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Glasgow AMA, Greene CM. Epithelial damage in the cystic fibrosis lung: the role of host and microbial factors. Expert Rev Respir Med 2022; 16:737-748. [PMID: 35833354 DOI: 10.1080/17476348.2022.2100350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The airway epithelium is a key system within the lung. It acts as a physical barrier to inhaled factors, and can actively remove unwanted microbes and particles from the lung via the mucociliary escalator. On a physiological level, it senses the presence of pathogens and initiates innate immune responses to combat their effects. Hydration of the airways is also controlled by the epithelium. Within the cystic fibrosis (CF) lung, these properties are suboptimal and contribute to the pulmonary manifestations of CF. AREAS COVERED In this review, we discuss how various host and microbial factors can contribute to airway epithelium dysfunction in the CF lung focusing on mechanisms relating to the mucociliary escalator and protease expression and function. We also explore how alterations in microRNA expression can impact the behavior of the airway epithelium. EXPERT OPINION Notwithstanding the unprecedented benefits that CFTR modulator drugs now provide to the health of CF sufferers, it will be important to delve more deeply into additional mechanisms underpinning CF lung disease such as those illustrated here in an attempt to counteract these aberrant processes and further enhance quality of life for people with CF.
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Affiliation(s)
- Arlene M A Glasgow
- Lung Biology Group, Department of Clinical Microbiology, Royal College of Surgeons in Ireland (RCSI), Education and Research Centre, Beaumont Hospital, Dublin, Ireland
| | - Catherine M Greene
- Lung Biology Group, Department of Clinical Microbiology, Royal College of Surgeons in Ireland (RCSI), Education and Research Centre, Beaumont Hospital, Dublin, Ireland
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2
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Tosco A, Castaldo A, Colombo C, Claut L, Carnovale V, Iacotucci P, Lucarelli M, Cimino G, Fabrizzi B, Caporelli N, Majo F, Ciciriello F, Padoan R, Poli P, Taccetti G, Centrone C, Casciaro R, Castellani C, Salvatore D, Colangelo C, Bonomi P, Castaldo G, Terlizzi V. Clinical outcomes of a large cohort of individuals with the F508del/5T;TG12 CFTR genotype. J Cyst Fibros 2022; 21:850-855. [PMID: 35523714 DOI: 10.1016/j.jcf.2022.04.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/16/2022] [Accepted: 04/26/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND In recent years, patients with cystic fibrosis (CF) conductance regulator (CFTR) variant poly(T) sequences have been increasingly reported with a wide spectrum of clinical severity. We describe the long-term clinical outcomes and progression to a CF diagnosis over time in a large Italian cohort of patients carrying the CFTR F508del/5T;TG12 genotype. METHODS A retrospective analysis of subjects from 10 CF centres in Italy with the F508del/5T;TG12 genotype was performed. Demographic, clinical, microbiological, and biochemical data, as well as information about the follow-ups and complications of the enroled patients, were collected. RESULTS A total of 129 subjects (54 females; median age: 15.0 years, range: 0-58 years; 59 older than 18 years) were included. In terms of initial diagnoses, 30 were CF (23.3%), 41 were CFTR-related disorder (CFTR-RD) (31.7%), and 58 were CF transmembrane conductance regulator-related metabolic syndrome/cystic fibrosis screen positive, inconclusive diagnosis (CRMS/CFSPID) (45.0%). After a median follow-up of 6.7 years (range 0.2-25 years), 15 patients progressed to CF, bringing the total number of CF diagnoses to 45/129 (34.9%). Most of these patients had mild lung diseases with pancreatic sufficiency and a low prevalence of CF-related complications. CONCLUSIONS At the end of the study, 34.9% of subjects with the CFTR F508del/5T;TG12 genotype were diagnosed with CF. We suggest including patients with the F508del/5T;TG12 genotype in long-term follow-ups.
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Affiliation(s)
- Antonella Tosco
- Paediatric Unit, Department of Translational Medical Sciences, Cystic Fibrosis Regional Reference Center, University of Naples Federico II, Naples, Italy
| | - Alice Castaldo
- Paediatric Unit, Department of Translational Medical Sciences, Cystic Fibrosis Regional Reference Center, University of Naples Federico II, Naples, Italy
| | - Carla Colombo
- Cystic Fibrosis Regional Reference Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Department of Pathophysiology and Transplantation, Milan, Italy
| | - Laura Claut
- Cystic Fibrosis Regional Reference Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Department of Pathophysiology and Transplantation, Milan, Italy
| | - Vincenzo Carnovale
- Department of Translational Medical Science, Cystic Fibrosis Center, Adult Unit, University of Naples "Federico II", Italy
| | - Paola Iacotucci
- Department of Translational Medical Science, Cystic Fibrosis Center, Adult Unit, University of Naples "Federico II", Italy
| | - Marco Lucarelli
- Dept of Experimental Medicine, Sapienza University of Rome, Rome, Italy; Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Giuseppe Cimino
- Cystic Fibrosis Regional Reference Center, A.O.U. Policlinico Umberto I, Rome, Italy
| | - Benedetta Fabrizzi
- Cystic Fibrosis Regional Reference Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Nicole Caporelli
- Cystic Fibrosis Regional Reference Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Fabio Majo
- Cystic Fibrosis Centre, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Fabiana Ciciriello
- Cystic Fibrosis Centre, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rita Padoan
- Cystic Fibrosis Regional Support Center, Department of Pediatrics, University of Brescia, ASST Spedali Civili Brescia, Brescia, Italy
| | - Piercarlo Poli
- Cystic Fibrosis Regional Support Center, Department of Pediatrics, University of Brescia, ASST Spedali Civili Brescia, Brescia, Italy
| | - Giovanni Taccetti
- Meyer Children's Hospital, Cystic Fibrosis Regional Reference Center, Department of Paediatric Medicine, Viale Gaetano Pieraccini 24, Florence, Italy
| | - Claudia Centrone
- Diagnostic Genetics Unit, Careggi University Hospital, Florence, Italy
| | | | | | | | | | | | - Giuseppe Castaldo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples, Naples, Italy; CEINGE-Advanced Biotechnology, Naples, Italy
| | - Vito Terlizzi
- Meyer Children's Hospital, Cystic Fibrosis Regional Reference Center, Department of Paediatric Medicine, Viale Gaetano Pieraccini 24, Florence, Italy.
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Iyer DN, Foo DCC, Lo OSH, Wan TMH, Li X, Sin RWY, Pang RWC, Law WL, Ng L. MiR-509-3p is oncogenic, targets the tumor suppressor PHLPP2, and functions as a novel tumor adjacent normal tissue based prognostic biomarker in colorectal cancer. BMC Cancer 2022; 22:351. [PMID: 35361144 PMCID: PMC8969217 DOI: 10.1186/s12885-021-09075-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/30/2021] [Indexed: 12/28/2022] Open
Abstract
Background Recently the role of microRNAs has been explored immensely as novel regulators and potential biomarkers in several cancers. MiR-509-3p is one such miRNA that has been observed to show a mixed expression in different cancers, while it’s expression and clinical relevance in colorectal cancer (CRC) has not yet been characterized. Methods We used quantitative PCR to evaluate the expression of miR-509-3p in fresh-frozen CRC tumor tissues and the corresponding tumor-adjacent normal (NAT) tissues from 103 patients. Subsequently, functional studies were performed to further interpret the role of the miRNA in CRC. Results MiR-509-3p was found to be overexpressed in CRC tissues in nearly 80% of cases and was associated with an aggressive disease presentation. Notably, a higher expression of the miRNA promoted cell proliferation, migration, and invasion of CRC cells in in vitro and in vivo models. Mechanistically, we confirmed that miR-509-3p directly binds the 3’UTR of the tumor suppressor PHLPP2 and inhibits its expression. Furthermore, within the previous 103 clinical tissue specimens, we observed an overexpression of miR-509-3p within the NAT tissue of patients associated with a poor disease prognosis. Using multivariate analysis, it was observed that the expression of miR-509-3p within the NAT tissue was an independent predictor of prognosis in CRC. At the cellular level, through indirect coculture experiments, miR-509-3p was observed to regulate the proliferative, migratory, and invasive behavior of normal colon cells. Conclusion MiR-509-3p strongly contributes to the development and progression of CRC and can potentially function as a prognostic biomarker in the disease. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-09075-x.
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Affiliation(s)
- Deepak Narayanan Iyer
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Dominic Chi-Chung Foo
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Oswens Siu-Hung Lo
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Timothy Ming-Hun Wan
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Xue Li
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ryan Wai-Yan Sin
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Roberta Wen-Chi Pang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Wai-Lun Law
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Lui Ng
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
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Cheng H, Yang S, Meng Q, Zheng B, Gu Y, Wang L, Song T, Xu C, Wang G, Han M, Shen L, Ding J, Li H, Ouyang J. Genetic analysis and intracytoplasmic sperm injection outcomes of Chinese patients with congenital bilateral absence of vas deferens. J Assist Reprod Genet 2022; 39:719-728. [PMID: 35119551 PMCID: PMC8995229 DOI: 10.1007/s10815-022-02417-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 01/27/2022] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Congenital bilateral absence of the vas deferens (CBAVD) is a major cause of obstructive azoospermia and male factor infertility. CBAVD is mainly caused by mutations in the genes encoding CFTR (cystic fibrosis transmembrane conductance regulator) and ADGRG2 (adhesion G protein-coupled receptor G2). This study aimed to describe CFTR and ADGRG2 variations in 46 Chinese CBAVD patients and evaluated sperm retrieval and assisted reproductive technology outcomes. METHODS The CFTR and ADGRG2 genes were sequenced and analyzed by whole-exome sequencing (WES), and variations were identified by Sanger sequencing. Bioinformatic analysis was performed. We retrospectively reviewed the outcomes of patients undergoing sperm retrieval surgery and intracytoplasmic sperm injection (ICSI). RESULTS In total, 35 of 46 (76.09%) patients carried at least one variation in CFTR, but no copy number variants or ADGRG2 variations were found. In addition to the IVS9-5 T allele, there were 27 CFTR variations, of which 4 variations were novel and predicted to be damaging by bioinformatics. Spermatozoa were successfully retrachieved in 46 patients, and 39 of the patients had their own offspring through ICSI. CONCLUSION There are no obvious hotspot CFTR mutations in Chinese CBAVD patients besides the IVS9-5 T allele. Therefore, WES might be the best detection method, and genetic counseling should be different from that provided to Caucasian populations. After proper counseling, all patients can undergo sperm retrieval from their epididymis or testis, and most of them can have their own children through ICSI.
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Affiliation(s)
- Hongbo Cheng
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000 Jiangsu China ,Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Shenmin Yang
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Qingxia Meng
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Bo Zheng
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Yidong Gu
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Luyun Wang
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Tao Song
- Department of Andrology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu China
| | - Chunlu Xu
- Department of Andrology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu China
| | - Gaigai Wang
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Mutian Han
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Liyan Shen
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Jie Ding
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Hong Li
- Center for Reproduction and Genetics, NHC Key Laboratory of Male Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.
| | - Jun Ouyang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu, China.
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5
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Johansson K, Woodruff PG, Ansel KM. Regulation of airway immunity by epithelial miRNAs. Immunol Rev 2021; 304:141-153. [PMID: 34549450 PMCID: PMC9135676 DOI: 10.1111/imr.13028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 02/07/2023]
Abstract
The airway epithelium is essential to protect the host from inhaled pathogens and particles. It maintains immune homeostasis and mediates tissue repair after injury. Inflammatory diseases of the airways are associated with failure of epithelial functions, including loss of barrier integrity that results in increased tissue permeability and immune activation; excessive mucus secretion and impaired mucociliary clearance that leads to airflow obstruction and microbial overgrowth; and dysregulation of cellular signals that promotes inflammation and alters tissue structure and airway reactivity. MicroRNAs play crucial roles in mounting appropriate cellular responses to environmental stimuli and preventing disease, using a common machinery and mechanism to regulate gene expression in epithelial cells, immune cells of hematopoietic origin, and other cellular components of the airways. Respiratory diseases are accompanied by dramatic changes in epithelial miRNA expression that drive persistent immune dysregulation. In this review, we discuss responses of the epithelium that promote airway immunopathology, with a focus on miRNAs that contribute to the breakdown of essential epithelial functions. We emphasize the emerging role of miRNAs in regulation of epithelial responses in respiratory health and their value as diagnostic and therapeutic targets.
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Affiliation(s)
- Kristina Johansson
- Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
- Sandler Asthma Basic Research Center, University of California, San Francisco, California, USA
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep and Allergy, University of California, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Prescott G. Woodruff
- Sandler Asthma Basic Research Center, University of California, San Francisco, California, USA
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep and Allergy, University of California, San Francisco, California, USA
- Cardiovascular Research Institute, University of California, San Francisco, California, USA
| | - K. Mark Ansel
- Sandler Asthma Basic Research Center, University of California, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
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6
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Dutta RK, Chinnapaiyan S, Santiago MJ, Rahman I, Unwalla HJ. Gene-specific MicroRNA antagonism protects against HIV Tat and TGF-β-mediated suppression of CFTR mRNA and function. Biomed Pharmacother 2021; 142:112090. [PMID: 34463266 DOI: 10.1016/j.biopha.2021.112090] [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: 06/30/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 10/20/2022] Open
Abstract
BACKGROUND MicroRNAs play an important role in health and disease. TGF-β signaling, upregulated by HIV Tat, and in chronic airway diseases and smokers upregulates miR-145-5p to suppress cystic fibrosis transmembrane conductance regulator (CFTR). CFTR suppression in chronic airway diseases like Cystic Fibrosis, COPD and smokers has been associated with suppressed MCC and recurrent lung infections and inflammation. This can explain the emergence of recurrent lung infections and inflammation in people living with HIV. METHODS Tat-induced aberrant microRNAome was identified by miRNA expression analysis. microRNA mimics and antagomirs were used to validate the identified miRNAs involved in Tat mediated CFTR mRNA suppression. CRISPR-based editing of the miRNA target sites in CFTR 3'UTR was used to determine rescue of CFTR mRNA and function in airway epithelial cell lines and in primary human bronchial epithelial cells exposed to TGF-β and Tat. FINDINGS HIV Tat upregulates miR-145-5p and miR-509-3p. The two miRNAs demonstrate co-operative effects in suppressing CFTR. CRISPR-based editing of the miRNA target site preserves CFTR mRNA and function in airway epithelial cells INTERPRETATION: Given the important roles of TGF-β signaling and the multitude of genes regulated by miRNAs, we demonstrate that CRISPR-based gene-specific microRNA antagonism approach can preserve CFTR mRNA and function in the context of HIV Tat and TGF-β signaling without suppressing expression of other genes regulated by miR-145-5p.
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Affiliation(s)
- R K Dutta
- Department of Immunology and Nanomedicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - S Chinnapaiyan
- Department of Immunology and Nanomedicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - M J Santiago
- Department of Immunology and Nanomedicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - I Rahman
- University of Rochester Medical Center, Departments of Environmental Medicine and Pulmonary Medicine, Rochester, NY 14642, USA
| | - H J Unwalla
- Department of Immunology and Nanomedicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA.
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Comegna M, Terlizzi V, Salvatore D, Colangelo C, Di Lullo AM, Zollo I, Taccetti G, Castaldo G, Amato F. Elexacaftor-Tezacaftor-Ivacaftor Therapy for Cystic Fibrosis Patients with The F508del/Unknown Genotype. Antibiotics (Basel) 2021; 10:antibiotics10070828. [PMID: 34356748 PMCID: PMC8300667 DOI: 10.3390/antibiotics10070828] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 01/07/2023] Open
Abstract
The new CFTR modulator combination, elexacaftor/tezacaftor/ivacaftor (Trikafta) was approved by the FDA in October 2019 for treatment of Cystic Fibrosis in patients 6 years of age or older who have at least one F508del mutation in one allele and a minimal-function or another F508del mutation in the other allele. However, there is a group of patients, in addition to those with rare mutations, in which despite the presence of a F508del in one allele, it was not possible to identify any mutation in the other allele. To date, these patients are excluded from treatment with Trikafta in Italy, where the CF patients carrying F508del/unknown represent about 1.3% (71 patients) of the overall Italian CF patients. In this paper we show that the Trikafta treatment of nasal epithelial cells, derived from F508del/Unknown patients, results in a significant rescue of CFTR activity. Based on our findings, we think that the F508del/Unknown patients considered in this study could obtain clinical benefits from Trikafta treatment, and we strongly suggest their eligibility for this type of treatment. This study, adding further evidence in the literature, once again confirms the validity of functional studies on nasal cells in the cystic fibrosis theratyping and personalized medicine.
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Affiliation(s)
- Marika Comegna
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini, 5, 80131 Naples, Italy; (M.C.); (I.Z.); (G.C.)
- CEINGE–Advanced Biotechnologies, Via G. Salvatore, 486, 80145 Naples, Italy
| | - Vito Terlizzi
- Cystic Fibrosis Regional Reference Center, Department of Pediatric Medicine, Anna Meyer Children’s University, Viale Pieraccini, 24, 50139 Florence, Italy; (V.T.); (G.T.)
| | - Donatello Salvatore
- Cystic Fibrosis Center, Hospital San Carlo, Via P. Petrone, 85100 Potenza, Italy; (D.S.); (C.C.)
| | - Carmela Colangelo
- Cystic Fibrosis Center, Hospital San Carlo, Via P. Petrone, 85100 Potenza, Italy; (D.S.); (C.C.)
| | - Antonella Miriam Di Lullo
- Department Reproductive Sciences and Dentistry, University of Naples Federico II of Neuroscience, Via Pansini, 5, 80131 Naples, Italy;
| | - Immacolata Zollo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini, 5, 80131 Naples, Italy; (M.C.); (I.Z.); (G.C.)
- CEINGE–Advanced Biotechnologies, Via G. Salvatore, 486, 80145 Naples, Italy
| | - Giovanni Taccetti
- Cystic Fibrosis Regional Reference Center, Department of Pediatric Medicine, Anna Meyer Children’s University, Viale Pieraccini, 24, 50139 Florence, Italy; (V.T.); (G.T.)
| | - Giuseppe Castaldo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini, 5, 80131 Naples, Italy; (M.C.); (I.Z.); (G.C.)
- CEINGE–Advanced Biotechnologies, Via G. Salvatore, 486, 80145 Naples, Italy
| | - Felice Amato
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini, 5, 80131 Naples, Italy; (M.C.); (I.Z.); (G.C.)
- CEINGE–Advanced Biotechnologies, Via G. Salvatore, 486, 80145 Naples, Italy
- Correspondence:
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8
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Comegna M, Conte G, Falanga AP, Marzano M, Cernera G, Di Lullo AM, Amato F, Borbone N, D'Errico S, Ungaro F, d'Angelo I, Oliviero G, Castaldo G. Assisting PNA transport through cystic fibrosis human airway epithelia with biodegradable hybrid lipid-polymer nanoparticles. Sci Rep 2021; 11:6393. [PMID: 33737583 PMCID: PMC7973768 DOI: 10.1038/s41598-021-85549-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/01/2021] [Indexed: 12/11/2022] Open
Abstract
Cystic fibrosis (CF) is characterized by an airway obstruction caused by a thick mucus due to a malfunctioning Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein. The sticky mucus restricts drugs in reaching target cells limiting the efficiency of treatments. The development of new approaches to enhance drug delivery to the lungs represents CF treatment's main challenge. In this work, we report the production and characterization of hybrid core–shell nanoparticles (hNPs) comprising a PLGA core and a dipalmitoylphosphatidylcholine (DPPC) shell engineered for inhalation. We loaded hNPs with a 7-mer peptide nucleic acid (PNA) previously considered for its ability to modulate the post-transcriptional regulation of the CFTR gene. We also investigated the in vitro release kinetics of hNPs and their efficacy in PNA delivery across the human epithelial airway barrier using an ex vivo model based on human primary nasal epithelial cells (HNEC) from CF patients. Confocal analyses and hNPs transport assay demonstrated the ability of hNPs to overcome the mucus barrier and release their PNA cargo within the cytoplasm, where it can exert its biological function.
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Affiliation(s)
- Marika Comegna
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131, Naples, Italy.,CEINGE-Biotecnologie Avanzate S.c.a.r.l., 80145, Naples, Italy
| | - Gemma Conte
- Di.S.T.A.Bi.F., University of Campania Luigi Vanvitelli, 81100, Caserta, Italy
| | | | - Maria Marzano
- Institute of Crystallography, National Research Council, 70126, Bari, Italy
| | - Gustavo Cernera
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131, Naples, Italy.,CEINGE-Biotecnologie Avanzate S.c.a.r.l., 80145, Naples, Italy
| | - Antonella Miriam Di Lullo
- ENT Section, Department of Neuroscience, Reproductive and Odontostomatological Sciences, University of Naples Federico II, 80131, Naples, Italy
| | - Felice Amato
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131, Naples, Italy.,CEINGE-Biotecnologie Avanzate S.c.a.r.l., 80145, Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Stefano D'Errico
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Francesca Ungaro
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Ivana d'Angelo
- Di.S.T.A.Bi.F., University of Campania Luigi Vanvitelli, 81100, Caserta, Italy.
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131, Naples, Italy.
| | - Giuseppe Castaldo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131, Naples, Italy.,CEINGE-Biotecnologie Avanzate S.c.a.r.l., 80145, Naples, Italy
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NGS Gene Panel Analysis Revealed Novel Mutations in Patients with Rare Congenital Diarrheal Disorders. Diagnostics (Basel) 2021; 11:diagnostics11020262. [PMID: 33567694 PMCID: PMC7915612 DOI: 10.3390/diagnostics11020262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 12/15/2022] Open
Abstract
Congenital diarrheal disorders (CDDs) are early-onset enteropathies generally inherited as autosomal recessive traits. Most patients with CDDs require rapid diagnosis as they need immediate and specific therapy to avoid a poor prognosis, but their clinical picture is often overlapping with a myriad of nongenetic diarrheal diseases. We developed a next-generation sequencing (NGS) panel for the analysis of 92 CDD-related genes, by which we analyzed patients suspect for CDD, among which were (i) three patients with sucrose-isomaltase deficiency; (ii) four patients with microvillous inclusion disease; (iii) five patients with congenital tufting enteropathy; (iv) eight patients with glucose-galactose malabsorption; (v) five patients with congenital chloride diarrhea. In all cases, we identified the mutations in the disease-gene, among which were several novel mutations for which we defined pathogenicity using a combination of bioinformatic tools. Although CDDs are rare, all together, they have an incidence of about 1%. Considering that the clinical picture of these disorders is often confusing, a CDD-related multigene NGS panel contributes to unequivocal and rapid diagnosis, which also reduces the need for invasive procedures.
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Abstract
Because CFTR gene studies now represent one of the most frequent genetic analyses routinely performed worldwide, the number of rare CFTR variants identified in various clinical situations, regularly increases. To provide appropriate diagnosis and prognosis to CF patients as well as appropriate genetic counseling to families, the clinical impact and the phenotypic spectrum of variants identified by diagnostic techniques need to be characterized. Three complementary locus specific databases, called CFTR1, CFTR2 and CFTR-France were developed to address these issues. Besides, the growing knowledge of the CF pathophysiology and the technical evolution in molecular biology allowed to identify candidate modifier genes, regulatory loci, epigenetic profiles and trans-regulators that could help to refine genotype-phenotype correlations at the individual level. These different factors may contribute to the large phenotypic variability between patients with CF, even when they carry identical CFTR variants, regarding lung function, meconium ileus susceptibility or the risk for developing CFTR-related diabetes and liver disease. Finally, the availability of new therapies that target the CFTR protein for numbers of CF patients led to the identification of 'good' and 'poor' responders, thus raising questions of pharmacogenetics factors that may influence treatment efficiency as a novel feature of the complexity of CF patients' management. © 2020 French Society of Pediatrics. Published by Elsevier Masson SAS. All rights reserved.
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De Palma FDE, Raia V, Kroemer G, Maiuri MC. The Multifaceted Roles of MicroRNAs in Cystic Fibrosis. Diagnostics (Basel) 2020; 10:E1102. [PMID: 33348555 PMCID: PMC7765910 DOI: 10.3390/diagnostics10121102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
Cystic fibrosis (CF) is a lifelong disorder affecting 1 in 3500 live births worldwide. It is a monogenetic autosomal recessive disease caused by loss-of-function mutations in the gene encoding the chloride channel cystic fibrosis transmembrane conductance regulator (CFTR), the impairment of which leads to ionic disequilibria in exocrine organs. This translates into a chronic multisystemic disease characterized by airway obstruction, respiratory infections, and pancreatic insufficiency as well as hepatobiliary and gastrointestinal dysfunction. Molecular characterization of the mutational heterogeneity of CFTR (affected by more than 2000 variants) improved the understanding and management of CF. However, these CFTR variants are linked to different clinical manifestations and phenotypes, and they affect response to treatments. Expanding evidence suggests that multisystemic disease affects CF pathology via impairing either CFTR or proteins regulated by CFTR. Thus, altering the expression of miRNAs in vivo could constitute an appealing strategy for developing new CF therapies. In this review, we will first describe the pathophysiology and clinical management of CF. Then, we will summarize the current knowledge on altered miRNAs in CF patients, with a focus on the miRNAs involved in the deregulation of CFTR and in the modulation of inflammation. We will highlight recent findings on the potential utility of measuring circulating miRNAs in CF as diagnostic, prognostic, and predictive biomarkers. Finally, we will provide an overview on potential miRNA-based therapeutic approaches.
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Affiliation(s)
- Fatima Domenica Elisa De Palma
- Equipe 11 Labellisée Ligue Contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université of Paris, 75006 Paris, France;
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, 94805 Villejuif, France
- CEINGE-Biotecnologie Avanzate, 80145 Naples, Italy
| | - Valeria Raia
- Pediatric Unit, Department of Translational Medical Sciences, Regional Cystic Fibrosis Center, Federico II University Naples, 80131 Naples, Italy;
| | - Guido Kroemer
- Equipe 11 Labellisée Ligue Contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université of Paris, 75006 Paris, France;
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, 94805 Villejuif, France
- Suzhou Institute for Systems Medicine, Chinese Academy of Sciences, Suzhou 215123, China
- Karolinska Institutet, Department of Women’s and Children’s Health, 17176 Stockholm, Sweden
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France
- Institut Universitaire de France, 75005 Paris, France
| | - Maria Chiara Maiuri
- Equipe 11 Labellisée Ligue Contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université of Paris, 75006 Paris, France;
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, 94805 Villejuif, France
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Fonseca C, Bicker J, Alves G, Falcão A, Fortuna A. Cystic fibrosis: Physiopathology and the latest pharmacological treatments. Pharmacol Res 2020; 162:105267. [PMID: 33127556 DOI: 10.1016/j.phrs.2020.105267] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/12/2020] [Accepted: 10/18/2020] [Indexed: 12/18/2022]
Abstract
Cystic fibrosis (CF) is a lethal autosomal recessive genetic disease, caused by a mutation in the cystic fibrosis transmembrane conductance regulator gene (CFTR), which primarily affects the lungs and digestive system. This gene encodes the CFTR protein, a distinctive membrane transporter of the ATP-binding cassette (ABC) superfamily. It functions as a chloride channel, allowing the balance and transport of chloride through the apical membrane of epithelial cells. Due to its ubiquitous location, mutations in the CFTR gene trigger multiple changes in ion transport and metabolic pathways, affecting various organs, as it will be herein explained. Pulmonary impairment is the most characteristic comorbidity of CF and respiratory failure is the main cause of death. This review presents the importance of an early diagnosis of CF to establish, as soon as possible, a primary therapy for symptomatic prevention and relief. It also mentions new therapeutic approaches that include CFTR modulators. They are correctors and/or potentiators of the deficient CFTR channel. In an attempt to overcome the disadvantages of CFTR modulators, the application of biotechnology techniques is addressed, such as gene therapy, gene editing, RNA therapy and therapeutic microRNAs. The potential of the intranasal administration route is another presented aspect.
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Affiliation(s)
- Carla Fonseca
- University of Coimbra, Faculty of Pharmacy, Coimbra, Portugal
| | - Joana Bicker
- University of Coimbra, Faculty of Pharmacy, Coimbra, Portugal; University of Coimbra, Coimbra Institute for Biomedical Imaging and Translational Research, Coimbra, Portugal
| | - Gilberto Alves
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Amílcar Falcão
- University of Coimbra, Faculty of Pharmacy, Coimbra, Portugal; University of Coimbra, Coimbra Institute for Biomedical Imaging and Translational Research, Coimbra, Portugal
| | - Ana Fortuna
- University of Coimbra, Faculty of Pharmacy, Coimbra, Portugal; University of Coimbra, Coimbra Institute for Biomedical Imaging and Translational Research, Coimbra, Portugal.
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Rezaei S, Mahjoubin-Tehran M, Aghaee-Bakhtiari SH, Jalili A, Movahedpour A, Khan H, Moghoofei M, Shojaei Z, R Hamblin M, Mirzaei H. Autophagy-related MicroRNAs in chronic lung diseases and lung cancer. Crit Rev Oncol Hematol 2020; 153:103063. [DOI: 10.1016/j.critrevonc.2020.103063] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 06/11/2020] [Accepted: 07/12/2020] [Indexed: 12/24/2022] Open
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The Role of MicroRNA in the Airway Surface Liquid Homeostasis. Int J Mol Sci 2020; 21:ijms21113848. [PMID: 32481719 PMCID: PMC7312818 DOI: 10.3390/ijms21113848] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/24/2020] [Accepted: 05/25/2020] [Indexed: 02/06/2023] Open
Abstract
Mucociliary clearance, mediated by a coordinated function of cilia bathing in the airway surface liquid (ASL) on the surface of airway epithelium, protects the host from inhaled pathogens and is an essential component of the innate immunity. ASL is composed of the superficial mucus layer and the deeper periciliary liquid. Ion channels, transporters, and pumps coordinate the transcellular and paracellular movement of ions and water to maintain the ASL volume and mucus hydration. microRNA (miRNA) is a class of non-coding, short single-stranded RNA regulating gene expression by post-transcriptional mechanisms. miRNAs have been increasingly recognized as essential regulators of ion channels and transporters responsible for ASL homeostasis. miRNAs also influence the airway host defense. We summarize the most up-to-date information on the role of miRNAs in ASL homeostasis and host-pathogen interactions in the airway and discuss concepts for miRNA-directed therapy.
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A Peptide Nucleic Acid (PNA) Masking the miR-145-5p Binding Site of the 3'UTR of the Cystic Fibrosis Transmembrane Conductance Regulator ( CFTR) mRNA Enhances CFTR Expression in Calu-3 Cells. Molecules 2020; 25:molecules25071677. [PMID: 32260566 PMCID: PMC7181265 DOI: 10.3390/molecules25071677] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 01/19/2023] Open
Abstract
Peptide nucleic acids (PNAs) have been demonstrated to be very useful tools for gene regulation at different levels and with different mechanisms of action. In the last few years the use of PNAs for targeting microRNAs (anti-miRNA PNAs) has provided impressive advancements. In particular, targeting of microRNAs involved in the repression of the expression of the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which is defective in cystic fibrosis (CF), is a key step in the development of new types of treatment protocols. In addition to the anti-miRNA therapeutic strategy, inhibition of miRNA functions can be reached by masking the miRNA binding sites present within the 3′UTR region of the target mRNAs. The objective of this study was to design a PNA masking the binding site of the microRNA miR-145-5p present within the 3′UTR of the CFTR mRNA and to determine its activity in inhibiting miR-145-5p function, with particular focus on the expression of both CFTR mRNA and CFTR protein in Calu-3 cells. The results obtained support the concept that the PNA masking the miR-145-5p binding site of the CFTR mRNA is able to interfere with miR-145-5p biological functions, leading to both an increase of CFTR mRNA and CFTR protein content.
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TAS2R38 is a novel modifier gene in patients with cystic fibrosis. Sci Rep 2020; 10:5806. [PMID: 32242045 PMCID: PMC7118092 DOI: 10.1038/s41598-020-62747-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/16/2020] [Indexed: 12/17/2022] Open
Abstract
The clinical manifestation of cystic fibrosis (CF) is heterogeneous also in patients with the same cystic fibrosis transmembrane regulator (CFTR) genotype and in affected sibling pairs. Other genes, inherited independently of CFTR, may modulate the clinical manifestation and complications of patients with CF, including the severity of chronic sinonasal disease and the occurrence of chronic Pseudomonas aeruginosa colonization. The T2R38 gene encodes a taste receptor and recently its functionality was related to the occurrence of sinonasal diseases and upper respiratory infections. We assessed the T2R38 genotype in 210 patients with CF and in 95 controls, relating the genotype to the severity of sinonasal disease and to the occurrence of P. aeruginosa pulmonary colonization. The frequency of the PAV allele i.e., the allele associated with the high functionality of the T2R38 protein, was significantly lower in i) CF patients with nasal polyposis requiring surgery, especially in patients who developed the complication before 14 years of age; and ii) in CF patients with chronic pulmonary colonization by P. aeruginosa, especially in patients who were colonized before 14 years of age, than in control subjects. These data suggest a role for T2R38 as a novel modifier gene of sinonasal disease severity and of pulmonary P. aeruginosa colonization in patients with CF.
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Wang H, An M, Liu Y, Hu K, Jin Y, Xu S, Chen B, Lu M. Genetic diagnosis and sperm retrieval outcomes for Chinese patients with congenital bilateral absence of vas deferens. Andrology 2020; 8:1064-1069. [PMID: 32020786 DOI: 10.1111/andr.12769] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 01/21/2020] [Accepted: 02/03/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Congenital bilateral absence of the vas deferens (CBAVD) is a frequent cause of obstructive azoospermia. CBAVD is mainly caused by mutations in the CFTR (cystic fibrosis transmembrane conductance regulator) gene and is also related to the X-linked ADGRG2 (adhesion G protein-coupled receptor G2) gene. Genetic screening and counseling strategies for Chinese CBAVD populations remain controversial because the genetic background of CBAVD in Chinese population is largely unknown. OBJECTIVES In this study, we aimed to study the mutation spectrum of CFTR and ADGRG2 in a group of CBAVD patients and to evaluate sperm retrieval outcomes in a subset of CBAVD patients. MATERIALS AND METHODS Next-generation targeted sequencing was used to identify mutations in the CFTR and ADGRG2 genes in 38 CBAVD patients. In addition, we followed and analyzed nine of the 38 patients who were undergoing sperm retrieval surgery. RESULTS In total, 27 of 38 (71.05%) patients carried at least one likely pathogenic or pathogenic mutation in CFTR or ADGRG2. In addition to the IVS9-5T allele, 15 CFTR and 1 ADGRG2 mutations were identified, including 4 novel mutations. CFTR hot-spot mutations were not identified in our study. Spermatozoon was successfully obtained in all nine patients who underwent MESA or TESE surgery, but most patients had spermatozoa with relatively low motility and high abnormality rates. DISCUSSION AND CONCLUSION Except for the IVS9-5T allele, hot-spot mutations of CFTR may not exist in Chinese CBAVD patients. Therefore, next-generation targeted sequencing for whole CFTR and ADGRG2 gene may be the appropriate genetic testing method, and genetic counseling may be different from Caucasian populations. We observed a high success rate of sperm retrieval with relatively low motility and high abnormality rates in Chinese CBAVD patients. However, this is only a weak conclusion due to the small sample size.
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Affiliation(s)
- Hongxiang Wang
- Department of Urology and Andrology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Miao An
- CarrierGene Biotechnologies Co., Ltd, Shanghai, China
| | - Yidong Liu
- Department of Urology and Andrology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Kai Hu
- Department of Urology and Andrology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Jin
- Department of Urology and Andrology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Shiran Xu
- Department of Urology and Andrology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Bin Chen
- Department of Urology and Andrology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Mujun Lu
- Department of Urology and Andrology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
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De Santi C, Fernández Fernández E, Gaul R, Vencken S, Glasgow A, Oglesby IK, Hurley K, Hawkins F, Mitash N, Mu F, Raoof R, Henshall DC, Cutrona MB, Simpson JC, Harvey BJ, Linnane B, McNally P, Cryan SA, MacLoughlin R, Swiatecka-Urban A, Greene CM. Precise Targeting of miRNA Sites Restores CFTR Activity in CF Bronchial Epithelial Cells. Mol Ther 2020; 28:1190-1199. [PMID: 32059764 DOI: 10.1016/j.ymthe.2020.02.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 03/02/2020] [Indexed: 01/19/2023] Open
Abstract
MicroRNAs that are overexpressed in cystic fibrosis (CF) bronchial epithelial cells (BEC) negatively regulate CFTR and nullify the beneficial effects of CFTR modulators. We hypothesized that it is possible to reverse microRNA-mediated inhibition of CFTR using CFTR-specific target site blockers (TSBs) and to develop a drug-device combination inhalation therapy for CF. Lead microRNA expression was quantified in a series of human CF and non-CF samples and in vitro models. A panel of CFTR 3' untranslated region (UTR)-specific locked nucleic acid antisense oligonucleotide TSBs was assessed for their ability to increase CFTR expression. Their effects on CFTR activity alone or in combination with CFTR modulators were measured in CF BEC models. TSB encapsulation in poly-lactic-co-glycolic acid (PLGA) nanoparticles was assessed as a proof of principle of delivery into CF BECs. TSBs targeting the CFTR 3' UTR 298-305:miR-145-5p or 166-173:miR-223-3p sites increased CFTR expression and anion channel activity and enhanced the effects of ivacaftor/lumacaftor or ivacaftor/tezacaftor in CF BECs. Biocompatible PLGA-TSB nanoparticles promoted CFTR expression in primary BECs and retained desirable biophysical characteristics following nebulization. Alone or in combination with CFTR modulators, aerosolized CFTR-targeting TSBs encapsulated in PLGA nanoparticles could represent a promising drug-device combination therapy for the treatment for CFTR dysfunction in the lung.
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Affiliation(s)
- Chiara De Santi
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin 9, Ireland.
| | | | - Rachel Gaul
- School of Pharmacy and Tissue Engineering Research Group, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Sebastian Vencken
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin 9, Ireland
| | - Arlene Glasgow
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin 9, Ireland
| | - Irene K Oglesby
- Department of Medicine, Royal College of Surgeons in Ireland, Dublin 9, Ireland
| | - Killian Hurley
- Department of Medicine, Royal College of Surgeons in Ireland, Dublin 9, Ireland
| | - Finn Hawkins
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Nilay Mitash
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Fangping Mu
- Center for Research Computing, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Rana Raoof
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - David C Henshall
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Meritxell B Cutrona
- School of Biology and Environmental Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Jeremy C Simpson
- School of Biology and Environmental Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Brian J Harvey
- Department of Molecular Medicine, Royal College of Surgeons in Ireland, Dublin 9, Ireland
| | - Barry Linnane
- University Hospital Limerick, Dooradoyle, Limerick, Ireland
| | - Paul McNally
- Department of Pediatrics, Royal College of Surgeons in Ireland, Dublin 2, Ireland; National Children's Research Centre, Children's Health Ireland at Crumlin, Dublin 12, Ireland
| | - Sally Ann Cryan
- School of Pharmacy and Tissue Engineering Research Group, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | | | | | - Catherine M Greene
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin 9, Ireland
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Alpha-1 Antitrypsin-A Target for MicroRNA-Based Therapeutic Development for Cystic Fibrosis. Int J Mol Sci 2020; 21:ijms21030836. [PMID: 32012925 PMCID: PMC7037267 DOI: 10.3390/ijms21030836] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 02/06/2023] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive genetic disorder arising from mutations to the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Disruption to normal ion homeostasis in the airway results in impaired mucociliary clearance, leaving the lung more vulnerable to recurrent and chronic bacterial infections. The CF lung endures an excess of neutrophilic inflammation, and whilst neutrophil serine proteases are a crucial part of the innate host defence to infection, a surplus of neutrophil elastase (NE) is understood to create a net destructive effect. Alpha-1 antitrypsin (A1AT) is a key antiprotease in the control of NE protease activity but is ineffective in the CF lung due to the huge imbalance of NE levels. Therapeutic strategies to boost levels of protective antiproteases such as A1AT in the lung remain an attractive research strategy to limit the damage from excess protease activity. microRNAs are small non-coding RNA molecules that bind specific cognate sequences to inhibit expression of target mRNAs. The inhibition of miRNAs which target the SERPINA1 (A1AT-encoding gene) mRNA represents a novel therapeutic approach for CF inflammation. This could involve the delivery of antagomirs that bind and sequester the target miRNA, or target site blockers that bind miRNA recognition elements within the target mRNA to prevent miRNA interaction. Therefore, miRNA targeted therapies offer an alternative strategy to drive endogenous A1AT production and thus supplement the antiprotease shield of the CF lung.
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Transforming Growth Factor-β1 Selectively Recruits microRNAs to the RNA-Induced Silencing Complex and Degrades CFTR mRNA under Permissive Conditions in Human Bronchial Epithelial Cells. Int J Mol Sci 2019; 20:ijms20194933. [PMID: 31590401 PMCID: PMC6801718 DOI: 10.3390/ijms20194933] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 09/27/2019] [Accepted: 10/05/2019] [Indexed: 12/23/2022] Open
Abstract
Mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene lead to cystic fibrosis (CF). The most common mutation F508del inhibits folding and processing of CFTR protein. FDA-approved correctors rescue the biosynthetic processing of F508del-CFTR protein, while potentiators improve the rescued CFTR channel function. Transforming growth factor (TGF-β1), overexpressed in many CF patients, blocks corrector/potentiator rescue by inhibiting CFTR mRNA in vitro. Increased TGF-β1 signaling and acquired CFTR dysfunction are present in other lung diseases. To study the mechanism of TGF-β1 repression of CFTR, we used molecular, biochemical, and functional approaches in primary human bronchial epithelial cells from over 50 donors. TGF-β1 destabilized CFTR mRNA in cells from lungs with chronic disease, including CF, and impaired F508del-CFTR rescue by new-generation correctors. TGF-β1 increased the active pool of selected micro(mi)RNAs validated as CFTR inhibitors, recruiting them to the RNA-induced silencing complex (RISC). Expression of F508del-CFTR globally modulated TGF-β1-induced changes in the miRNA landscape, creating a permissive environment required for degradation of F508del-CFTR mRNA. In conclusion, TGF-β1 may impede the full benefit of corrector/potentiator therapy in CF patients. Studying miRNA recruitment to RISC under disease-specific conditions may help to better characterize the miRNAs utilized by TGF-β1 to destabilize CFTR mRNA.
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Transcriptional consequences of impaired immune cell responses induced by cystic fibrosis plasma characterized via dual RNA sequencing. BMC Med Genomics 2019; 12:66. [PMID: 31118097 PMCID: PMC6532208 DOI: 10.1186/s12920-019-0529-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 05/13/2019] [Indexed: 02/07/2023] Open
Abstract
Background In cystic fibrosis (CF), impaired immune cell responses, driven by the dysfunctional CF transmembrane conductance regulator (CFTR) gene, may determine the disease severity but clinical heterogeneity remains a major therapeutic challenge. The characterization of molecular mechanisms underlying impaired immune responses in CF may reveal novel targets with therapeutic potential. Therefore, we utilized simultaneous RNA sequencing targeted at identifying differentially expressed genes, transcripts, and miRNAs that characterize impaired immune responses triggered by CF and its phenotypes. Methods Peripheral blood mononuclear cells (PBMCs) extracted from a healthy donor were stimulated with plasma from CF patients (n = 9) and healthy controls (n = 3). The PBMCs were cultured (1 × 105 cells/well) for 9 h at 37 ° C in 5% CO2. After culture, total RNA was extracted from each sample and used for simultaneous total RNA and miRNA sequencing. Results Analysis of expression signatures from peripheral blood mononuclear cells induced by plasma of CF patients and healthy controls identified 151 genes, 154 individual transcripts, and 41 miRNAs differentially expressed in CF compared to HC while the expression signatures of 285 genes, 241 individual transcripts, and seven miRNAs differed due to CF phenotypes. Top immune pathways influenced by CF included agranulocyte adhesion, diapedesis signaling, and IL17 signaling, while those influenced by CF phenotypes included natural killer cell signaling and PI3K signaling in B lymphocytes. Upstream regulator analysis indicated dysregulation of CCL5, NF-κB and IL1A due to CF while dysregulation of TREM1 and TP53 regulators were associated with CF phenotype. Five miRNAs showed inverse expression patterns with three target genes relevant in CF-associated impaired immune pathways while two miRNAs showed inverse expression patterns with two target genes relevant to a dysregulated immune pathway associated with CF phenotypes. Conclusions Our results indicate that miRNAs and individual transcript variants are relevant molecular targets contributing to impaired immune cell responses in CF. Electronic supplementary material The online version of this article (10.1186/s12920-019-0529-0) contains supplementary material, which is available to authorized users.
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Finotti A, Fabbri E, Lampronti I, Gasparello J, Borgatti M, Gambari R. MicroRNAs and Long Non-coding RNAs in Genetic Diseases. Mol Diagn Ther 2019; 23:155-171. [PMID: 30610665 PMCID: PMC6469593 DOI: 10.1007/s40291-018-0380-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Since the discovery and classification of non-coding RNAs, their roles have gained great attention. In this respect, microRNAs and long non-coding RNAs have been firmly demonstrated to be linked to regulation of gene expression and onset of human diseases, including rare genetic diseases; therefore they are suitable targets for therapeutic intervention. This issue, in the context of rare genetic diseases, is being considered by an increasing number of research groups and is of key interest to the health community. In the case of rare genetic diseases, the possibility of developing personalized therapy in precision medicine has attracted the attention of researchers and clinicians involved in developing "orphan medicinal products" and proposing these to the European Medicines Agency (EMA) and to the Food and Drug Administration (FDA) Office of Orphan Products Development (OOPD) in the United States. The major focuses of these activities are the evaluation and development of products (drugs, biologics, devices, or medical foods) considered to be promising for diagnosis and/or treatment of rare diseases or conditions, including rare genetic diseases. In an increasing number of rare genetic diseases, analysis of microRNAs and long non-coding RNAs has been proven a promising strategy. These diseases include, but are not limited to, Duchenne muscular dystrophy, cystic fibrosis, Rett syndrome, and β-thalassemia. In conclusion, a large number of approaches based on targeting microRNAs and long non-coding RNAs are expected in the field of molecular diagnosis and therapy, with a facilitated technological transfer in the case of rare genetic diseases, in virtue of the existing regulation concerning these diseases.
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Affiliation(s)
- Alessia Finotti
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Enrica Fabbri
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Ilaria Lampronti
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Jessica Gasparello
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy.
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23
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Terlizzi V, Lucarelli M, Salvatore D, Angioni A, Bisogno A, Braggion C, Buzzetti R, Carnovale V, Casciaro R, Castaldo G, Cirilli N, Collura M, Colombo C, Di Lullo AM, Elce A, Lucidi V, Madarena E, Padoan R, Quattrucci S, Raia V, Seia M, Termini L, Zarrilli F. Clinical expression of cystic fibrosis in a large cohort of Italian siblings. BMC Pulm Med 2018; 18:196. [PMID: 30577776 PMCID: PMC6303904 DOI: 10.1186/s12890-018-0766-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 12/12/2018] [Indexed: 02/10/2023] Open
Abstract
Background A clinical heterogeneity was reported in patients with Cystic Fibrosis (CF) with the same CFTR genotype and between siblings with CF. Methods We investigated all clinical aspects in a cohort of 101 pairs of siblings with CF (including 6 triplets) followed since diagnosis. Results Severe lung disease had a 22.2% concordance in sib-pairs, occurred early and the FEV1% at 12 years was predictive of the severity of lung disease in the adulthood. Similarly, CF liver disease occurred early (median: 15 years) and showed a concordance of 27.8% in sib-pairs suggesting a scarce contribution of genetic factors; in fact, only 2/15 patients with liver disease in discordant sib-pairs had a deficiency of alpha-1-antitrypsin (a known modifier gene of CF liver phenotype). CF related diabetes was found in 22 pairs (in 6 in both the siblings). It occurred later (median: 32.5 years) and is strongly associated with liver disease. Colonization by P. aeruginosa and nasal polyposis that required surgery had a concordance > 50% in sib-pairs and were poorly correlated to other clinical parameters. The pancreatic status was highly concordant in pairs of siblings (i.e., 95.1%) but a different pancreatic status was observed in patients with the same CFTR mutations. This suggests a close relationship of the pancreatic status with the “whole” CFTR genotype, including mutations in regulatory regions that may modulate the levels of CFTR expression. Finally, a severe course of CF was evident in a number of patients with pancreatic sufficiency. Conclusions Physicians involved in care of patients with CF and in genetic counseling must be aware of the clinical heterogeneity of CF even in sib-pairs that, at the state of the art, is difficult to explain. Electronic supplementary material The online version of this article (10.1186/s12890-018-0766-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vito Terlizzi
- Dipartimento di Pediatria, Centro Regionale Toscano per la Fibrosi Cistica, Azienda Ospedaliero-Universitaria Meyer, Viale Gaetano Pieraccini 24, 50139, Florence, Italy.
| | - Marco Lucarelli
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza Università e Policlinico Umberto I, Rome, Italy
| | - Donatello Salvatore
- Centro Regionale Fibrosi Cistica, Centro Pediatrico Bambino Gesù Basilicata, AOR San Carlo, Potenza, Italy
| | - Adriano Angioni
- Laboratorio di Genetica Medica, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Arianna Bisogno
- Centro Regionale Fibrosi Cistica, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Cesare Braggion
- Dipartimento di Pediatria, Centro Regionale Toscano per la Fibrosi Cistica, Azienda Ospedaliero-Universitaria Meyer, Viale Gaetano Pieraccini 24, 50139, Florence, Italy
| | | | - Vincenzo Carnovale
- Centro Regionale Fibrosi Cistica Adulti, Dipartimento di Scienze Mediche Traslazionali, Università di Napoli Federico II, Naples, Italy
| | - Rosaria Casciaro
- Centro Regionale Fibrosi Cistica, U.O.C. Pneumologia, IRCCS G. Gaslini, Genua, Italy
| | - Giuseppe Castaldo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy.,CEINGE-Biotecnologie avanzate, Naples, Italy
| | - Natalia Cirilli
- Centro Regionale Fibrosi Cistica, Dipartimento Materno-Infantile, Ospedali Riuniti Ancona, Ancona, Italy
| | - Mirella Collura
- CRR Fibrosi Cistica, Ospedale dei Bambini, ARNAS Civico, Palermo, Italy
| | - Carla Colombo
- Centro Regionale Fibrosi Cistica, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Antonella Miriam Di Lullo
- Dipartimento di Neuroscienze, Scienze Riproduttive ed Odontostomatologica, Università di Napoli Federico II, Naples, Italy
| | | | - Vincenzina Lucidi
- Unità Regionale di Fibrosi Cistica, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Elisa Madarena
- Centro Regionale Fibrosi Cistica, Ospedale Giovanni Paolo II, Lamezia, Italy
| | - Rita Padoan
- Centro Regionale di supporto Fibrosi Cistica, Dipartimento di Pediatria, Università di Brescia, AO Spedali Civili, Brescia, Italy
| | - Serena Quattrucci
- Centro Fibrosi Cistica Regione Lazio, Dipartimento di Pediatria e Neuropsichiatria Infantile, Sapienza Università-Policlinico Umberto I, Rome, Italy
| | - Valeria Raia
- Centro Regionale Fibrosi Cistica, Sezione Pediatrica, Dipartimento di Scienze Mediche Traslazionali, Università di Napoli Federico II, Naples, Italy
| | - Manuela Seia
- Laboratorio di Genetica Medica, Fondazione IRCCS Policlinico Ca' Granda Ospedale, Milan, Italy
| | - Lisa Termini
- Ospedale dei Bambini G. Di Cristina, Centro Regionale Fibrosi Cistica, Palermo, Italy
| | - Federica Zarrilli
- Dipartimento di Bioscienze e Territorio, Università del Molise, Isernia, Italy
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24
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Stolzenburg LR, Harris A. The role of microRNAs in chronic respiratory disease: recent insights. Biol Chem 2018; 399:219-234. [PMID: 29148977 DOI: 10.1515/hsz-2017-0249] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 10/24/2017] [Indexed: 01/16/2023]
Abstract
Chronic respiratory diseases encompass a group of diverse conditions affecting the airways, which all impair lung function over time. They include cystic fibrosis (CF), idiopathic pulmonary fibrosis (IPF), chronic obstructive pulmonary disease (COPD) and asthma, which together affect hundreds of millions of people worldwide. MicroRNAs (miRNAs), a class of small non-coding RNAs involved in post-transcriptional gene repression, are now recognized as major regulators in the development and progression of chronic lung disease. Alterations in miRNA abundance occur in lung tissue, inflammatory cells, and freely circulating in blood and are thought to function both as drivers and modifiers of disease. Their importance in lung pathology has prompted the development of miRNA-based therapies and biomarker tools. Here, we review the current literature on miRNA expression and function in chronic respiratory disease and highlight further research that is needed to propel miRNA treatments for lung disorders towards the clinic.
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Affiliation(s)
- Lindsay R Stolzenburg
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA.,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ann Harris
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA.,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44016, USA
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25
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Comegna M, Amato F, Liguori R, Berni Canani R, Spagnuolo MI, Morroni M, Guarino A, Castaldo G. Two cases of microvillous inclusion disease caused by novel mutations in MYO5B gene. Clin Case Rep 2018; 6:2451-2456. [PMID: 30564347 PMCID: PMC6293129 DOI: 10.1002/ccr3.1879] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/29/2018] [Accepted: 09/19/2018] [Indexed: 12/13/2022] Open
Abstract
Microvillous inclusion disease (MVID) typically appears with severe chronic diarrhea in the few days after birth and rapidly causes dehydration and metabolic acidosis. In this context, presenting two novel cases, we underline the crucial importance of mutation analysis for the diagnosis of this disease that may be easily misdiagnosed.
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Affiliation(s)
- Marika Comegna
- Dipartimento di Medicina Molecolare e Biotecnologie MedicheUniversità di Napoli Federico IINaplesItaly
- CEINGE‐Biotecnologie AvanzateNaplesItaly
| | - Felice Amato
- Dipartimento di Medicina Molecolare e Biotecnologie MedicheUniversità di Napoli Federico IINaplesItaly
- CEINGE‐Biotecnologie AvanzateNaplesItaly
| | - Renato Liguori
- Dipartimento di Medicina Molecolare e Biotecnologie MedicheUniversità di Napoli Federico IINaplesItaly
- CEINGE‐Biotecnologie AvanzateNaplesItaly
| | - Roberto Berni Canani
- Dipartimento di Medicina Molecolare e Biotecnologie MedicheUniversità di Napoli Federico IINaplesItaly
- Dipartimento di Scienze Mediche Traslazionali, Sezione di PediatriaUniversità di Napoli Federico IINaplesItaly
- European Laboratory for the Investigation of Food‐Induced DiseasesUniversità di Napoli Federico IINaplesItaly
| | - Maria Immacolata Spagnuolo
- Dipartimento di Scienze Mediche Traslazionali, Sezione di PediatriaUniversità di Napoli Federico IINaplesItaly
| | - Manrico Morroni
- Dipartimento di Medicina Sperimentale e Clinica, Sezione di Neuroscienze e Biologia cellulareUniversità Politecnica delle MarcheAnconaItaly
| | - Alfredo Guarino
- Dipartimento di Scienze Mediche Traslazionali, Sezione di PediatriaUniversità di Napoli Federico IINaplesItaly
| | - Giuseppe Castaldo
- Dipartimento di Medicina Molecolare e Biotecnologie MedicheUniversità di Napoli Federico IINaplesItaly
- CEINGE‐Biotecnologie AvanzateNaplesItaly
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26
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Bardin P, Sonneville F, Corvol H, Tabary O. Emerging microRNA Therapeutic Approaches for Cystic Fibrosis. Front Pharmacol 2018; 9:1113. [PMID: 30349480 PMCID: PMC6186820 DOI: 10.3389/fphar.2018.01113] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/10/2018] [Indexed: 12/12/2022] Open
Abstract
Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene and remains the most common life-shortening diseases affecting the exocrine organs. The absence of this channel results in an imbalance of ion concentrations across the cell membrane and results in more abnormal secretion and mucus plugging in the gastrointestinal tract and in the lungs of CF patients. The direct introduction of fully functional CFTR by gene therapy has long been pursued as a therapeutical option to restore CFTR function independent of the specific CFTR mutation, but the different clinical trials failed to propose persuasive evidence of this strategy. The last ten years has led to the development of new pharmacotherapies which can activate CFTR function in a mutation-specific manner. Although approximately 2,000 different disease-associated mutations have been identified, a single codon deletion, F508del, is by far the most common and is present on at least one allele in approximately 70% of the patients in CF populations. This strategy is limited by chemistry, the knowledge on CFTR and the heterogenicity of the patients. New research efforts in CF aim to develop other therapeutical approaches to combine different strategies. Targeting RNA appears as a new and an important opportunity to modulate dysregulated biological processes. Abnormal miRNA activity has been linked to numerous diseases, and over the last decade, the critical role of miRNA in regulating biological processes has fostered interest in how miRNA binds to and interacts explicitly with the target protein. Herein, this review describes the different strategies to identify dysregulated miRNA opens up a new concept and new opportunities to correct CFTR deficiency. This review describes therapeutic applications of antisense techniques currently under investigation in CF.
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Affiliation(s)
- Pauline Bardin
- INSERM UMR-S938, Centre de Recherche Saint Antoine, Faculté des Sciences, Sorbonne Université, Paris, France
| | - Florence Sonneville
- INSERM UMR-S938, Centre de Recherche Saint Antoine, Faculté des Sciences, Sorbonne Université, Paris, France
| | - Harriet Corvol
- INSERM UMR-S938, Centre de Recherche Saint Antoine, Faculté des Sciences, Sorbonne Université, Paris, France.,Paediatric Respiratory Department, Hôpital Trousseau, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Olivier Tabary
- INSERM UMR-S938, Centre de Recherche Saint Antoine, Faculté des Sciences, Sorbonne Université, Paris, France
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27
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Krause K, Kopp BT, Tazi MF, Caution K, Hamilton K, Badr A, Shrestha C, Tumin D, Hayes D, Robledo-Avila F, Hall-Stoodley L, Klamer BG, Zhang X, Partida-Sanchez S, Parinandi NL, Kirkby SE, Dakhlallah D, McCoy KS, Cormet-Boyaka E, Amer AO. The expression of Mirc1/Mir17-92 cluster in sputum samples correlates with pulmonary exacerbations in cystic fibrosis patients. J Cyst Fibros 2018; 17:454-461. [PMID: 29241629 PMCID: PMC5995663 DOI: 10.1016/j.jcf.2017.11.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/27/2017] [Accepted: 11/16/2017] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Cystic fibrosis (CF) is a multi-organ disorder characterized by chronic sino-pulmonary infections and inflammation. Many patients with CF suffer from repeated pulmonary exacerbations that are predictors of worsened long-term morbidity and mortality. There are no reliable markers that associate with the onset or progression of an exacerbation or pulmonary deterioration. Previously, we found that the Mirc1/Mir17-92a cluster which is comprised of 6 microRNAs (Mirs) is highly expressed in CF mice and negatively regulates autophagy which in turn improves CF transmembrane conductance regulator (CFTR) function. Therefore, here we sought to examine the expression of individual Mirs within the Mirc1/Mir17-92 cluster in human cells and biological fluids and determine their role as biomarkers of pulmonary exacerbations and response to treatment. METHODS Mirc1/Mir17-92 cluster expression was measured in human CF and non-CF plasma, blood-derived neutrophils, and sputum samples. Values were correlated with pulmonary function, exacerbations and use of CFTR modulators. RESULTS Mirc1/Mir17-92 cluster expression was not significantly elevated in CF neutrophils nor plasma when compared to the non-CF cohort. Cluster expression in CF sputum was significantly higher than its expression in plasma. Elevated CF sputum Mirc1/Mir17-92 cluster expression positively correlated with pulmonary exacerbations and negatively correlated with lung function. Patients with CF undergoing treatment with the CFTR modulator Ivacaftor/Lumacaftor did not demonstrate significant change in the expression Mirc1/Mir17-92 cluster after six months of treatment. CONCLUSIONS Mirc1/Mir17-92 cluster expression is a promising biomarker of respiratory status in patients with CF including pulmonary exacerbation.
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Affiliation(s)
- Kathrin Krause
- Department of Microbial Infection and Immunity, Columbus, OH, USA; Dorothy M. Davis Heart and Lung Research Institute, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, USA
| | - Benjamin T Kopp
- Department of Pediatrics, Columbus, OH, USA; Nationwide Children's Hospital, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, USA
| | - Mia F Tazi
- Department of Microbial Infection and Immunity, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, USA
| | - Kyle Caution
- Department of Microbial Infection and Immunity, Columbus, OH, USA; Dorothy M. Davis Heart and Lung Research Institute, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, USA
| | - Kaitlin Hamilton
- Department of Microbial Infection and Immunity, Columbus, OH, USA; Dorothy M. Davis Heart and Lung Research Institute, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, USA
| | - Asmaa Badr
- Department of Microbial Infection and Immunity, Columbus, OH, USA; Dorothy M. Davis Heart and Lung Research Institute, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, USA
| | - Chandra Shrestha
- Department of Pediatrics, Columbus, OH, USA; Nationwide Children's Hospital, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, USA
| | - Dmitry Tumin
- Department of Anesthesiology & Pain Medicine, Columbus, OH, USA; Nationwide Children's Hospital, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, USA
| | - Don Hayes
- Department of Pediatrics, Columbus, OH, USA; Nationwide Children's Hospital, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, USA
| | - Frank Robledo-Avila
- Department of Pediatrics, Columbus, OH, USA; Nationwide Children's Hospital, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, USA
| | - Luanne Hall-Stoodley
- Department of Microbial Infection and Immunity, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, USA
| | - Brett G Klamer
- Center for Biostatistics, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, USA
| | - Xiaoli Zhang
- Center for Biostatistics, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, USA
| | - Santiago Partida-Sanchez
- Department of Pediatrics, Columbus, OH, USA; Nationwide Children's Hospital, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, USA
| | - Narasimham L Parinandi
- Dorothy M. Davis Heart and Lung Research Institute, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, USA
| | - Stephen E Kirkby
- Department of Pediatrics, Columbus, OH, USA; Nationwide Children's Hospital, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, USA
| | - Duaa Dakhlallah
- Microbiology, Immunology and Cell Biology Department, West Virginia University, Morgantown, WV, USA
| | - Karen S McCoy
- Department of Pediatrics, Columbus, OH, USA; Nationwide Children's Hospital, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, USA
| | - Estelle Cormet-Boyaka
- Department of Veterinary Biosciences, Columbus, OH, USA; Dorothy M. Davis Heart and Lung Research Institute, Columbus, OH, USA
| | - Amal O Amer
- Department of Microbial Infection and Immunity, Columbus, OH, USA; Dorothy M. Davis Heart and Lung Research Institute, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, USA.
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28
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Abstract
Non-coding RNAs (ncRNAs) are an abundant class of RNAs that include small ncRNAs, long non-coding RNAs (lncRNA) and pseudogenes. The human ncRNA atlas includes thousands of these specialised RNA molecules that are further subcategorised based on their size or function. Two of the more well-known and widely studied ncRNA species are microRNAs (miRNAs) and lncRNAs. These are regulatory RNAs and their altered expression has been implicated in the pathogenesis of a variety of human diseases. Failure to express a functional cystic fibrosis (CF) transmembrane receptor (CFTR) chloride ion channel in epithelial cells underpins CF. Secondary to the CFTR defect, it is known that other pathways can be altered and these may contribute to the pathophysiology of CF lung disease in particular. For example, quantitative alterations in expression of some ncRNAs are associated with CF. In recent years, there has been a series of published studies exploring ncRNA expression and function in CF. The majority have focussed principally on miRNAs, with just a handful of reports to date on lncRNAs. The present study reviews what is currently known about ncRNA expression and function in CF, and discusses the possibility of applying this knowledge to the clinical management of CF in the near future.
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Affiliation(s)
- Arlene M.A. Glasgow
- Lung Biology Group, Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland
| | - Chiara De Santi
- Lung Biology Group, Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland
| | - Catherine M. Greene
- Lung Biology Group, Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland
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29
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Fernandez Fernandez E, De Santi C, De Rose V, Greene CM. CFTR dysfunction in cystic fibrosis and chronic obstructive pulmonary disease. Expert Rev Respir Med 2018; 12:483-492. [PMID: 29750581 DOI: 10.1080/17476348.2018.1475235] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Obstructive lung diseases such as cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) are causes of high morbidity and mortality worldwide. CF is a multiorgan genetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene and is characterized by progressive chronic obstructive lung disease. Most cases of COPD are a result of noxious particles, mainly cigarette smoke but also other environmental pollutants. Areas covered: Although the pathogenesis and pathophysiology of CF and COPD differ, they do share key phenotypic features and because of these similarities there is great interest in exploring common mechanisms and/or factors affected by CFTR mutations and environmental insults involved in COPD. Various molecular, cellular and clinical studies have confirmed that CFTR protein dysfunction is common in both the CF and COPD airways. This review provides an update of our understanding of the role of dysfunctional CFTR in both respiratory diseases. Expert commentary: Drugs developed for people with CF to improve mutant CFTR function and enhance CFTR ion channel activity might also be beneficial in patients with COPD. A move toward personalized therapy using, for example, microRNA modulators in conjunction with CFTR potentiators or correctors, could enhance treatment of both diseases.
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Affiliation(s)
- Elena Fernandez Fernandez
- a Lung Biology Group, Department of Clinical Microbiology , RCSI Education & Research Centre, Beaumont Hospital , Dublin 9 , Ireland
| | - Chiara De Santi
- a Lung Biology Group, Department of Clinical Microbiology , RCSI Education & Research Centre, Beaumont Hospital , Dublin 9 , Ireland
| | - Virginia De Rose
- b Department of Clinical and Biological Sciences , University of Torino , Torino , Italy
| | - Catherine M Greene
- a Lung Biology Group, Department of Clinical Microbiology , RCSI Education & Research Centre, Beaumont Hospital , Dublin 9 , Ireland
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30
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Di Lullo AM, Scorza M, Amato F, Comegna M, Raia V, Maiuri L, Ilardi G, Cantone E, Castaldo G, Iengo M. An "ex vivo model" contributing to the diagnosis and evaluation of new drugs in cystic fibrosis. ACTA OTORHINOLARYNGOLOGICA ITALICA 2018; 37:207-213. [PMID: 27897275 PMCID: PMC5463510 DOI: 10.14639/0392-100x-1328] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 07/25/2016] [Indexed: 01/09/2023]
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the cystic fibrosis transmembrane regulator (CFTR) gene. About 2000 mutations have been described so far. We setup an ex vivo model of human nasal epithelial cells (HNECs) to study CF patients testing the effect of novel mutations and molecular therapies. We performed sampling (by brushing), followed by culture and analysis of HNECs using a series of molecular techniques. We performed 50 brushings from CF patients and controls. Using cultured cells, we: i) demonstrated the widely heterogeneous CFTR expression in patients and in controls; ii) defined the splicing effect of a CFTR mutation; iii) assessed the CFTR gating activity in patients bearing different mutations; iv) demonstrated that butyrate significantly enhances CFTR expression. Based on our data, we can conclude: 1) HNEC brushing is performed without anaesthesia and is well tolerated in all CF patients (children and adults); 2) HNECs can be preserved for up to 48 hours before culture allowings multicentre studies; 3) HNECs culture can be considered a suitable model to study the molecular effects of new CFTR gene mutations and/or uncertain meaning specific mutations of carriers; 4) an ex vivo model of HNECs may be used to evaluate, before human use, the effect of new drugs on patients’ cells bearing specific CFTR mutations; 5) the methodology is adequate for a quantitative measurement, by fluorescence, of the CFTR gating activity of the HNECs from patients with different genotypes identifying: a) CF patients bearing two severe mutations with an activity < 10% (compared to controls – 100%); b) CF patients bearing at least a mild mutation with an activity of 10-20%; c) CF carriers (heterozygous subjects) with an activity between 40-70%.
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Affiliation(s)
- A M Di Lullo
- Department of Neuroscience, Section of Otorhinolaryngology, University of Naples "Federico II", Italy.,CEINGE-Advanced Biotechnologies scarl, Naples, Italy.,Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Italy
| | - M Scorza
- CEINGE-Advanced Biotechnologies scarl, Naples, Italy.,Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Italy
| | - F Amato
- CEINGE-Advanced Biotechnologies scarl, Naples, Italy.,Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Italy
| | - M Comegna
- CEINGE-Advanced Biotechnologies scarl, Naples, Italy.,Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Italy
| | - V Raia
- Department of Translational Medical Sciences, University of Naples "Federico II", Italy
| | - L Maiuri
- Department of Science and Technology Innovation, University of Piemonte Orientale, Novara, Italy
| | - G Ilardi
- European Institute for Research in Cystic Fibrosis, San Raffaele Hospital, Milan, Italy
| | - E Cantone
- Department of Neuroscience, Section of Otorhinolaryngology, University of Naples "Federico II", Italy
| | - G Castaldo
- CEINGE-Advanced Biotechnologies scarl, Naples, Italy.,Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Italy
| | - M Iengo
- Department of Neuroscience, Section of Otorhinolaryngology, University of Naples "Federico II", Italy
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31
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McNally P, Greene CM. Cystic fibrosis: a model for precision medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2018. [DOI: 10.1080/23808993.2018.1444990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Paul McNally
- Department of Paediatrics, Royal College of Surgeons in Ireland, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
- Cystic Fibrosis Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
| | - Catherine M. Greene
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin, Ireland
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32
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De Santi C, Gadi S, Swiatecka-Urban A, Greene CM. Identification of a novel functional miR-143-5p recognition element in the Cystic Fibrosis Transmembrane Conductance Regulator 3'UTR. AIMS GENETICS 2018; 5:53-62. [PMID: 31435512 PMCID: PMC6690249 DOI: 10.3934/genet.2018.1.53] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 02/08/2018] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs involved in regulation of gene expression. They bind in a sequence-specific manner to miRNA recognition elements (MREs) located in the 3' untranslated region (UTR) of target mRNAs and prevent mRNA translation. MiRNA expression is dysregulated in cystic fibrosis (CF), affecting several biological processes including ion conductance in the epithelial cells of the lung. We previously reported that miR-143 is up-regulated in CF bronchial brushings compared to non-CF. Here we identified two predicted binding sites for miR-143-5p (starting at residues 558 and 644) on the CFTR mRNA, and aimed to assess whether CFTR is a true molecular target of miR-143-5p. Expression of miR-143-5p was found to be up-regulated in a panel of CF vs non-CF cell lines (1.7-fold, P = 0.0165), and its levels were increased in vitro after 20 hours treatment with bronchoalveolar lavage fluid from CF patients compared to vehicle-treated cells (3.3-fold, P = 0.0319). Luciferase assays were performed to elucidate direct miRNA::target interactions and showed that miR-143-5p significantly decreased the reporter activity when carrying the wild-type full length sequence of CFTR 3'UTR (minus 15%, P = 0.005). This repression was rescued by the disruption of the first, but not the second, predicted MRE, suggesting that the residue starting at 558 was the actual active binding site. In conclusion, we here showed that miR-143-5p modestly but significantly inhibits CFTR, improving the knowledge on functional MREs within the CFTR 3'UTR. This could lead to the development of novel therapeutic strategies where miRNA-mediated CFTR repression is blocked thereby possibly increasing the efficacy of the currently available CFTR modulators.
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Affiliation(s)
- Chiara De Santi
- Lung Biology Group, Department of Clinical Microbiology, RCSI Education & Research Centre, Beaumont Hospital, Dublin 9, Ireland
| | - Sucharitha Gadi
- Lung Biology Group, Department of Clinical Microbiology, RCSI Education & Research Centre, Beaumont Hospital, Dublin 9, Ireland
| | - Agnieszka Swiatecka-Urban
- Children's Hospital of Pittsburgh of UPMC, Department of Cell Biology, University of Pittsburgh School of Medicine Pittsburgh, PA, USA
| | - Catherine M Greene
- Lung Biology Group, Department of Clinical Microbiology, RCSI Education & Research Centre, Beaumont Hospital, Dublin 9, Ireland
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Fabbri E, Tamanini A, Jakova T, Gasparello J, Manicardi A, Corradini R, Sabbioni G, Finotti A, Borgatti M, Lampronti I, Munari S, Dechecchi MC, Cabrini G, Gambari R. A Peptide Nucleic Acid against MicroRNA miR-145-5p Enhances the Expression of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) in Calu-3 Cells. Molecules 2017; 23:molecules23010071. [PMID: 29286300 PMCID: PMC6017273 DOI: 10.3390/molecules23010071] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/05/2017] [Accepted: 12/14/2017] [Indexed: 01/18/2023] Open
Abstract
Peptide nucleic acids (PNAs) are very useful tools for gene regulation at different levels, but in particular in the last years their use for targeting microRNA (anti-miR PNAs) has provided impressive advancements. In this respect, microRNAs related to the repression of cystic fibrosis transmembrane conductance regulator (CFTR) gene, which is defective in cystic fibrosis, are of great importance in the development of new type of treatments. In this paper we propose the use of an anti-miR PNA for targeting miR-145, a microRNA reported to suppress CFTR expression. Octaarginine-anti-miR PNA conjugates were delivered to Calu-3 cells, exerting sequence dependent targeting of miR-145-5p. This allowed to enhance expression of the miR-145 regulated CFTR gene, analyzed at mRNA (RT-qPCR, Reverse Transcription quantitative Polymerase Chain Reaction) and CFTR protein (Western blotting) level.
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Affiliation(s)
- Enrica Fabbri
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
| | - Anna Tamanini
- Laboratory of Molecular Pathology, University-Hospital, 37126 Verona, Italy.
| | - Tiziana Jakova
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy.
| | - Jessica Gasparello
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
| | - Alex Manicardi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy.
| | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy.
| | - Giuseppe Sabbioni
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
| | - Alessia Finotti
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
| | - Ilaria Lampronti
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
| | - Silvia Munari
- Laboratory of Molecular Pathology, University-Hospital, 37126 Verona, Italy.
| | | | - Giulio Cabrini
- Laboratory of Molecular Pathology, University-Hospital, 37126 Verona, Italy.
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
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34
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Narożna B, Langwiński W, Szczepankiewicz A. Non-Coding RNAs in Pediatric Airway Diseases. Genes (Basel) 2017; 8:genes8120348. [PMID: 29186897 PMCID: PMC5748666 DOI: 10.3390/genes8120348] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/18/2017] [Accepted: 11/21/2017] [Indexed: 12/18/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are involved in the regulation of numerous biological processes and pathways and therefore have been extensively studied in human diseases. Previous reports have shown that non-coding RNAs play a crucial role in the pathogenesis and aberrant regulation of respiratory diseases. The altered expression of microRNAs (miRNAs) and long non-coding RNAs in blood and also locally in sputum or exhaled breath condensate influences lung function, immune response, and disease phenotype and may be used for the development of biomarkers specific for airway disease. In this review, we provide an overview of the recent works studying the non-coding RNAs in airway diseases, with a particular focus on chronic respiratory diseases of childhood. We have chosen the most common chronic respiratory condition—asthma—and the most severe, chronic disease of the airways—cystic fibrosis. Study of the altered expression of non-coding RNAs in these diseases may be key to better understanding their pathogenesis and improving diagnosis, while also holding promise for the development of therapeutic strategies using the regulatory potential of non-coding RNAs.
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Affiliation(s)
- Beata Narożna
- Laboratory of Molecular and Cell Biology, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, 60-512 Poznan, Poland.
| | - Wojciech Langwiński
- Laboratory of Molecular and Cell Biology, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, 60-512 Poznan, Poland.
| | - Aleksandra Szczepankiewicz
- Laboratory of Molecular and Cell Biology, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, 60-512 Poznan, Poland.
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35
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Bartoszewska S, Kamysz W, Jakiela B, Sanak M, Króliczewski J, Bebok Z, Bartoszewski R, Collawn JF. miR-200b downregulates CFTR during hypoxia in human lung epithelial cells. Cell Mol Biol Lett 2017; 22:23. [PMID: 29167681 PMCID: PMC5688675 DOI: 10.1186/s11658-017-0054-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/17/2017] [Indexed: 12/28/2022] Open
Abstract
Background Hypoxic conditions induce the expression of hypoxia-inducible factors (HIFs) that allow cells to adapt to the changing conditions and alter the expression of a number of genes including the cystic fibrosis transmembrane conductance regulator (CFTR). CFTR is a low abundance mRNA in airway epithelial cells even during normoxic conditions, but during hypoxia its mRNA expression decreases even further. Methods In the current studies, we examined the kinetics of hypoxia-induced changes in CFTR mRNA and protein levels in two human airway epithelial cell lines, Calu-3 and 16HBE14o-, and in normal primary bronchial epithelial cells. Our goal was to examine the posttranscriptional modifications that affected CFTR expression during hypoxia. We utilized in silico predictive protocols to establish potential miRNAs that could potentially regulate CFTR message stability and identified miR-200b as a candidate molecule. Results Analysis of each of the epithelial cell types during prolonged hypoxia revealed that CFTR expression decreased after 12 h during a time when miR-200b was continuously upregulated. Furthermore, manipulation of the miRNA levels during normoxia and hypoxia using miR-200b mimics and antagomirs decreased and increased CFTR mRNA levels, respectively, and thus established that miR-200b downregulates CFTR message levels during hypoxic conditions. Conclusion The data suggest that miR-200b may be a suitable target for modulating CFTR levels in vivo. Electronic supplementary material The online version of this article (10.1186/s11658-017-0054-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sylwia Bartoszewska
- Department of Inorganic Chemistry, Medical University of Gdansk, Gdansk, Poland
| | - Wojciech Kamysz
- Department of Inorganic Chemistry, Medical University of Gdansk, Gdansk, Poland
| | - Bogdan Jakiela
- Department of Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Marek Sanak
- Department of Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Jarosław Króliczewski
- Department of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Zsuzsa Bebok
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA
| | - Rafal Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland
| | - James F Collawn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA
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36
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Delavan B, Roberts R, Huang R, Bao W, Tong W, Liu Z. Computational drug repositioning for rare diseases in the era of precision medicine. Drug Discov Today 2017; 23:382-394. [PMID: 29055182 DOI: 10.1016/j.drudis.2017.10.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/19/2017] [Accepted: 10/11/2017] [Indexed: 12/12/2022]
Abstract
There are tremendous unmet needs in drug development for rare diseases. Computational drug repositioning is a promising approach and has been successfully applied to the development of treatments for diseases. However, how to utilize this knowledge and effectively conduct and implement computational drug repositioning approaches for rare disease therapies is still an open issue. Here, we focus on the means of utilizing accumulated genomic data for accelerating and facilitating drug repositioning for rare diseases. First, we summarize the current genome landscape of rare diseases. Second, we propose several promising bioinformatics approaches and pipelines for computational drug repositioning for rare diseases. Finally, we discuss recent regulatory incentives and other enablers in rare disease drug development and outline the remaining challenges.
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Affiliation(s)
- Brian Delavan
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA; University of Arkansas at Little Rock, Little Rock, AR 72204, USA
| | - Ruth Roberts
- ApconiX, BioHub at Alderley Park, Alderley Edge SK10 4TG, UK; University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health Rockville, MD 20850, USA
| | | | - Weida Tong
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Zhichao Liu
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
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37
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Lucarelli M, Porcaro L, Biffignandi A, Costantino L, Giannone V, Alberti L, Bruno SM, Corbetta C, Torresani E, Colombo C, Seia M. A New Targeted CFTR Mutation Panel Based on Next-Generation Sequencing Technology. J Mol Diagn 2017; 19:788-800. [PMID: 28736296 DOI: 10.1016/j.jmoldx.2017.06.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 06/01/2017] [Accepted: 06/07/2017] [Indexed: 01/16/2023] Open
Abstract
Searching for mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR) is a key step in the diagnosis of and neonatal and carrier screening for cystic fibrosis (CF), and it has implications for prognosis and personalized therapy. The large number of mutations and genetic and phenotypic variability make this search a complex task. Herein, we developed, validated, and tested a laboratory assay for an extended search for mutations in CFTR using a next-generation sequencing-based method, with a panel of 188 CFTR mutations customized for the Italian population. Overall, 1426 dried blood spots from neonatal screening, 402 genomic DNA samples from various origins, and 1138 genomic DNA samples from patients with CF were analyzed. The assay showed excellent analytical and diagnostic operative characteristics. We identified and experimentally validated 159 (of 188) CFTR mutations. The assay achieved detection rates of 95.0% and 95.6% in two large-scale case series of CF patients from central and northern Italy, respectively. These detection rates are among the highest reported so far with a genetic test for CF based on a mutation panel. This assay appears to be well suited for diagnostics, neonatal and carrier screening, and assisted reproduction, and it represents a considerable advantage in CF genetic counseling.
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Affiliation(s)
- Marco Lucarelli
- Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy; Pasteur Institute Cenci Bolognetti Foundation, Sapienza University, Rome, Italy.
| | - Luigi Porcaro
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alice Biffignandi
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lucy Costantino
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Giannone
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luisella Alberti
- Newborn Screening Laboratory, ASST Fatebenefratelli Sacco-PO Ospedale dei Bambini "V. Buzzi", Milan, Italy
| | - Sabina Maria Bruno
- Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Carlo Corbetta
- Newborn Screening Laboratory, ASST Fatebenefratelli Sacco-PO Ospedale dei Bambini "V. Buzzi", Milan, Italy
| | - Erminio Torresani
- Unit of Microbiology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Carla Colombo
- Cystic Fibrosis Centre, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Manuela Seia
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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38
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Peptide Nucleic Acids as miRNA Target Protectors for the Treatment of Cystic Fibrosis. Molecules 2017; 22:molecules22071144. [PMID: 28698463 PMCID: PMC6152032 DOI: 10.3390/molecules22071144] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/03/2017] [Accepted: 07/04/2017] [Indexed: 12/12/2022] Open
Abstract
Cystic Fibrosis (CF) is one of the most common life shortening conditions in Caucasians. CF is caused by mutations in the CF Transmembrane Conductance Regulator (CFTR) gene which result in reduced or altered CFTR functionality. Several microRNAs (miRNAs) downregulate the expression of CFTR, thus causing or exacerbating the symptoms of CF. In this context, the design of anti-miRNA agents represents a valid functional tool, but its translation to the clinic might lead to unpredictable side effects because of the interference with the expression of other genes regulated by the same miRNAs. Herein, for the first time, is proposed the use of peptide nucleic acids (PNAs) to protect specific sequences in the 3’UTR (untranslated region) of the CFTR messenger RNA (mRNA) by action of miRNAs. Two PNAs (7 and 13 bases long) carrying the tetrapeptide Gly-SerP-SerP-Gly at their C-end, fully complementary to the 3’UTR sequence recognized by miR-509-3p, have been synthesized and the structural features of target PNA/RNA heteroduplexes have been investigated by spectroscopic and molecular dynamics studies. The co-transfection of the pLuc-CFTR-3´UTR vector with different combinations of PNAs, miR-509-3p, and controls in A549 cells demonstrated the ability of the longer PNA to rescue the luciferase activity by up to 70% of the control, thus supporting the use of suitable PNAs to counteract the reduction in the CFTR expression.
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39
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Abstract
Cystic fibrosis is a complex genetic disease hallmarked by repetitive infectious exacerbations that leads to destruction of airway architecture, acute on chronic inflammatory changes, and deterioration in lung function. Predicting an exacerbation may help preempt some of these changes by the initiation of swift antibiotic and anti-inflammatory therapy. A search for biomarkers that could predict exacerbations or help guide duration of antibiotic therapy is being aggressively sought. In this review, we discuss the most recent and promising biomarkers that hopefully will assist in the future management of the CF patient.
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40
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Lucarelli M. New era of cystic fibrosis: Full mutational analysis and personalized therapy. World J Med Genet 2017; 7:1-9. [DOI: 10.5496/wjmg.v7.i1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/19/2016] [Accepted: 02/21/2017] [Indexed: 02/07/2023] Open
Abstract
Despite its apparently simple genetics, cystic fibrosis (CF) is a rather complex genetic disease. A lot of variability in the steps of the path from the cystic fibrosis transmembrane conductance regulator (CFTR) gene to the clinical manifestations originates an uncertain genotype - phenotype relationship. A major determinant of this uncertainty is the incomplete knowledge of the CFTR mutated genotypes, due to the high number of CFTR mutations and to the higher number of their combinations in trans and in cis. Also the very limited knowledge of functional effects of CFTR mutated alleles severely impairs our diagnostic and prognostic ability. The final phenotypic modulation exerted by CFTR modifier genes and interactome further complicates the framework. The next generation sequencing approach is a rapid, low-cost and high-throughput tool that allows a near complete structural characterization of CFTR mutated genotypes, as well as of genotypes of several other genes cooperating to the final CF clinical manifestations. This powerful method perfectly complements the new personalized therapeutic approach for CF. Drugs active on specific CFTR mutational classes are already available for CF patients or are in phase 3 trials. A complete genetic characterization has been becoming crucial for a correct personalized therapy. However, the need of a functional classification of each CFTR mutation potently arises. Future big efforts towards an ever more detailed knowledge of both structural and functional CFTR defects, coupled to parallel personalized therapeutic interventions decisive for CF cure can be foreseen.
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Affiliation(s)
- Marco Lucarelli
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00161 Rome, Italy
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41
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Biswas R, Kumar P, Pollard HB. Regulation of mRNA turnover in cystic fibrosis lung disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27863009 DOI: 10.1002/wrna.1408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/13/2016] [Accepted: 10/16/2016] [Indexed: 01/07/2023]
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease due to mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, F508del-CFTR being the most frequent mutation. The CF lung is characterized by a hyperinflammatory phenotype and is regulated by multiple factors that coordinate its pathophysiology. In CF the expression of CFTR as well as proinflammatory genes are regulated at the level of messenger RNA (mRNA) stability, which subsequently affect translation. These mechanisms are mediated by inflammatory RNA-binding proteins as well as small endogenous noncoding microRNAs, in coordination with cellular signaling pathways. These regulatory factors exhibit altered expression and function in vivo in the CF lung, and play a key role in the pathophysiology of CF lung disease. In this review, we have described the role of mRNA stability and associated regulatory mechanisms in CF lung disease. WIREs RNA 2017, 8:e1408. doi: 10.1002/wrna.1408 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Roopa Biswas
- Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Parameet Kumar
- Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Harvey B Pollard
- Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
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42
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Terlizzi V, Castaldo G, Salvatore D, Lucarelli M, Raia V, Angioni A, Carnovale V, Cirilli N, Casciaro R, Colombo C, Di Lullo AM, Elce A, Iacotucci P, Comegna M, Scorza M, Lucidi V, Perfetti A, Cimino R, Quattrucci S, Seia M, Sofia VM, Zarrilli F, Amato F. Genotype-phenotype correlation and functional studies in patients with cystic fibrosis bearing CFTR complex alleles. J Med Genet 2016; 54:224-235. [PMID: 27738188 DOI: 10.1136/jmedgenet-2016-103985] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 09/12/2016] [Accepted: 09/22/2016] [Indexed: 01/08/2023]
Abstract
BACKGROUND The effect of complex alleles in cystic fibrosis (CF) is poorly defined for the lack of functional studies. OBJECTIVES To describe the genotype-phenotype correlation and the results of either in vitro and ex vivo studies performed on nasal epithelial cells (NEC) in a cohort of patients with CF carrying cystic fibrosis transmembrane conductance regulator (CFTR) complex alleles. METHODS We studied 70 homozygous, compound heterozygous or heterozygous for CFTR mutations: p.[Arg74Trp;Val201Met;Asp1270Asn], n=8; p.[Ile148Thr;Ile1023_Val1024del], n=5; p.[Arg117Leu;Leu997Phe], n=6; c.[1210-34TG[12];1210-12T[5];2930C>T], n=3; p.[Arg74Trp;Asp1270Asn], n=4; p.Asp1270Asn, n=2; p.Ile148Thr, n=6; p.Leu997Phe, n=36. In 39 patients, we analysed the CFTR gating activity on NEC in comparison with patients with CF (n=8) and carriers (n=4). Finally, we analysed in vitro the p.[Arg74Trp;Val201Met;Asp1270Asn] complex allele. RESULTS The p.[Ile148Thr;Ile1023_Val1024del] caused severe CF in five compound heterozygous with a class I-II mutation. Their CFTR activity on NEC was comparable with patients with two class I-II mutations (mean 7.3% vs 6.9%). The p.[Arg74Trp;Asp1270Asn] and the p.Asp1270Asn have scarce functional effects, while p.[Arg74Trp;Val201Met;Asp1270Asn] caused mild CF in four of five subjects carrying a class I-II mutation in trans, or CFTR-related disorders (CFTR-RD) in three having in trans a class IV-V mutation. The p.[Arg74Trp;Val201Met;Asp1270Asn] causes significantly (p<0.001) higher CFTR activity compared with compound heterozygous for class I-II mutations. Furthermore, five of six compounds heterozygous with the p.[Arg117Leu;Leu997Phe] had mild CF, whereas the p.Leu997Phe, in trans with a class I-II CFTR mutation, caused CFTR-RD or a healthy status (CFTR activity: 21.3-36.9%). Finally, compounds heterozygous for the c.[1210-34TG[12];1210-12T[5];2930C>T] and a class I-II mutation had mild CF or CFTR-RD (gating activity: 18.5-19.0%). CONCLUSIONS The effect of complex alleles partially depends on the mutation in trans. Although larger studies are necessary, the CFTR activity on NEC is a rapid contributory tool to classify patients with CFTR dysfunction.
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Affiliation(s)
- Vito Terlizzi
- Dipartimento di Pediatria, Centro Regionale Toscano per la Fibrosi Cistica, Azienda Ospedaliero-Universitaria Meyer, Florence, Italy
| | - Giuseppe Castaldo
- CEINGE-Biotecnologie Avanzate, Naples, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy
| | | | - Marco Lucarelli
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza Università e Policlinico Umberto I, Rome, Italy
| | - Valeria Raia
- Centro Regionale Fibrosi Cistica, Sezione Pediatrica, Dipartimento di Scienze Mediche Traslazionali, Università di Napoli Federico II, Naples, Italy
| | - Adriano Angioni
- Laboratorio di Genetica Medica, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Vincenzo Carnovale
- Dipartimento di Scienze Mediche Traslazionali, Centro Regionale Fibrosi Cistica, Sezione Adulti, Università di Napoli Federico II, Naples, Italy
| | - Natalia Cirilli
- Dipartimento Materno-Infantile, Ospedali Riuniti Ancona, Centro Regionale Fibrosi Cistica, Ancona, Italy
| | - Rosaria Casciaro
- Dipartimento di Pediatria, Centro Regionale Fibrosi Cistica, IRCCS G. Gaslini, Genova, Italy
| | - Carla Colombo
- Centro Regionale Fibrosi Cistica, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Antonella Miriam Di Lullo
- CEINGE-Biotecnologie Avanzate, Naples, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy.,Dipartimento di Neuroscienze, Sezione di ORL, Università di Napoli Federico II, Naples, Italy
| | | | - Paola Iacotucci
- Dipartimento di Scienze Mediche Traslazionali, Centro Regionale Fibrosi Cistica, Sezione Adulti, Università di Napoli Federico II, Naples, Italy
| | - Marika Comegna
- CEINGE-Biotecnologie Avanzate, Naples, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy
| | - Manuela Scorza
- CEINGE-Biotecnologie Avanzate, Naples, Italy.,Dipartimento di Biotecnologie e Bioscienze, Università di Milano Bicocca, Milan, Italy
| | - Vincenzina Lucidi
- Unità di Fibrosi Cistica, IRCCS Ospedale Pediatrico Bambin Gesù, Rome, Italy
| | | | - Roberta Cimino
- Dipartimento di Scienze Neurologiche, Riproduttive ed Odontostomatologiche, Università di Napoli Federico II, Naples, Italy
| | - Serena Quattrucci
- Centro Fibrosi Cistica, Sapienza Università e Policlinico Umberto I, Rome, Italy
| | - Manuela Seia
- Laboratorio Genetica Medica, Ospedale Maggiore Policlinico, Milano, Italy
| | | | - Federica Zarrilli
- Dipartimento di Bioscienze e Territorio, Università del Molise, Isernia, Italy
| | - Felice Amato
- CEINGE-Biotecnologie Avanzate, Naples, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy
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43
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Moisan S, Berlivet S, Ka C, Le Gac G, Dostie J, Férec C. Analysis of long-range interactions in primary human cells identifies cooperative CFTR regulatory elements. Nucleic Acids Res 2015; 44:2564-76. [PMID: 26615198 PMCID: PMC4824072 DOI: 10.1093/nar/gkv1300] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 11/07/2015] [Indexed: 12/19/2022] Open
Abstract
A mechanism by which control DNA elements regulate transcription over large linear genomic distances is by achieving close physical proximity with genes, and looping of the intervening chromatin paths. Alterations of such regulatory 'chromatin looping' systems are likely to play a critical role in human genetic disease at large. Here, we studied the spatial organization of a ≈790 kb locus encompassing the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Dysregulation of CFTR is responsible for cystic fibrosis, which is the most common lethal genetic disorder in Caucasian populations. CFTR is a relatively large gene of 189 kb with a rather complex tissue-specific and temporal expression profile. We used chromatin conformation at the CFTR locus to identify new DNA sequences that regulate its transcription. By comparing 5C chromatin interaction maps of the CFTR locus in expressing and non-expressing human primary cells, we identified several new contact points between the CFTR promoter and its surroundings, in addition to regions featuring previously described regulatory elements. We demonstrate that two of these novel interacting regions cooperatively increase CFTR expression, and suggest that the new enhancer elements located on either side of the gene are brought together through chromatin looping via CTCF.
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Affiliation(s)
- Stéphanie Moisan
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Inserm U1078, Université de Brest, SFR ScInBioS, CHRU de Brest, Établissement Français du Sang - Bretagne, Brest, France
| | - Soizik Berlivet
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada
| | - Chandran Ka
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Inserm U1078, Université de Brest, SFR ScInBioS, CHRU de Brest, Établissement Français du Sang - Bretagne, Brest, France
| | - Gérald Le Gac
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Inserm U1078, Université de Brest, SFR ScInBioS, CHRU de Brest, Établissement Français du Sang - Bretagne, Brest, France
| | - Josée Dostie
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada
| | - Claude Férec
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Inserm U1078, Université de Brest, SFR ScInBioS, CHRU de Brest, Établissement Français du Sang - Bretagne, Brest, France
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44
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Ebrahimi A, Sadroddiny E. MicroRNAs in lung diseases: Recent findings and their pathophysiological implications. Pulm Pharmacol Ther 2015; 34:55-63. [PMID: 26319446 DOI: 10.1016/j.pupt.2015.08.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/04/2015] [Accepted: 08/24/2015] [Indexed: 12/14/2022]
Abstract
Lung diseases are one of the leading causes of mortality and morbidity worldwide and effective therapies are imperfect. Nonetheless, recently some novel strategies have been developed to treat and curtail their debilitating impact. Some of the treatments include the role of MicroRNAs (miRNAs) in stemming the spread of lung morbidities. Micro RNAs are small non-coding RNAs which are known as important players in the posttranscriptional regulation of gene expression in mammalian cells by regulating translation. MiRNAs are involved in basic regulatory mechanisms of cells including influencing inflammation. MiRNA dysregulation, resulting in aberrant expression of a gene, is suggested to play a key role in susceptibility of diseases. MiRNAs are involved in the pathogenesis of lung diseases such as cystic fibrosis, lung cancer, asthma, chronic obstructive pulmonary disease, and Idiopathic pulmonary fibrosis. A better understanding of the involvement of miRNAs in pathogenesis of these diseases could result in the development of new therapeutic and diagnostic tools. In this review, we provide an overview of the current understanding of miRNA biogenesis and role as well as recent insights into role of some miRNAs in different pulmonary diseases.
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Affiliation(s)
- Ammar Ebrahimi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Esmaeil Sadroddiny
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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45
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Castaldo G, Amato F. Editorial Comment to p.Leu636Pro mutation is associated with cystic fibrosis transmembrane conductance regulator-related disorders (congenital bilateral absence of vas deferens). Int J Urol 2015; 22:804. [DOI: 10.1111/iju.12823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Giuseppe Castaldo
- Department of Molecular Medicine and Medical Biotechnology; University of Naples Federico II; Naples Italy
- CEINGE-Advanced Biotechnology Scarl; Naples Italy
| | - Felice Amato
- Department of Molecular Medicine and Medical Biotechnology; University of Naples Federico II; Naples Italy
- CEINGE-Advanced Biotechnology Scarl; Naples Italy
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46
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Hu LH, Ji JT, Li ZS. Potential application of miRNAs as diagnostic and therapeutic tools in chronic pancreatitis. J Cell Mol Med 2015; 19:2049-57. [PMID: 26149296 PMCID: PMC4568909 DOI: 10.1111/jcmm.12603] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 03/25/2015] [Indexed: 02/06/2023] Open
Abstract
Chronic pancreatitis (CP) is a progressive inflammatory disease typified by end-stage fibrosis. This disease can also increase the risk of pancreatic cancer. The associated diagnosis, pain and other complications further add to the burden of disease management. In recent years, significant progress has been achieved in identifying miRNAs and their physiological functions, including mRNA repression and protein expression control. Given the extensive effort made on miRNA research, a close correlation has been discovered between certain types of miRNAs and disease progression, particularly for tissue fibrosis. Designing miRNA-related tools for disease diagnosis and therapeutic treatments presents a novel and potential research frontier. In the current review, we discuss various miRNAs closely interacting with CP, as well as the possible development of targeted miRNA therapies in managing this disease.
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Affiliation(s)
- Liang-Hao Hu
- Department of Gastroenterology, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Jun-Tao Ji
- Department of Gastroenterology, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Zhao-Shen Li
- Department of Gastroenterology, Changhai Hospital, The Second Military Medical University, Shanghai, China
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47
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MicroRNA Dysregulation in Cystic Fibrosis. Mediators Inflamm 2015; 2015:529642. [PMID: 26185362 PMCID: PMC4491587 DOI: 10.1155/2015/529642] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 01/06/2015] [Indexed: 12/19/2022] Open
Abstract
The cystic fibrosis lung is a complex milieu comprising multiple factors that coordinate its physiology. MicroRNAs are regulatory factors involved in most biological processes and it is becoming increasingly clear that they play a key role in the development and manifestations of CF lung disease. These small noncoding RNAs act posttranscriptionally to inhibit protein production. Their involvement in the pathogenesis of CF lung disease stems from the fact that their expression is altered in vivo in the CF lung due to intrinsic and extrinsic factors; to date defective chloride ion conductance, endoplasmic reticulum stress, inflammation, and infection have been implicated in altering endogenous miRNA expression in this setting. Here, the current state-of-the-art and biological consequences of altered microRNA expression in cystic fibrosis are reviewed.
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48
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Canani RB, Castaldo G, Bacchetta R, Martín MG, Goulet O. Congenital diarrhoeal disorders: advances in this evolving web of inherited enteropathies. Nat Rev Gastroenterol Hepatol 2015; 12:293-302. [PMID: 25782092 PMCID: PMC7599016 DOI: 10.1038/nrgastro.2015.44] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Congenital diarrhoeal disorders (CDDs) represent an evolving web of rare chronic enteropathies, with a typical onset early in life. In many of these conditions, severe chronic diarrhoea represents the primary clinical manifestation, whereas in others diarrhoea is only a component of a more complex multi-organ or systemic disorder. Typically, within the first days of life, diarrhoea leads to a life-threatening condition highlighted by severe dehydration and serum electrolyte abnormalities. Thus, in the vast majority of cases appropriate therapy must be started immediately to prevent dehydration and long-term, sometimes severe, complications. The number of well-characterized disorders attributed to CDDs has gradually increased over the past several years, and many new genes have been identified and functionally related to CDDs, opening new diagnostic and therapeutic perspectives. Molecular analysis has changed the diagnostic scenario in CDDs, and led to a reduction in invasive and expensive procedures. Major advances have been made in terms of pathogenesis, enabling a better understanding not only of these rare conditions but also of more common diseases mechanisms.
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Affiliation(s)
- Roberto Berni Canani
- Department of Translational Medical Science, University of Naples Federico II, Via S. Pansini 5 80131, Naples, Italy
| | - Giuseppe Castaldo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via S. Pansini 5 80131, Naples, Italy
| | - Rosa Bacchetta
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford School of Medicine, 265 Campus Drive West, Stanford, CA 94305, USA
| | - Martín G. Martín
- Department of Pediatrics, Division of Gastroenterology and Nutrition, Mattel Children’s Hospital and the David Geffen School of Medicine, University of California Los Angeles, 757 Westwood Plaza Los Angeles, CA 90095, USA
| | - Olivier Goulet
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, University Paris Descartes Hôpital Necker Enfants Malades, 149 Rue de Sèvres, 75015 Paris, France
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49
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Sonneville F, Ruffin M, Guillot L, Rousselet N, Le Rouzic P, Corvol H, Tabary O. New insights about miRNAs in cystic fibrosis. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 185:897-908. [PMID: 25687559 DOI: 10.1016/j.ajpath.2014.12.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 01/08/2023]
Abstract
The molecular basis of cystic fibrosis (CF) is a mutation-related defect in the epithelial-cell chloride channel called CF transmembrane conductance regulator (CFTR). This defect alters chloride ion transport and impairs water transport across the cell membrane. Marked clinical heterogeneity occurs even among patients carrying the same mutation in the CFTR gene. Recent studies suggest that such heterogeneity could be related to epigenetic factors and/or miRNAs, which are small noncoding RNAs that modulate the expression of various proteins via post-transcriptional inhibition of gene expression. In the respiratory system, it has been shown that the dysregulation of miRNAs could participate in and lead to pathogenicity in several diseases. In CF airways, recent studies have proposed that miRNAs may modulate disease progression by affecting the production of either CFTR or various proteins that are dysregulated in the CF lung. Herein, we provide an overview of studies showing how miRNAs may modulate CF pathology and the efforts to develop miRNA-based treatments and/or to consider miRNAs as biomarkers. The identification of miRNAs involved in CF disease progression opens up new avenues toward treatments targeting selected clinical components of CF, independently from the CFTR mutation.
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Affiliation(s)
- Florence Sonneville
- Inserm UMR_S938, CDR Saint-Antoine, Paris, France; Sorbonne Universités, UPMC University Paris 06, Paris, France
| | - Manon Ruffin
- Inserm UMR_S938, CDR Saint-Antoine, Paris, France; Sorbonne Universités, UPMC University Paris 06, Paris, France
| | - Loïc Guillot
- Inserm UMR_S938, CDR Saint-Antoine, Paris, France; Sorbonne Universités, UPMC University Paris 06, Paris, France
| | - Nathalie Rousselet
- Inserm UMR_S938, CDR Saint-Antoine, Paris, France; Sorbonne Universités, UPMC University Paris 06, Paris, France
| | - Philippe Le Rouzic
- Inserm UMR_S938, CDR Saint-Antoine, Paris, France; Sorbonne Universités, UPMC University Paris 06, Paris, France
| | - Harriet Corvol
- Inserm UMR_S938, CDR Saint-Antoine, Paris, France; Sorbonne Universités, UPMC University Paris 06, Paris, France; Paediatric Respiratory Department, Hôpital Trousseau, AP-HP, Paris, France
| | - Olivier Tabary
- Inserm UMR_S938, CDR Saint-Antoine, Paris, France; Sorbonne Universités, UPMC University Paris 06, Paris, France.
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50
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Bonini J, Varilh J, Raynal C, Thèze C, Beyne E, Audrezet MP, Ferec C, Bienvenu T, Girodon E, Tuffery-Giraud S, Des Georges M, Claustres M, Taulan-Cadars M. Small-scale high-throughput sequencing-based identification of new therapeutic tools in cystic fibrosis. Genet Med 2015; 17:796-806. [PMID: 25569440 DOI: 10.1038/gim.2014.194] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/24/2014] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Although 97-99% of CFTR mutations have been identified, great efforts must be made to detect yet-unidentified mutations. METHODS We developed a small-scale next-generation sequencing approach for reliably and quickly scanning the entire gene, including noncoding regions, to identify new mutations. We applied this approach to 18 samples from patients suffering from cystic fibrosis (CF) in whom only one mutation had hitherto been identified. RESULTS Using an in-house bioinformatics pipeline, we could rapidly identify a second disease-causing CFTR mutation for 16 of 18 samples. Of them, c.1680-883A>G was found in three unrelated CF patients. Analysis of minigenes and patients' transcripts showed that this mutation results in aberrantly spliced transcripts because of the inclusion of a pseudoexon. It is located only three base pairs from the c.1680-886A>G mutation (1811+1.6kbA>G), the fourth most frequent mutation in southwestern Europe. We next tested the effect of antisense oligonucleotides targeting splice sites on these two mutations on pseudoexon skipping. Oligonucleotide transfection resulted in the restoration of the full-length, in-frame CFTR transcript, demonstrating the effect of antisense oligonucleotide-induced pseudoexon skipping in CF. CONCLUSION Our data confirm the importance of analyzing noncoding regions to find unidentified mutations, which is essential to designing targeted therapeutic approaches.
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Affiliation(s)
- Jennifer Bonini
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France.,Université Montpellier I, UFR de Médecine, Montpellier, France
| | - Jessica Varilh
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - Caroline Raynal
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - Corinne Thèze
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - Emmanuelle Beyne
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | | | - Claude Ferec
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHRU, Brest, France
| | - Thierry Bienvenu
- AP-HP, Service de Biochimie et Génétique Moléculaires, Groupe Hospitalier Cochin Broca Hôtel Dieu, Paris, France
| | - Emmanuelle Girodon
- AP-HP, Service de Biochimie et Génétique Moléculaires, Groupe Hospitalier Cochin Broca Hôtel Dieu, Paris, France
| | - Sylvie Tuffery-Giraud
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France.,Université Montpellier I, UFR de Médecine, Montpellier, France
| | - Marie Des Georges
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - Mireille Claustres
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France.,Université Montpellier I, UFR de Médecine, Montpellier, France
| | - Magali Taulan-Cadars
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France.,Université Montpellier I, UFR de Médecine, Montpellier, France
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