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Mujammami M, Nimer RM, Al Mogren M, Almalki R, Alabdaljabar MS, Benabdelkamel H, Abdel Rahman AM. Metabolomics Panel Associated with Cystic Fibrosis-Related Diabetes toward Biomarker Discovery. ACS OMEGA 2024; 9:32873-32880. [PMID: 39100315 PMCID: PMC11292812 DOI: 10.1021/acsomega.4c03626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/08/2024] [Accepted: 07/10/2024] [Indexed: 08/06/2024]
Abstract
The most prevalent comorbidity among cystic fibrosis (CF) patients is cystic fibrosis-related diabetes (CFRD). CFRD has been linked to one of the worse clinical outcomes and a higher mortality. Improved clinical results have been related to earlier diagnosis and treatment of CFRD. Therefore, the present study aimed to investigate the metabolome of human serum of patients with CFRD. This might aid in identifying novel biomarkers linked with the pathophysiology of CFRD and its diagnosis. The liquid chromatography-high-resolution mass spectrometry (LC-HRMS) metabolomics approach was utilized for serum samples from patients with CF (n = 36) and healthy controls (n = 36). Nine patients in the CF group had CFRD, and 27 were non-CFRD patients (nCFRD). A total of 2328 metabolites were significantly altered in CF compared with the healthy control. Among those, 799 significantly dysregulated metabolites were identified between CFRD and nCFRD. Arachidonic acid (AA), ascorbate, and aldarate metabolism were the most common metabolic pathways dysregulated in CF. l-Homocysteic acid (l-HCA) levels were significantly reduced in CF and CFRD compared to the control and nCFRD, respectively. In addition, gamma-glutamylglycine and l-5-hydroxytryptophan (5-HTP) had the highest discrimination between CFRD and nCFRD with AUC (0.716 and 0.683, respectively). These biomarkers might serve as diagnostic biomarkers and aid in understanding potential metabolic changes linked to CF and CFRD.
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Affiliation(s)
- Muhammad Mujammami
- Endocrinology
and Diabetes Unit, Department of Medicine, College of Medicine, King Saud University, Riyadh 12372, Saudi Arabia
- Diabetes
University Center, King Saud University Medical City, King Saud University, Riyadh 12372, Saudi Arabia
| | - Refat M. Nimer
- Department
of Medical Laboratory Sciences, Jordan University
of Science and Technology, Irbid 22110, Jordan
| | - Maha Al Mogren
- Metabolomics
Section, Department of Clinical Genomics, Center for Genomics Medicine, King Faisal Specialist Hospital and Research Centre
(KFSHRC), Riyadh 11211, Saudi Arabia
| | - Reem Almalki
- Metabolomics
Section, Department of Clinical Genomics, Center for Genomics Medicine, King Faisal Specialist Hospital and Research Centre
(KFSHRC), Riyadh 11211, Saudi Arabia
| | | | - Hicham Benabdelkamel
- Proteomics
Resource Unit, Obesity Research Center, College of Medicine, King Saud University, Riyadh 11362, Saudi Arabia
| | - Anas M. Abdel Rahman
- Metabolomics
Section, Department of Clinical Genomics, Center for Genomics Medicine, King Faisal Specialist Hospital and Research Centre
(KFSHRC), Riyadh 11211, Saudi Arabia
- Department
of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
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2
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Putman MS, Norris AW, Hull RL, Rickels MR, Sussel L, Blackman SM, Chan CL, Ode KL, Daley T, Stecenko AA, Moran A, Helmick MJ, Cray S, Alvarez JA, Stallings VA, Tuggle KL, Clancy JP, Eggerman TL, Engelhardt JF, Kelly A. Cystic Fibrosis-Related Diabetes Workshop: Research Priorities Spanning Disease Pathophysiology, Diagnosis, and Outcomes. Diabetes Care 2023; 46:1112-1123. [PMID: 37125948 PMCID: PMC10234745 DOI: 10.2337/dc23-0380] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/27/2023] [Indexed: 05/02/2023]
Abstract
Cystic fibrosis (CF) is a recessive disorder arising from mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR) protein. CFTR is expressed in numerous tissues, with high expression in the airways, small and large intestine, pancreatic and hepatobiliary ducts, and male reproductive tract. CFTR loss in these tissues disrupts regulation of salt, bicarbonate, and water balance across their epithelia, resulting in a systemic disorder with progressive organ dysfunction and damage. Pancreatic exocrine damage ultimately manifests as pancreatic exocrine insufficiency that begins as early as infancy. Pancreatic remodeling accompanies this early damage, during which abnormal glucose tolerance can be observed in toddlers. With increasing age, however, insulin secretion defects progress such that CF-related diabetes (CFRD) occurs in 20% of teens and up to half of adults with CF. The relevance of CFRD is highlighted by its association with increased morbidity, mortality, and patient burden. While clinical research on CFRD has greatly assisted in the care of individuals with CFRD, key knowledge gaps on CFRD pathogenesis remain. Furthermore, the wide use of CFTR modulators to restore CFTR activity is changing the CFRD clinical landscape and the field's understanding of CFRD pathogenesis. For these reasons, the National Institute of Diabetes and Digestive and Kidney Diseases and the Cystic Fibrosis Foundation sponsored a CFRD Scientific Workshop, 23-25 June 2021, to define knowledge gaps and needed research areas. This article describes the findings from this workshop and plots a path for CFRD research that is needed over the next decade.
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Affiliation(s)
- Melissa S. Putman
- Division of Pediatric Endocrinology, Boston Children’s Hospital, Boston, MA
- Diabetes Research Center, Massachusetts General Hospital, Boston, MA
| | - Andrew W. Norris
- Department of Pediatrics, University of Iowa, Iowa City, IA
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA
| | - Rebecca L. Hull
- Division of Metabolism, Endocrinology, and Nutrition, Department of Medicine, University of Washington, Seattle, WA
- Research Service, VA Puget Sound Health Care System, Seattle
| | - Michael R. Rickels
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Lori Sussel
- Department of Pediatrics, Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Scott M. Blackman
- Division of Pediatric Endocrinology and Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Christine L. Chan
- Department of Pediatrics, Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Katie Larson Ode
- Department of Pediatrics, University of Iowa, Iowa City, IA
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA
| | - Tanicia Daley
- Division of Endocrinology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Children’s Healthcare of Atlanta, Atlanta, GA
| | - Arlene A. Stecenko
- Division of Pulmonology, Asthma, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University, Atlanta, GA
| | - Antoinette Moran
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | | | | | - Jessica A. Alvarez
- Division of Endocrinology, Metabolism, and Lipids, Department of Medicine, Emory School of Medicine, Atlanta, GA
| | - Virginia A. Stallings
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, The University of Pennsylvania, Philadelphia, PA
| | | | | | - Thomas L. Eggerman
- Division of Diabetes, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - John F. Engelhardt
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Andrea Kelly
- Department of Pediatrics, The University of Pennsylvania, Philadelphia, PA
- Division of Endocrinology and Diabetes, The Children’s Hospital of Philadelphia, Philadelphia, PA
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3
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Putman MS, Norris AW, Hull RL, Rickels MR, Sussel L, Blackman SM, Chan CL, Ode KL, Daley T, Stecenko AA, Moran A, Helmick MJ, Cray S, Alvarez JA, Stallings VA, Tuggle KL, Clancy JP, Eggerman TL, Engelhardt JF, Kelly A. Cystic Fibrosis-Related Diabetes Workshop: Research Priorities Spanning Disease Pathophysiology, Diagnosis, and Outcomes. Diabetes 2023; 72:677-689. [PMID: 37125945 PMCID: PMC10202770 DOI: 10.2337/db22-0949] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/27/2023] [Indexed: 05/02/2023]
Abstract
Cystic fibrosis (CF) is a recessive disorder arising from mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR) protein. CFTR is expressed in numerous tissues, with high expression in the airways, small and large intestine, pancreatic and hepatobiliary ducts, and male reproductive tract. CFTR loss in these tissues disrupts regulation of salt, bicarbonate, and water balance across their epithelia, resulting in a systemic disorder with progressive organ dysfunction and damage. Pancreatic exocrine damage ultimately manifests as pancreatic exocrine insufficiency that begins as early as infancy. Pancreatic remodeling accompanies this early damage, during which abnormal glucose tolerance can be observed in toddlers. With increasing age, however, insulin secretion defects progress such that CF-related diabetes (CFRD) occurs in 20% of teens and up to half of adults with CF. The relevance of CFRD is highlighted by its association with increased morbidity, mortality, and patient burden. While clinical research on CFRD has greatly assisted in the care of individuals with CFRD, key knowledge gaps on CFRD pathogenesis remain. Furthermore, the wide use of CFTR modulators to restore CFTR activity is changing the CFRD clinical landscape and the field's understanding of CFRD pathogenesis. For these reasons, the National Institute of Diabetes and Digestive and Kidney Diseases and the Cystic Fibrosis Foundation sponsored a CFRD Scientific Workshop, 23-25 June 2021, to define knowledge gaps and needed research areas. This article describes the findings from this workshop and plots a path for CFRD research that is needed over the next decade.
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Affiliation(s)
- Melissa S. Putman
- Division of Pediatric Endocrinology, Boston Children’s Hospital, Boston, MA
- Diabetes Research Center, Massachusetts General Hospital, Boston, MA
| | - Andrew W. Norris
- Department of Pediatrics, University of Iowa, Iowa City, IA
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA
| | - Rebecca L. Hull
- Division of Metabolism, Endocrinology, and Nutrition, Department of Medicine, University of Washington, Seattle, WA
- Research Service, VA Puget Sound Health Care System, Seattle, WA
| | - Michael R. Rickels
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Lori Sussel
- Department of Pediatrics, Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Scott M. Blackman
- Division of Pediatric Endocrinology and Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Christine L. Chan
- Department of Pediatrics, Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Katie Larson Ode
- Department of Pediatrics, University of Iowa, Iowa City, IA
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA
| | - Tanicia Daley
- Division of Endocrinology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Children’s Healthcare of Atlanta, Atlanta, GA
| | - Arlene A. Stecenko
- Division of Pulmonology, Asthma, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University, Atlanta, GA
| | - Antoinette Moran
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | | | | | - Jessica A. Alvarez
- Division of Endocrinology, Metabolism, and Lipids, Department of Medicine, Emory School of Medicine, Atlanta, GA
| | - Virginia A. Stallings
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, The University of Pennsylvania, Philadelphia, PA
| | | | | | - Thomas L. Eggerman
- Division of Diabetes, Endocrinology, and Metabolic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - John F. Engelhardt
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Andrea Kelly
- Department of Pediatrics, The University of Pennsylvania, Philadelphia, PA
- Division of Endocrinology and Diabetes, The Children’s Hospital of Philadelphia, Philadelphia, PA
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4
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Hicks R, Ode KL, Vigers T, Chan CL. A provider survey of cystic fibrosis related diabetes screening and management practices at North American CF centers. Front Endocrinol (Lausanne) 2023; 14:1183288. [PMID: 37274323 PMCID: PMC10232971 DOI: 10.3389/fendo.2023.1183288] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/01/2023] [Indexed: 06/06/2023] Open
Abstract
Background Cystic Fibrosis Foundation (CFF) Guidelines recommend annual screening for cystic fibrosis related diabetes (CFRD) with an oral glucose tolerance test (OGTT). However, screening rates remain consistently low. We conducted surveys of 1) US CF center directors and 2) Endocrinologists affiliated with the CFF-sponsored EnVision program to characterize CFRD screening practices, describe provider perceived barriers to screening, and identify strategies for improving screening. Methods The surveys queried OGTT protocols, alternate screening strategies, and perceived barriers to screening. CF center characteristics and procedures for coordinating OGTTs were compared between centers achieving ≥50% versus <50% OGTT completion. Endocrinologists received additional questions regarding OGTT interpretation and management. Results The survey response rate was 18% (51/290) from CF Centers and 63% (25/40) from Endocrinologists. The majority (57%) of CF centers utilized 2 OGTT timepoints (0,120 min). The majority (72%) of Endocrinologists utilized 3 timepoints (0,60,120 min). Four percent of CF centers and 8% of Endocrinologists utilized other timepoints. Forty-nine percent of CF centers reported ≥50% OGTT completion in the past year. Completion of ≥50% OGTT was 5 times more likely when patient reminders were consistently provided (p = 0.017). Both CF Centers and Endocrinologists employed alternative screening strategies including HbA1c (64%, 92%), fasting plasma glucose (49%, 67%), continuous glucose monitoring (30%, 58%), and home fingerstick monitoring (55%, 50%). Discussion OGTT is the gold standard screening method for CFRD, but completion rates remain suboptimal, practice variation exists, and many providers utilize alternate screening strategies. Systematic reminders may improve completion rates. Studies to improve our approach to CFRD screening are urgently needed.
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Affiliation(s)
- Rebecca Hicks
- University of California, Los Angeles, Division of Pediatric Endocrinology, Los Angeles, CA, United States
| | - Katie Larson Ode
- Department of Pediatrics, University of Iowa, Iowa City, IA, United States
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA, United States
| | - Tim Vigers
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Christine L. Chan
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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5
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Xiao T, Dong X, Lu Y, Zhou W. High-Resolution and Multidimensional Phenotypes Can Complement Genomics Data to Diagnose Diseases in the Neonatal Population. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:204-215. [PMID: 37197647 PMCID: PMC10110825 DOI: 10.1007/s43657-022-00071-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 08/03/2022] [Accepted: 08/08/2022] [Indexed: 05/19/2023]
Abstract
Advances in genomic medicine have greatly improved our understanding of human diseases. However, phenome is not well understood. High-resolution and multidimensional phenotypes have shed light on the mechanisms underlying neonatal diseases in greater details and have the potential to optimize clinical strategies. In this review, we first highlight the value of analyzing traditional phenotypes using a data science approach in the neonatal population. We then discuss recent research on high-resolution, multidimensional, and structured phenotypes in neonatal critical diseases. Finally, we briefly introduce current technologies available for the analysis of multidimensional data and the value that can be provided by integrating these data into clinical practice. In summary, a time series of multidimensional phenome can improve our understanding of disease mechanisms and diagnostic decision-making, stratify patients, and provide clinicians with optimized strategies for therapeutic intervention; however, the available technologies for collecting multidimensional data and the best platform for connecting multiple modalities should be considered.
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Affiliation(s)
- Tiantian Xiao
- Division of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, 399 Wanyuan Road, Shanghai, 201102 China
- Department of Neonatology, Chengdu Women’s and Children’s Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610000 China
| | - Xinran Dong
- Center for Molecular Medicine, Pediatric Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, 201102 China
| | - Yulan Lu
- Center for Molecular Medicine, Pediatric Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, 201102 China
| | - Wenhao Zhou
- Division of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, 399 Wanyuan Road, Shanghai, 201102 China
- Center for Molecular Medicine, Pediatric Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, 201102 China
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6
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Radtke T, Kriemler S, Stein L, Karila C, Urquhart DS, Orenstein DM, Lands LC, Schindler C, Eber E, Haile SR, Hebestreit H. Cystic fibrosis related diabetes is not associated with maximal aerobic exercise capacity in cystic fibrosis: a cross-sectional analysis of an international multicenter trial. J Cyst Fibros 2023; 22:31-38. [PMID: 35803884 DOI: 10.1016/j.jcf.2022.06.012] [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: 04/15/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Previous studies have reported differences in aerobic exercise capacity, expressed as peak oxygen uptake (VO2peak), between people with and without cystic fibrosis (CF) related diabetes (CFRD). However, none of the studies controlled for the potential influence of physical activity on VO2peak. We investigated associations between CFRD and VO2peak following rigorous control for confounders including objectively measured physical activity. METHODS Baseline data from the international multicenter trial ACTIVATE-CF with participants ≥12 years performing up to 4 h per week of vigorous physical activity were used for this project. Multivariable models were computed to study associations between CFRD and VO2peak (mL.min-1) adjusting for a set of pre-defined covariates: age, sex, weight, forced expiratory volume in 1 s (FEV1), breathing reserve index, Pseudomonas aeruginosa infection, and physical activity (aerobic step counts from pedometry). Variables were selected based on their potential confounding effect on the association between VO2peak and CFRD. RESULTS Among 117 randomized individuals, 103 (52% female) had a maximal exercise test and were included in the analysis. Participants with (n = 19) and without (n = 84) CFRD did not differ in FEV1, physical activity, nutritional status, and other clinical characteristics. There were also no differences in VO2peak (mL.min-1 or mL.kg-1.min-1 or% predicted). In the final multivariable model, all pre-defined covariates were significant predictors of VO2peak (mL.min-1), however CFRD [coefficient 82.1, 95% CI -69.5 to 233.8, p = 0.28] was not. CONCLUSIONS This study suggests no meaningful differences in VO2peak between people with and without CFRD given comparable levels of physical activity.
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Affiliation(s)
- Thomas Radtke
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland.
| | - Susi Kriemler
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Lothar Stein
- Hannover Medical School, Institute of Sports Medicine, Hannover, Germany
| | - Chantal Karila
- Service de pneumologie et allergologie pédiatriques - Hôpital Necker Enfants malades - APHP - Université Paris Descartes, Paris, France
| | - Don S Urquhart
- Department of Paediatric Respiratory and Sleep Medicine, Royal Hospital for Children and Young People, Edinburgh, UK
| | - David M Orenstein
- Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, USA
| | - Larry C Lands
- Montreal Children's Hospital - McGill University Health, Montreal, QC, Canada
| | - Christian Schindler
- Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland; Faculty of Medicine, University of Basel, Basel, Switzerland
| | - Ernst Eber
- Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Sarah R Haile
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
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Mastromatteo S, Chen A, Gong J, Lin F, Thiruvahindrapuram B, Sung WW, Whitney J, Wang Z, Patel RV, Keenan K, Halevy A, Panjwani N, Avolio J, Wang C, Côté-Maurais G, Bégin S, Adam D, Brochiero E, Bjornson C, Chilvers M, Price A, Parkins M, van Wylick R, Mateos-Corral D, Hughes D, Smith MJ, Morrison N, Tullis E, Stephenson AL, Wilcox P, Quon BS, Leung WM, Solomon M, Sun L, Ratjen F, Strug LJ. High-quality read-based phasing of cystic fibrosis cohort informs genetic understanding of disease modification. HGG ADVANCES 2023; 4:100156. [PMID: 36386424 PMCID: PMC9647008 DOI: 10.1016/j.xhgg.2022.100156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Phasing of heterozygous alleles is critical for interpretation of cis-effects of disease-relevant variation. We sequenced 477 individuals with cystic fibrosis (CF) using linked-read sequencing, which display an average phase block N50 of 4.39 Mb. We use these samples to construct a graph representation of CFTR haplotypes, demonstrating its utility for understanding complex CF alleles. These are visualized in a Web app, CFTbaRcodes, that enables interactive exploration of CFTR haplotypes present in this cohort. We perform fine-mapping and phasing of the chr7q35 trypsinogen locus associated with CF meconium ileus, an intestinal obstruction at birth associated with more severe CF outcomes and pancreatic disease. A 20-kb deletion polymorphism and a PRSS2 missense variant p.Thr8Ile (rs62473563) are shown to independently contribute to meconium ileus risk (p = 0.0028, p = 0.011, respectively) and are PRSS2 pancreas eQTLs (p = 9.5 × 10−7 and p = 1.4 × 10−4, respectively), suggesting the mechanism by which these polymorphisms contribute to CF. The phase information from linked reads provides a putative causal explanation for variation at a CF-relevant locus, which also has implications for the genetic basis of non-CF pancreatitis, to which this locus has been reported to contribute.
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8
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Kelly A, Marks BE, Stalvey MS. Endocrine Complications of Cystic Fibrosis. Clin Chest Med 2022; 43:773-789. [PMID: 36344080 DOI: 10.1016/j.ccm.2022.06.013] [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: 11/06/2022]
Abstract
Endocrine comorbidities have become increasingly important medical considerations as improving cystic fibrosis (CF) care increases life expectancy. Although the underlying pathophysiology of CF-related diabetes remains elusive, the use of novel technologies and therapeutics seeks to improve both CF-related outcomes and quality of life. Improvements in the overall health of those with CF have tempered concerns about pubertal delay and short stature; however, other comorbidities such as hypogonadism and bone disease are increasingly recognized. Following the introduction of highly effective modulator therapies there are many lessons to be learned about their long-term impact on endocrine comorbidities.
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Affiliation(s)
- Andrea Kelly
- Division of Endocrinology & Diabetes, University of Pennsylvania Perelman School of Medicine, Children's Hospital of Philadelphia, Room 14363, Roberts Building for Pediatric Research, 2716 South Street, Philadelphia, PA 19146, USA
| | - Brynn E Marks
- Division of Endocrinology & Diabetes, Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Children's Hospital of Philadelphia, Room 7547, The Hub for Clinical Collaboration, 3501 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Michael S Stalvey
- Department of Pediatrics, UAB Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Children's of Alabama, CPPII M30, 1600 7th Avenue South, Birmingham, AL 35233-1711, USA; Department of Medicine, UAB Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Children's of Alabama, CPPII M30, 1600 7th Avenue South, Birmingham, AL 35233-1711, USA.
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9
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Mésinèle J, Ruffin M, Guillot L, Corvol H. Modifier Factors of Cystic Fibrosis Phenotypes: A Focus on Modifier Genes. Int J Mol Sci 2022; 23:ijms232214205. [PMID: 36430680 PMCID: PMC9698440 DOI: 10.3390/ijms232214205] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
Although cystic fibrosis (CF) is recognized as a monogenic disease, due to variants within the CFTR (Cystic Fibrosis Transmembrane Regulator) gene, an extreme clinical heterogeneity is described among people with CF (pwCF). Apart from the exocrine pancreatic status, most studies agree that there is little association between CFTR variants and disease phenotypes. Environmental factors have been shown to contribute to this heterogeneity, accounting for almost 50% of the variability of the lung function of pwCF. Nevertheless, pwCF with similar CFTR variants and sharing the same environment (such as in siblings) may have highly variable clinical manifestations not explained by CFTR variants, and only partly explained by environmental factors. It is recognized that genetic variants located outside the CFTR locus, named "modifier genes", influence the clinical expression of the disease. This short review discusses the latest studies that have described modifier factors associated with the various CF phenotypes as well as the response to the recent CFTR modulator therapies.
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Affiliation(s)
- Julie Mésinèle
- Sorbonne Université, Inserm U938, Centre de Recherche Saint-Antoine (CRSA), 75012 Paris, France
- Inovarion, 75005 Paris, France
| | - Manon Ruffin
- Sorbonne Université, Inserm U938, Centre de Recherche Saint-Antoine (CRSA), 75012 Paris, France
| | - Loïc Guillot
- Sorbonne Université, Inserm U938, Centre de Recherche Saint-Antoine (CRSA), 75012 Paris, France
- Correspondence: (L.G.); (H.C.)
| | - Harriet Corvol
- Sorbonne Université, Inserm U938, Centre de Recherche Saint-Antoine (CRSA), 75012 Paris, France
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Trousseau, Service de Pneumologie Pédiatrique, 75012 Paris, France
- Correspondence: (L.G.); (H.C.)
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10
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Dong X, Xiao T, Chen B, Lu Y, Zhou W. Precision medicine via the integration of phenotype-genotype information in neonatal genome project. FUNDAMENTAL RESEARCH 2022; 2:873-884. [PMID: 38933389 PMCID: PMC11197532 DOI: 10.1016/j.fmre.2022.07.003] [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: 04/26/2022] [Revised: 07/07/2022] [Accepted: 07/10/2022] [Indexed: 11/21/2022] Open
Abstract
The explosion of next-generation sequencing (NGS) has enabled the widespread use of genomic data in precision medicine. Currently, several neonatal genome projects have emerged to explore the advantages of NGS to diagnose or screen for rare genetic disorders. These projects have made remarkable achievements, but still the genome data could be further explored with the assistance of phenotype collection. In contrast, longitudinal birth cohorts are great examples to record and apply phenotypic information in clinical studies starting at the neonatal period, especially the trajectory analyses for health development or disease progression. It is obvious that efficient integration of genotype and phenotype benefits not only the clinical management of rare genetic disorders but also the risk assessment of complex diseases. Here, we first summarize the recent neonatal genome projects as well as some longitudinal birth cohorts. Then, we propose two simplified strategies by integrating genotypic and phenotypic information in precision medicine based on current studies. Finally, research collaborations, sociological issues, and future perspectives are discussed. How to maximize neonatal genomic information to benefit the pediatric population remains an area in need of more research and effort.
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Affiliation(s)
- Xinran Dong
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Tiantian Xiao
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
- Department of Neonatology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610066, China
| | - Bin Chen
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Yulan Lu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
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Aksit MA, Ling H, Pace RG, Raraigh KS, Onchiri F, Faino AV, Pagel K, Pugh E, Stilp AM, Sun Q, Blue EE, Wright FA, Zhou YH, Bamshad MJ, Gibson RL, Knowles MR, Cutting GR, Blackman SM. Pleiotropic modifiers of age-related diabetes and neonatal intestinal obstruction in cystic fibrosis. Am J Hum Genet 2022; 109:1894-1908. [PMID: 36206743 PMCID: PMC9606479 DOI: 10.1016/j.ajhg.2022.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 09/12/2022] [Indexed: 01/25/2023] Open
Abstract
Individuals with cystic fibrosis (CF) develop complications of the gastrointestinal tract influenced by genetic variants outside of CFTR. Cystic fibrosis-related diabetes (CFRD) is a distinct form of diabetes with a variable age of onset that occurs frequently in individuals with CF, while meconium ileus (MI) is a severe neonatal intestinal obstruction affecting ∼20% of newborns with CF. CFRD and MI are slightly correlated traits with previous evidence of overlap in their genetic architectures. To better understand the genetic commonality between CFRD and MI, we used whole-genome-sequencing data from the CF Genome Project to perform genome-wide association. These analyses revealed variants at 11 loci (6 not previously identified) that associated with MI and at 12 loci (5 not previously identified) that associated with CFRD. Of these, variants at SLC26A9, CEBPB, and PRSS1 associated with both traits; variants at SLC26A9 and CEBPB increased risk for both traits, while variants at PRSS1, the higher-risk alleles for CFRD, conferred lower risk for MI. Furthermore, common and rare variants within the SLC26A9 locus associated with MI only or CFRD only. As expected, different loci modify risk of CFRD and MI; however, a subset exhibit pleiotropic effects indicating etiologic and mechanistic overlap between these two otherwise distinct complications of CF.
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Affiliation(s)
- Melis A Aksit
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Hua Ling
- Department of Genetic Medicine, Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rhonda G Pace
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karen S Raraigh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Frankline Onchiri
- Children's Core for Biostatistics, Epidemiology and Analytics in Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Anna V Faino
- Children's Core for Biostatistics, Epidemiology and Analytics in Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Kymberleigh Pagel
- The Institute for Computational Medicine, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Elizabeth Pugh
- Department of Genetic Medicine, Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Elizabeth E Blue
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Fred A Wright
- Department of Statistics, North Carolina State University, Raleigh, NC 27797, USA; Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27797, USA; Department of Biological Sciences, North Carolina State University, Raleigh, NC 27797, USA
| | - Yi-Hui Zhou
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27797, USA
| | - Michael J Bamshad
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Center for Clinical and Translational Research, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Ronald L Gibson
- Center for Clinical and Translational Research, Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Pediatrics, Division of Pulmonary & Sleep Medicine, University of Washington School of Medicine/Seattle Children's Hospital, Seattle, WA, USA
| | - Michael R Knowles
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Garry R Cutting
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Scott M Blackman
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Division of Pediatric Endocrinology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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Wrigley-Carr HE, van Dorst JM, Ooi CY. Intestinal dysbiosis and inflammation in cystic fibrosis impacts gut and multi-organ axes. MEDICINE IN MICROECOLOGY 2022. [DOI: 10.1016/j.medmic.2022.100057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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13
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Genetic evidence supports the development of SLC26A9 targeting therapies for the treatment of lung disease. NPJ Genom Med 2022; 7:28. [PMID: 35396391 PMCID: PMC8993824 DOI: 10.1038/s41525-022-00299-9] [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: 12/30/2021] [Accepted: 03/04/2022] [Indexed: 12/19/2022] Open
Abstract
Over 400 variants in the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) are CF-causing. CFTR modulators target variants to improve lung function, but marked variability in response exists and current therapies do not address all CF-causing variants highlighting unmet needs. Alternative epithelial ion channel/transporters such as SLC26A9 could compensate for CFTR dysfunction, providing therapeutic targets that may benefit all individuals with CF. We investigate the relationship between rs7512462, a marker of SLC26A9 activity, and lung function pre- and post-treatment with CFTR modulators in Canadian and US CF cohorts, in the general population, and in those with chronic obstructive pulmonary disease (COPD). Rs7512462 CC genotype is associated with greater lung function in CF individuals with minimal function variants (for which there are currently no approved therapies; p = 0.008); and for gating (p = 0.033) and p.Phe508del/ p.Phe508del (p = 0.006) genotypes upon treatment with CFTR modulators. In parallel, human nasal epithelia with CC and p.Phe508del/p.Phe508del after Ussing chamber analysis of a combination of approved and experimental modulator treatments show greater CFTR function (p = 0.0022). Beyond CF, rs7512462 is associated with peak expiratory flow in a meta-analysis of the UK Biobank and Spirometa Consortium (p = 2.74 × 10-44) and provides p = 0.0891 in an analysis of COPD case-control status in the UK Biobank defined by spirometry. These findings support SLC26A9 as a therapeutic target to improve lung function for all people with CF and in individuals with other obstructive lung diseases.
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Rachel M, Biesiadecki M, Galiniak S. Cystic Fibrosis-Related Diabetes in Poland. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19074069. [PMID: 35409752 PMCID: PMC8998285 DOI: 10.3390/ijerph19074069] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/14/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023]
Abstract
Cystic fibrosis (CF) is the most common autosomal recessive inherited monogenic disease in Caucasians. As medical technology progresses and the quality of patient care improves, the survival time of patients with CF has increased, which results in more frequent comorbidities such as cystic fibrosis-related diabetes (CFRD). CFRD is the result of abnormal glucose metabolism characterized primarily by insulin deficiency, exacerbated periodically by insulin resistance. The aim of our study was to analyze the epidemiology of patients with CFRD in Poland on the basis of data collected from six CF treatment centers. Analyses were performed on 1157 CF patients who were treated at one of the six CF care centers. CFRD was diagnosed according to standard criteria. All data including demographics, types of CFTR mutations, CFRD duration, and microorganisms in the sputum were obtained from the patients’ medical history. Our study indicates that the prevalence of CFRD in Poland is 12.9%. CFRD was most often diagnosed between the ages of 11 and 20 (60% of patients), while 23% of patients were diagnosed between 21 and 30 years of age. Furthermore, we observed that approximately 3–5% of patients under the age of 10 had CFRD. We found out that the type of mutation did not affect the frequency of CFRD development. Factors that increased the risk of developing CFRD include underweight and chronic Pseudomonas aeruginosa infection. Due to the extended lifespan of CF patients, the number of CFRD patients is currently increasing. We believe that the results of our study may complement information from other studies or may be useful in planning health policy in Poland.
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Affiliation(s)
- Marta Rachel
- Institute of Medical Sciences, Medical College, Rzeszów University, Warzywna 1a, 35-310 Rzeszów, Poland; (M.B.); (S.G.)
- Department of Allergology and Cystic Fibrosis, State Hospital 2 in Rzeszow, Lwowska 60, 35-301 Rzeszów, Poland
- Correspondence: ; Tel.: +48-17-866-46-67
| | - Marek Biesiadecki
- Institute of Medical Sciences, Medical College, Rzeszów University, Warzywna 1a, 35-310 Rzeszów, Poland; (M.B.); (S.G.)
| | - Sabina Galiniak
- Institute of Medical Sciences, Medical College, Rzeszów University, Warzywna 1a, 35-310 Rzeszów, Poland; (M.B.); (S.G.)
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15
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The role of genetic modifiers, inflammation and CFTR in the pathogenesis of Cystic fibrosis related diabetes. J Clin Transl Endocrinol 2022; 27:100287. [PMID: 34976741 PMCID: PMC8688704 DOI: 10.1016/j.jcte.2021.100287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/11/2021] [Accepted: 11/27/2021] [Indexed: 11/20/2022] Open
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Coderre L, Debieche L, Plourde J, Rabasa-Lhoret R, Lesage S. The Potential Causes of Cystic Fibrosis-Related Diabetes. Front Endocrinol (Lausanne) 2021; 12:702823. [PMID: 34394004 PMCID: PMC8361832 DOI: 10.3389/fendo.2021.702823] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/06/2021] [Indexed: 12/16/2022] Open
Abstract
Cystic fibrosis (CF) is a genetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR). Cystic fibrosis-related diabetes (CFRD) is the most common comorbidity, affecting more than 50% of adult CF patients. Despite this high prevalence, the etiology of CFRD remains incompletely understood. Studies in young CF children show pancreatic islet disorganization, abnormal glucose tolerance, and delayed first-phase insulin secretion suggesting that islet dysfunction is an early feature of CF. Since insulin-producing pancreatic β-cells express very low levels of CFTR, CFRD likely results from β-cell extrinsic factors. In the vicinity of β-cells, CFTR is expressed in both the exocrine pancreas and the immune system. In the exocrine pancreas, CFTR mutations lead to the obstruction of the pancreatic ductal canal, inflammation, and immune cell infiltration, ultimately causing the destruction of the exocrine pancreas and remodeling of islets. Both inflammation and ductal cells have a direct effect on insulin secretion and could participate in CFRD development. CFTR mutations are also associated with inflammatory responses and excessive cytokine production by various immune cells, which infiltrate the pancreas and exert a negative impact on insulin secretion, causing dysregulation of glucose homeostasis in CF adults. In addition, the function of macrophages in shaping pancreatic islet development may be impaired by CFTR mutations, further contributing to the pancreatic islet structural defects as well as impaired first-phase insulin secretion observed in very young children. This review discusses the different factors that may contribute to CFRD.
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Affiliation(s)
- Lise Coderre
- Immunology-Oncology Section, Maisonneuve-Rosemont Hospital Research Center, Montréal, QC, Canada
| | - Lyna Debieche
- Immunology-Oncology Section, Maisonneuve-Rosemont Hospital Research Center, Montréal, QC, Canada
- Département de médecine, Université de Montréal, Montréal, QC, Canada
| | - Joëlle Plourde
- Immunology-Oncology Section, Maisonneuve-Rosemont Hospital Research Center, Montréal, QC, Canada
- Département de médecine, Université de Montréal, Montréal, QC, Canada
| | - Rémi Rabasa-Lhoret
- Division of Cardiovascular and Metabolic Diseases, Institut de recherche clinique de Montréal, Montréal, QC, Canada
- Département de nutrition, Université de Montréal, Montréal, QC, Canada
- Cystic Fibrosis Clinic, Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC, Canada
| | - Sylvie Lesage
- Immunology-Oncology Section, Maisonneuve-Rosemont Hospital Research Center, Montréal, QC, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC, Canada
- *Correspondence: Sylvie Lesage,
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