1
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Raraigh KS, Lewis MH, Collaco JM, Corey M, Penland CM, Stephenson AL, Rommens JM, Castellani C, Cutting GR. Caution advised in the use of CFTR modulator treatment for individuals harboring specific CFTR variants. J Cyst Fibros 2022; 21:856-860. [DOI: 10.1016/j.jcf.2022.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/09/2022] [Accepted: 04/24/2022] [Indexed: 10/18/2022]
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2
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He G, Panjwani N, Avolio J, Ouyang H, Keshavjee S, Rommens JM, Gonska T, Moraes TJ, Strug LJ. Expression of cystic fibrosis lung disease modifier genes in human airway models. J Cyst Fibros 2022; 21:616-622. [DOI: 10.1016/j.jcf.2022.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/05/2022] [Accepted: 02/09/2022] [Indexed: 12/13/2022]
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Lin YC, Keenan K, Gong J, Panjwani N, Avolio J, Lin F, Adam D, Barrett P, Bégin S, Berthiaume Y, Bilodeau L, Bjornson C, Brusky J, Burgess C, Chilvers M, Consunji-Araneta R, Côté-Maurais G, Dale A, Donnelly C, Fairservice L, Griffin K, Henderson N, Hillaby A, Hughes D, Iqbal S, Itterman J, Jackson M, Karlsen E, Kosteniuk L, Lazosky L, Leung W, Levesque V, Maille É, Mateos-Corral D, McMahon V, Merjaneh M, Morrison N, Parkins M, Pike J, Price A, Quon BS, Reisman J, Smith C, Smith MJ, Vadeboncoeur N, Veniott D, Viczko T, Wilcox P, van Wylick R, Cutting G, Tullis E, Ratjen F, Rommens JM, Sun L, Solomon M, Stephenson AL, Brochiero E, Blackman S, Corvol H, Strug LJ. Correction to: Cystic fibrosis-related diabetes onset can be predicted using biomarkers measured at birth. Genet Med 2021; 23:2235-2236. [PMID: 34389817 PMCID: PMC8553623 DOI: 10.1038/s41436-021-01281-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Yu-Chung Lin
- Department of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Katherine Keenan
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jiafen Gong
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Naim Panjwani
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Julie Avolio
- Program in Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Fan Lin
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Damien Adam
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.,CRCHUM, Montréal, QC, Canada
| | | | | | - Yves Berthiaume
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Lara Bilodeau
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec-Université Laval, Québec City, QC, Canada
| | | | - Janna Brusky
- Jim Pattison Children's Hospital, Saskatoon, SK, Canada
| | | | - Mark Chilvers
- British Columbia Children's Hospital, Vancouver, BC, Canada
| | | | | | - Andrea Dale
- Queen Elizabeth II Health Sciences Centre, Halifax, NS, Canada
| | | | | | | | | | | | | | - Shaikh Iqbal
- The Children's Hospital of Winnipeg, Winnipeg, MB, Canada
| | | | - Mary Jackson
- Royal University Hospital, Saskatoon, SK, Canada
| | | | | | | | - Winnie Leung
- University of Alberta Hospital, Edmonton, AB, Canada
| | | | | | | | | | | | - Nancy Morrison
- Queen Elizabeth II Health Sciences Centre, Halifax, NS, Canada
| | | | | | - April Price
- The Children's Hospital of Western Ontario, London, ON, Canada
| | | | - Joe Reisman
- The Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Clare Smith
- Foothills Medical Centre, Calgary, AB, Canada
| | - Mary Jane Smith
- Janeway Children's Health & Rehabilitation Centre, St. John's, NL, Canada
| | - Nathalie Vadeboncoeur
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec-Université Laval, Québec City, QC, Canada
| | | | - Terry Viczko
- British Columbia Children's Hospital, Vancouver, BC, Canada
| | | | | | - Garry Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Felix Ratjen
- Program in Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada.,Division of Respiratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Johanna M Rommens
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Lei Sun
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | - Melinda Solomon
- Division of Respiratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | | | - Emmanuelle Brochiero
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.,CRCHUM, Montréal, QC, Canada
| | - Scott Blackman
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Harriet Corvol
- Assistance Publique-Hôpitaux de Paris, Hôpital Trousseau, Pediatric Pulmonary Department, Paris, France.,Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre de Recherche Saint Antoine, Paris, France
| | - Lisa J Strug
- Department of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada. .,Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada. .,Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada. .,The Center for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada. .,Department of Computer Science, University of Toronto, Toronto, ON, Canada.
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4
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Lin YC, Keenan K, Gong J, Panjwani N, Avolio J, Lin F, Adam D, Barrett P, Bégin S, Berthiaume Y, Bilodeau L, Bjornson C, Brusky J, Burgess C, Chilvers M, Consunji-Araneta R, Côté-Maurais G, Dale A, Donnelly C, Fairservice L, Griffin K, Henderson N, Hillaby A, Hughes D, Iqbal S, Itterman J, Jackson M, Karlsen E, Kosteniuk L, Lazosky L, Leung W, Levesque V, Maille É, Mateos-Corral D, McMahon V, Merjaneh M, Morrison N, Parkins M, Pike J, Price A, Quon BS, Reisman J, Smith C, Smith MJ, Vadeboncoeur N, Veniott D, Viczko T, Wilcox P, van Wylick R, Cutting G, Tullis E, Ratjen F, Rommens JM, Sun L, Solomon M, Stephenson AL, Brochiero E, Blackman S, Corvol H, Strug LJ. Cystic fibrosis-related diabetes onset can be predicted using biomarkers measured at birth. Genet Med 2021; 23:927-933. [PMID: 33500570 PMCID: PMC8105168 DOI: 10.1038/s41436-020-01073-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 12/16/2022] Open
Abstract
Purpose Cystic fibrosis (CF), caused by pathogenic variants in the CF transmembrane conductance regulator (CFTR), affects multiple organs including the exocrine pancreas, which is a causal contributor to cystic fibrosis–related diabetes (CFRD). Untreated CFRD causes increased CF-related mortality whereas early detection can improve outcomes. Methods Using genetic and easily accessible clinical measures available at birth, we constructed a CFRD prediction model using the Canadian CF Gene Modifier Study (CGS; n = 1,958) and validated it in the French CF Gene Modifier Study (FGMS; n = 1,003). We investigated genetic variants shown to associate with CF disease severity across multiple organs in genome-wide association studies. Results The strongest predictors included sex, CFTR severity score, and several genetic variants including one annotated to PRSS1, which encodes cationic trypsinogen. The final model defined in the CGS shows excellent agreement when validated on the FGMS, and the risk classifier shows slightly better performance at predicting CFRD risk later in life in both studies. Conclusion We demonstrated clinical utility by comparing CFRD prevalence rates between the top 10% of individuals with the highest risk and the bottom 10% with the lowest risk. A web-based application was developed to provide practitioners with patient-specific CFRD risk to guide CFRD monitoring and treatment.
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Affiliation(s)
- Yu-Chung Lin
- Department of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Katherine Keenan
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jiafen Gong
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Naim Panjwani
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Julie Avolio
- Program in Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Fan Lin
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Damien Adam
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.,CRCHUM, Montréal, QC, Canada
| | | | | | - Yves Berthiaume
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Lara Bilodeau
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec-Université Laval, Québec City, QC, Canada
| | | | - Janna Brusky
- Jim Pattison Children's Hospital, Saskatoon, SK, Canada
| | | | - Mark Chilvers
- British Columbia Children's Hospital, Vancouver, BC, Canada
| | | | | | - Andrea Dale
- Queen Elizabeth II Health Sciences Centre, Halifax, NS, Canada
| | | | | | | | | | | | | | - Shaikh Iqbal
- The Children's Hospital of Winnipeg, Winnipeg, MB, Canada
| | | | - Mary Jackson
- Royal University Hospital, Saskatoon, SK, Canada
| | | | | | | | - Winnie Leung
- University of Alberta Hospital, Edmonton, AB, Canada
| | | | | | | | | | | | - Nancy Morrison
- Queen Elizabeth II Health Sciences Centre, Halifax, NS, Canada
| | | | | | - April Price
- The Children's Hospital of Western Ontario, London, ON, Canada
| | | | - Joe Reisman
- The Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Clare Smith
- Foothills Medical Centre, Calgary, AB, Canada
| | - Mary Jane Smith
- Janeway Children's Health & Rehabilitation Centre, St. John's, NL, Canada
| | - Nathalie Vadeboncoeur
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec-Université Laval, Québec City, QC, Canada
| | | | - Terry Viczko
- British Columbia Children's Hospital, Vancouver, BC, Canada
| | | | | | - Garry Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Felix Ratjen
- Program in Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada.,Division of Respiratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Johanna M Rommens
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Lei Sun
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | - Melinda Solomon
- Division of Respiratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | | | - Emmanuelle Brochiero
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.,CRCHUM, Montréal, QC, Canada
| | - Scott Blackman
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Harriet Corvol
- Assistance Publique-Hôpitaux de Paris, Hôpital Trousseau, Pediatric Pulmonary Department, Paris, France.,Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre de Recherche Saint Antoine, Paris, France
| | - Lisa J Strug
- Department of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada. .,Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada. .,Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada. .,The Center for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada. .,Department of Computer Science, University of Toronto, Toronto, ON, Canada.
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5
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Rauscher R, Bampi GB, Guevara-Ferrer M, Santos LA, Joshi D, Mark D, Strug LJ, Rommens JM, Ballmann M, Sorscher EJ, Oliver KE, Ignatova Z. Positive epistasis between disease-causing missense mutations and silent polymorphism with effect on mRNA translation velocity. Proc Natl Acad Sci U S A 2021; 118:e2010612118. [PMID: 33468668 PMCID: PMC7848603 DOI: 10.1073/pnas.2010612118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Epistasis refers to the dependence of a mutation on other mutation(s) and the genetic context in general. In the context of human disorders, epistasis complicates the spectrum of disease symptoms and has been proposed as a major contributor to variations in disease outcome. The nonadditive relationship between mutations and the lack of complete understanding of the underlying physiological effects limit our ability to predict phenotypic outcome. Here, we report positive epistasis between intragenic mutations in the cystic fibrosis transmembrane conductance regulator (CFTR)-the gene responsible for cystic fibrosis (CF) pathology. We identified a synonymous single-nucleotide polymorphism (sSNP) that is invariant for the CFTR amino acid sequence but inverts translation speed at the affected codon. This sSNP in cis exhibits positive epistatic effects on some CF disease-causing missense mutations. Individually, both mutations alter CFTR structure and function, yet when combined, they lead to enhanced protein expression and activity. The most robust effect was observed when the sSNP was present in combination with missense mutations that, along with the primary amino acid change, also alter the speed of translation at the affected codon. Functional studies revealed that synergistic alteration in ribosomal velocity is the underlying mechanism; alteration of translation speed likely increases the time window for establishing crucial domain-domain interactions that are otherwise perturbed by each individual mutation.
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Affiliation(s)
- Robert Rauscher
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Giovana B Bampi
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Marta Guevara-Ferrer
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Leonardo A Santos
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Disha Joshi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322
- Children's Healthcare of Atlanta, Atlanta, GA 30322
| | - David Mark
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Lisa J Strug
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto M5G 0A4, Canada
- Department of Statistical Sciences, Computer Science and Division of Biostatistics, University of Toronto, Toronto M5G 0A4, Canada
| | - Johanna M Rommens
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto M5G 0A4, Canada
| | | | - Eric J Sorscher
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322
- Children's Healthcare of Atlanta, Atlanta, GA 30322
| | - Kathryn E Oliver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322
- Children's Healthcare of Atlanta, Atlanta, GA 30322
| | - Zoya Ignatova
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany;
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6
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Panjwani N, Wang F, Mastromatteo S, Bao A, Wang C, He G, Gong J, Rommens JM, Sun L, Strug LJ. LocusFocus: Web-based colocalization for the annotation and functional follow-up of GWAS. PLoS Comput Biol 2020; 16:e1008336. [PMID: 33090994 PMCID: PMC7608978 DOI: 10.1371/journal.pcbi.1008336] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 11/03/2020] [Accepted: 09/13/2020] [Indexed: 01/10/2023] Open
Abstract
Genome-wide association studies (GWAS) have primarily identified trait-associated loci in the non-coding genome. Colocalization analyses of SNP associations from GWAS with expression quantitative trait loci (eQTL) evidence enable the generation of hypotheses about responsible mechanism, genes and tissues of origin to guide functional characterization. Here, we present a web-based colocalization browsing and testing tool named LocusFocus (https://locusfocus.research.sickkids.ca). LocusFocus formally tests colocalization using our established Simple Sum method to identify the most relevant genes and tissues for a particular GWAS locus in the presence of high linkage disequilibrium and/or allelic heterogeneity. We demonstrate the utility of LocusFocus, following up on a genome-wide significant locus from a GWAS of meconium ileus (an intestinal obstruction in cystic fibrosis). Using LocusFocus for colocalization analysis with eQTL data suggests variation in ATP12A gene expression in the pancreas rather than intestine is responsible for the GWAS locus. LocusFocus has no operating system dependencies and may be installed in a local web server. LocusFocus is available under the MIT license, with full documentation and source code accessible on GitHub at https://github.com/naim-panjwani/LocusFocus.
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Affiliation(s)
- Naim Panjwani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Fan Wang
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Scott Mastromatteo
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Allen Bao
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Cheng Wang
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gengming He
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jiafen Gong
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Johanna M. Rommens
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Lei Sun
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Lisa J. Strug
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- * E-mail:
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7
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Aksit MA, Pace RG, Vecchio-Pagán B, Ling H, Rommens JM, Boelle PY, Guillot L, Raraigh KS, Pugh E, Zhang P, Strug LJ, Drumm ML, Knowles MR, Cutting GR, Corvol H, Blackman SM. Genetic Modifiers of Cystic Fibrosis-Related Diabetes Have Extensive Overlap With Type 2 Diabetes and Related Traits. J Clin Endocrinol Metab 2020; 105:5599821. [PMID: 31697830 PMCID: PMC7236628 DOI: 10.1210/clinem/dgz102] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/02/2019] [Indexed: 02/08/2023]
Abstract
CONTEXT Individuals with cystic fibrosis (CF) develop a distinct form of diabetes characterized by β-cell dysfunction and islet amyloid accumulation similar to type 2 diabetes (T2D), but generally have normal insulin sensitivity. CF-related diabetes (CFRD) risk is determined by both CFTR, the gene responsible for CF, and other genetic variants. OBJECTIVE To identify genetic modifiers of CFRD and determine the genetic overlap with other types of diabetes. DESIGN AND PATIENTS A genome-wide association study was conducted for CFRD onset on 5740 individuals with CF. Weighted polygenic risk scores (PRSs) for type 1 diabetes (T1D), T2D, and diabetes endophenotypes were tested for association with CFRD. RESULTS Genome-wide significance was obtained for variants at a novel locus (PTMA) and 2 known CFRD genetic modifiers (TCF7L2 and SLC26A9). PTMA and SLC26A9 variants were CF-specific; TCF7L2 variants also associated with T2D. CFRD was strongly associated with PRSs for T2D, insulin secretion, postchallenge glucose concentration, and fasting plasma glucose, and less strongly with T1D PRSs. CFRD was inconsistently associated with PRSs for insulin sensitivity and was not associated with a PRS for islet autoimmunity. A CFRD PRS comprising variants selected from these PRSs (with a false discovery rate < 0.1) and the genome-wide significant variants was associated with CFRD in a replication population. CONCLUSIONS CFRD and T2D have more etiologic and mechanistic overlap than previously known, aligning along pathways involving β-cell function rather than insulin sensitivity. Two CFRD risk loci are unrelated to T2D and may affect multiple aspects of CF. An 18-variant PRS stratifies risk of CFRD in an independent population.
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Affiliation(s)
- Melis A Aksit
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rhonda G Pace
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - Hua Ling
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Johanna M Rommens
- The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
| | - Pierre-Yves Boelle
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, iPLESP, AP-HP, Hôpital Saint-Antoine, Paris, France
| | - Loic Guillot
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Karen S Raraigh
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Peng Zhang
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Lisa J Strug
- The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
| | | | - Michael R Knowles
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Garry R Cutting
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Harriet Corvol
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Scott M Blackman
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Division of Pediatric Endocrinology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Correspondence and Reprint Requests: Scott M. Blackman, McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205. E-mail:
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8
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McCague AF, Raraigh KS, Pellicore MJ, Davis-Marcisak EF, Evans TA, Han ST, Lu Z, Joynt AT, Sharma N, Castellani C, Collaco JM, Corey M, Lewis MH, Penland CM, Rommens JM, Stephenson AL, Sosnay PR, Cutting GR. Correlating Cystic Fibrosis Transmembrane Conductance Regulator Function with Clinical Features to Inform Precision Treatment of Cystic Fibrosis. Am J Respir Crit Care Med 2020; 199:1116-1126. [PMID: 30888834 DOI: 10.1164/rccm.201901-0145oc] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Rationale: The advent of precision treatment for cystic fibrosis using small-molecule therapeutics has created a need to estimate potential clinical improvements attributable to increases in cystic fibrosis transmembrane conductance regulator (CFTR) function. Objectives: To derive CFTR function of a variety of CFTR genotypes and correlate with key clinical features (sweat chloride concentration, pancreatic exocrine status, and lung function) to develop benchmarks for assessing response to CFTR modulators. Methods: CFTR function assigned to 226 unique CFTR genotypes was correlated with the clinical data of 54,671 individuals enrolled in the Clinical and Functional Translation of CFTR (CFTR2) project. Cross-sectional FEV1% predicted measurements were plotted by age at which measurement was obtained. Shifts in sweat chloride concentration and lung function reported in CFTR modulator trials were compared with function-phenotype correlations to assess potential efficacy of therapies. Measurements and Main Results: CFTR genotype function exhibited a logarithmic relationship with each clinical feature. Modest increases in CFTR function related to differing genotypes were associated with clinically relevant improvements in cross-sectional FEV1% predicted over a range of ages (6-82 yr). Therapeutic responses to modulators corresponded closely to predictions from the CFTR2-derived relationship between CFTR genotype function and phenotype. Conclusions: Increasing CFTR function in individuals with severe disease will have a proportionally greater effect on outcomes than similar increases in CFTR function in individuals with mild disease and should reverse a substantial fraction of the disease process. This study provides reference standards for clinical outcomes that may be achieved by increasing CFTR function.
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Affiliation(s)
- Allison F McCague
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | - Karen S Raraigh
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | | | | | - Taylor A Evans
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | - Sangwoo T Han
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | - Zhongzhou Lu
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | - Anya T Joynt
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | - Neeraj Sharma
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | - Carlo Castellani
- 2 Cystic Fibrosis Center, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Joseph M Collaco
- 3 Eudowood Division of Pediatric Respiratory Sciences, School of Medicine
| | | | | | | | - Johanna M Rommens
- 7 Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anne L Stephenson
- 8 Department of Respirology, Adult Cystic Fibrosis Program, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Patrick R Sosnay
- 9 Pulmonary and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Garry R Cutting
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
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9
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Nguyen TL, Aung YK, Evans CF, Dite GS, Stone J, MacInnis RJ, Dowty JG, Bickerstaffe A, Aujard K, Rommens JM, Song YM, Sung J, Jenkins MA, Southey MC, Giles GG, Apicella C, Hopper JL. Mammographic density defined by higher than conventional brightness thresholds better predicts breast cancer risk. Int J Epidemiol 2018; 46:652-661. [PMID: 28338721 PMCID: PMC5837222 DOI: 10.1093/ije/dyw212] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2016] [Indexed: 11/24/2022] Open
Abstract
Background: Mammographic density defined by the conventional pixel brightness threshold, and adjusted for age and body mass index (BMI), is a well-established risk factor for breast cancer. We asked if higher thresholds better separate women with and without breast cancer. Methods: We studied Australian women, 354 with breast cancer over-sampled for early-onset and family history, and 944 unaffected controls frequency-matched for age at mammogram. We measured mammographic dense area and percent density using the CUMULUS software at the conventional threshold, which we call Cumulus, and at two increasingly higher thresholds, which we call Altocumulus and Cirrocumulus, respectively. All measures were Box–Cox transformed and adjusted for age and BMI. We estimated the odds per adjusted standard deviation (OPERA) using logistic regression and the area under the receiver operating characteristic curve (AUC). Results:Altocumulus and Cirrocumulus were correlated with Cumulus (r ∼ 0.8 and 0.6, respectively). For dense area, the OPERA was 1.62, 1.74 and 1.73 for Cumulus, Altocumulus and Cirrocumulus, respectively (all P < 0.001). After adjusting for Altocumulus and Cirrocumulus, Cumulus was not significant (P > 0.6). The OPERAs for percent density were less but gave similar findings. The mean of the standardized adjusted Altocumulus and Cirrocumulus dense area measures was the best predictor; OPERA = 1.87 [95% confidence interval (CI): 1.64–2.14] and AUC = 0.68 (0.65–0.71). Conclusions: The areas of higher mammographically dense regions are associated with almost 30% stronger breast cancer risk gradient, explain the risk association of the conventional measure and might be more aetiologically important. This has substantial implications for clinical translation and molecular, genetic and epidemiological research.
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Affiliation(s)
- Tuong L Nguyen
- Centre for Epidemiology and Biostatistics, University of Melbourne, Carlton, VIC, Australia
| | - Ye K Aung
- Centre for Epidemiology and Biostatistics, University of Melbourne, Carlton, VIC, Australia
| | - Christopher F Evans
- Centre for Epidemiology and Biostatistics, University of Melbourne, Carlton, VIC, Australia
| | - Gillian S Dite
- Centre for Epidemiology and Biostatistics, University of Melbourne, Carlton, VIC, Australia
| | - Jennifer Stone
- Curtin UWA Centre for Genetic Origins of Health and Disease, Curtin University and The University of Western Australia, Perth, WA, Australia
| | - Robert J MacInnis
- Centre for Epidemiology and Biostatistics, University of Melbourne, Carlton, VIC, Australia
| | - James G Dowty
- Centre for Epidemiology and Biostatistics, University of Melbourne, Carlton, VIC, Australia
| | - Adrian Bickerstaffe
- Centre for Epidemiology and Biostatistics, University of Melbourne, Carlton, VIC, Australia
| | - Kelly Aujard
- Centre for Epidemiology and Biostatistics, University of Melbourne, Carlton, VIC, Australia
| | - Johanna M Rommens
- Program in Genetics and Genomic Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Yun-Mi Song
- Department of Family Medicine, Sungkyunkwan University School of Medicine, Seoul, South Korea and
| | - Joohon Sung
- Department of Epidemiology, School of Public Health, Seoul National University, Seoul, Korea.,Institute of Health and Environment, Seoul National University, Seoul, Korea
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, University of Melbourne, Carlton, VIC, Australia
| | | | - Graham G Giles
- Centre for Epidemiology and Biostatistics, University of Melbourne, Carlton, VIC, Australia.,Cancer Council Victoria, Melbourne, VIC, Australia
| | - Carmel Apicella
- Centre for Epidemiology and Biostatistics, University of Melbourne, Carlton, VIC, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, University of Melbourne, Carlton, VIC, Australia.,Department of Epidemiology, School of Public Health, Seoul National University, Seoul, Korea.,Institute of Health and Environment, Seoul National University, Seoul, Korea
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10
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Collaco JM, Blackman SM, Raraigh KS, Corvol H, Rommens JM, Pace RG, Boelle PY, McGready J, Sosnay PR, Strug LJ, Knowles MR, Cutting GR. Sources of Variation in Sweat Chloride Measurements in Cystic Fibrosis. Am J Respir Crit Care Med 2016; 194:1375-1382. [PMID: 27258095 PMCID: PMC5148144 DOI: 10.1164/rccm.201603-0459oc] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/03/2016] [Indexed: 01/20/2023] Open
Abstract
RATIONALE Expanding the use of cystic fibrosis transmembrane conductance regulator (CFTR) potentiators and correctors for the treatment of cystic fibrosis (CF) requires precise and accurate biomarkers. Sweat chloride concentration provides an in vivo assessment of CFTR function, but it is unknown the degree to which CFTR mutations account for sweat chloride variation. OBJECTIVES To estimate potential sources of variation for sweat chloride measurements, including demographic factors, testing variability, recording biases, and CFTR genotype itself. METHODS A total of 2,639 sweat chloride measurements were obtained in 1,761 twins/siblings from the CF Twin-Sibling Study, French CF Modifier Gene Study, and Canadian Consortium for Genetic Studies. Variance component estimation was performed by nested mixed modeling. MEASUREMENTS AND MAIN RESULTS Across the tested CF population as a whole, CFTR gene mutations were found to be the primary determinant of sweat chloride variability (56.1% of variation) with contributions from variation over time (e.g., factors related to testing on different days; 13.8%), environmental factors (e.g., climate, family diet; 13.5%), other residual factors (e.g., test variability; 9.9%), and unique individual factors (e.g., modifier genes, unique exposures; 6.8%) (likelihood ratio test, P < 0.001). Twin analysis suggested that modifier genes did not play a significant role because the heritability estimate was negligible (H2 = 0; 95% confidence interval, 0.0-0.35). For an individual with CF, variation in sweat chloride was primarily caused by variation over time (58.1%) with the remainder attributable to residual/random factors (41.9%). CONCLUSIONS Variation in the CFTR gene is the predominant cause of sweat chloride variation; most of the non-CFTR variation is caused by testing variability and unique environmental factors. If test precision and accuracy can be improved, sweat chloride measurement could be a valuable biomarker for assessing response to therapies directed at mutant CFTR.
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Affiliation(s)
| | | | | | - Harriet Corvol
- Assistance Publique-Hôpitaux de Paris, Trousseau Hospital, Paris, France
- Institut National de la Santé et la Recherche Médicale, Paris, France
| | - Johanna M. Rommens
- The Hospital for Sick Children and the University of Toronto, Toronto, Canada
| | - Rhonda G. Pace
- Marsico Lung Institute/Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Pierre-Yves Boelle
- Institut National de la Santé et la Recherche Médicale, Paris, France
- Sorbonne Universités, Université Pierre et Marie Curie, Paris, France; and
- Assistance Publique-Hôpitaux de Paris, Saint-Antoine Hospital, Paris, France
| | - John McGready
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | | | - Lisa J. Strug
- The Hospital for Sick Children and the University of Toronto, Toronto, Canada
| | - Michael R. Knowles
- Marsico Lung Institute/Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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11
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Strug LJ, Gonska T, He G, Keenan K, Ip W, Boëlle PY, Lin F, Panjwani N, Gong J, Li W, Soave D, Xiao B, Tullis E, Rabin H, Parkins MD, Price A, Zuberbuhler PC, Corvol H, Ratjen F, Sun L, Bear CE, Rommens JM. Cystic fibrosis gene modifier SLC26A9 modulates airway response to CFTR-directed therapeutics. Hum Mol Genet 2016; 25:4590-4600. [PMID: 28171547 PMCID: PMC5886039 DOI: 10.1093/hmg/ddw290] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/12/2016] [Accepted: 08/25/2016] [Indexed: 12/18/2022] Open
Abstract
Cystic fibrosis is realizing the promise of personalized medicine. Recent advances in drug development that target the causal CFTR directly result in lung function improvement, but variability in response is demanding better prediction of outcomes to improve management decisions. The genetic modifier SLC26A9 contributes to disease severity in the CF pancreas and intestine at birth and here we assess its relationship with disease severity and therapeutic response in the airways. SLC26A9 association with lung disease was assessed in individuals from the Canadian and French CF Gene Modifier consortia with CFTR-gating mutations and in those homozygous for the common Phe508del mutation. Variability in response to a CFTR-directed therapy attributed to SLC26A9 genotype was assessed in Canadian patients with gating mutations. A primary airway model system determined if SLC26A9 shows modification of Phe508del CFTR function upon treatment with a CFTR corrector. In those with gating mutations that retain cell surface-localized CFTR we show that SLC26A9 modifies lung function while this is not the case in individuals homozygous for Phe508del where cell surface expression is lacking. Treatment response to ivacaftor, which aims to improve CFTR-channel opening probability in patients with gating mutations, shows substantial variability in response, 28% of which can be explained by rs7512462 in SLC26A9 (P = 0.0006). When homozygous Phe508del primary bronchial cells are treated to restore surface CFTR, SLC26A9 likewise modifies treatment response (P = 0.02). Our findings indicate that SLC26A9 airway modification requires CFTR at the cell surface, and that a common variant in SLC26A9 may predict response to CFTR-directed therapeutics.
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Affiliation(s)
- Lisa J. Strug
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Ontario, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tanja Gonska
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gengming He
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Katherine Keenan
- Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wan Ip
- Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pierre-Yves Boëlle
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris 06, Paris, France
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital St. Antoine, Biostatistics Department; Inserm U1136, Paris, France
| | - Fan Lin
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Naim Panjwani
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jiafen Gong
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Weili Li
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - David Soave
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Ontario, Canada
| | - Bowei Xiao
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elizabeth Tullis
- Department of Respiratory Medicine and Li Ka Shing Knowledge Institute, St. Michael’s Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Harvey Rabin
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
- The Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, Alberta, Canada
| | - Michael D. Parkins
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
- The Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, Alberta, Canada
| | - April Price
- Division of Paediatric Respirology, Department of Paediatrics, Children's Hospital at London Health Sciences Centre, London, Ontario, Canada
| | | | - Harriet Corvol
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris 06, Paris, France
- AP-HP, Hôpital Trousseau, Pediatric Pulmonary Department; Institut National de la Santé et al Recherche Medicale (INSERM) U938, Paris, France
| | - Felix Ratjen
- Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Respiratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lei Sun
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Ontario, Canada
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Christine E. Bear
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, CanadaDepartments of
- Biochemistry
- Physiology
| | - Johanna M. Rommens
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
- Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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12
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Sosnay PR, Castellani C, Penland CM, Rommens JM, Lewis M, Raraigh KS, Corey M, Cutting GR. Bias in CFTR screening panels. Genet Med 2015; 18:209. [PMID: 26513347 DOI: 10.1038/gim.2015.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 06/09/2015] [Indexed: 11/09/2022] Open
Affiliation(s)
- Patrick R Sosnay
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Carlo Castellani
- Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | | | - Johanna M Rommens
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michelle Lewis
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Karen S Raraigh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Mary Corey
- Program in Child Evaluative Health Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Garry R Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
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13
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Zambetti NA, Bindels EMJ, Van Strien PMH, Valkhof MG, Adisty MN, Hoogenboezem RM, Sanders MA, Rommens JM, Touw IP, Raaijmakers MHGP. Deficiency of the ribosome biogenesis gene Sbds in hematopoietic stem and progenitor cells causes neutropenia in mice by attenuating lineage progression in myelocytes. Haematologica 2015; 100:1285-93. [PMID: 26185170 DOI: 10.3324/haematol.2015.131573] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/06/2015] [Indexed: 01/10/2023] Open
Abstract
Shwachman-Diamond syndrome is a congenital bone marrow failure disorder characterized by debilitating neutropenia. The disease is associated with loss-of-function mutations in the SBDS gene, implicated in ribosome biogenesis, but the cellular and molecular events driving cell specific phenotypes in ribosomopathies remain poorly defined. Here, we established what is to our knowledge the first mammalian model of neutropenia in Shwachman-Diamond syndrome through targeted downregulation of Sbds in hematopoietic stem and progenitor cells expressing the myeloid transcription factor CCAAT/enhancer binding protein α (Cebpa). Sbds deficiency in the myeloid lineage specifically affected myelocytes and their downstream progeny while, unexpectedly, it was well tolerated by rapidly cycling hematopoietic progenitor cells. Molecular insights provided by massive parallel sequencing supported cellular observations of impaired cell cycle exit and formation of secondary granules associated with the defect of myeloid lineage progression in myelocytes. Mechanistically, Sbds deficiency activated the p53 tumor suppressor pathway and induced apoptosis in these cells. Collectively, the data reveal a previously unanticipated, selective dependency of myelocytes and downstream progeny, but not rapidly cycling progenitors, on this ubiquitous ribosome biogenesis protein, thus providing a cellular basis for the understanding of myeloid lineage biased defects in Shwachman-Diamond syndrome.
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Affiliation(s)
- Noemi A Zambetti
- Department of Hematology, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Eric M J Bindels
- Department of Hematology, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Paulina M H Van Strien
- Department of Hematology, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Marijke G Valkhof
- Department of Hematology, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands Current address: Laboratory for Cell Therapy, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Maria N Adisty
- Department of Hematology, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Remco M Hoogenboezem
- Department of Hematology, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Mathijs A Sanders
- Department of Hematology, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Johanna M Rommens
- Program in Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Department of Molecular Genetics, University of Toronto, ON, Canada
| | - Ivo P Touw
- Department of Hematology, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Marc H G P Raaijmakers
- Department of Hematology, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
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14
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Soave D, Corvol H, Panjwani N, Gong J, Li W, Boëlle PY, Durie PR, Paterson AD, Rommens JM, Strug LJ, Sun L. A Joint Location-Scale Test Improves Power to Detect Associated SNPs, Gene Sets, and Pathways. Am J Hum Genet 2015; 97:125-38. [PMID: 26140448 PMCID: PMC4572492 DOI: 10.1016/j.ajhg.2015.05.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 05/26/2015] [Indexed: 11/28/2022] Open
Abstract
Gene-based, pathway, and other multivariate association methods are motivated by the possibility of GxG and GxE interactions; however, accounting for such interactions is limited by the challenges associated with adequate modeling information. Here we propose an easy-to-implement joint location-scale (JLS) association testing framework for single-variant and multivariate analysis that accounts for interactions without explicitly modeling them. We apply the JLS method to a gene-set analysis of cystic fibrosis (CF) lung disease, which is influenced by multiple environmental and genetic factors. We identify and replicate an association between the constituents of the apical plasma membrane and CF lung disease (p = 0.0099 and p = 0.0180, respectively) and highlight a role for the SLC9A3-SLC9A3R1/2-EZR complex in contributing to CF lung disease. Many association studies could benefit from re-analysis with the JLS method that leverages complex genetic architecture for SNP, gene, and pathway identification. Analytical verification, simulation, and additional proof-of-principle applications support our approach.
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Affiliation(s)
- David Soave
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada; Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Harriet Corvol
- Assistance Publique-Hôpitaux de Paris (AP-HP), Trousseau Hospital, Pediatric Pulmonology Department; Institut National de la Santé et la Recherche Médicale (INSERM), UMR_S 938, CDR Saint-Antoine, 75012 Paris, France; Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris 06, 75005 Paris, France
| | - Naim Panjwani
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jiafen Gong
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Weili Li
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada; Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Pierre-Yves Boëlle
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris 06, 75005 Paris, France; AP-HP, Saint-Antoine Hospital, Biostatistics Department, INSERM, UMR_S 1136, 75012 Paris, France
| | - Peter R Durie
- Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Andrew D Paterson
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Johanna M Rommens
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Lisa J Strug
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada; Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.
| | - Lei Sun
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada; Department of Statistical Sciences, University of Toronto, Toronto, ON M5S 3G3, Canada.
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15
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Tourlakis ME, Zhang S, Ball HL, Gandhi R, Liu H, Zhong J, Yuan JS, Guidos CJ, Durie PR, Rommens JM. In Vivo Senescence in the Sbds-Deficient Murine Pancreas: Cell-Type Specific Consequences of Translation Insufficiency. PLoS Genet 2015; 11:e1005288. [PMID: 26057580 PMCID: PMC4461263 DOI: 10.1371/journal.pgen.1005288] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 05/18/2015] [Indexed: 01/01/2023] Open
Abstract
Genetic models of ribosome dysfunction show selective organ failure, highlighting a gap in our understanding of cell-type specific responses to translation insufficiency. Translation defects underlie a growing list of inherited and acquired cancer-predisposition syndromes referred to as ribosomopathies. We sought to identify molecular mechanisms underlying organ failure in a recessive ribosomopathy, with particular emphasis on the pancreas, an organ with a high and reiterative requirement for protein synthesis. Biallelic loss of function mutations in SBDS are associated with the ribosomopathy Shwachman-Diamond syndrome, which is typified by pancreatic dysfunction, bone marrow failure, skeletal abnormalities and neurological phenotypes. Targeted disruption of Sbds in the murine pancreas resulted in p53 stabilization early in the postnatal period, specifically in acinar cells. Decreased Myc expression was observed and atrophy of the adult SDS pancreas could be explained by the senescence of acinar cells, characterized by induction of Tgfβ, p15Ink4b and components of the senescence-associated secretory program. This is the first report of senescence, a tumour suppression mechanism, in association with SDS or in response to a ribosomopathy. Genetic ablation of p53 largely resolved digestive enzyme synthesis and acinar compartment hypoplasia, but resulted in decreased cell size, a hallmark of decreased translation capacity. Moreover, p53 ablation resulted in expression of acinar dedifferentiation markers and extensive apoptosis. Our findings indicate a protective role for p53 and senescence in response to Sbds ablation in the pancreas. In contrast to the pancreas, the Tgfβ molecular signature was not detected in fetal bone marrow, liver or brain of mouse models with constitutive Sbds ablation. Nevertheless, as observed with the adult pancreas phenotype, disease phenotypes of embryonic tissues, including marked neuronal cell death due to apoptosis, were determined to be p53-dependent. Our findings therefore point to cell/tissue-specific responses to p53-activation that include distinction between apoptosis and senescence pathways, in the context of translation disruption. Growth of all living things relies on protein synthesis. Failure of components of the complex protein synthesis machinery underlies a growing list of inherited and acquired multi—organ syndromes referred to as ribosomopathies. While ribosomes, the critical working components of the protein synthesis machinery, are required in all cell types to translate the genetic code, only certain organs manifest clinical symptoms in ribosomopathies, indicating specific cell-type features of protein synthesis control. Further, many of these diseases result in cancer despite an inherent deficit in growth. Here we report a range of consequences of protein synthesis insufficiency with loss of a broadly expressed ribosome factor, leading to growth impairment and cell cycle arrest at different stages. Apparent induction of p53-dependent cell death and arrest pathways included apoptosis in the fetal brain and senescence in the mature exocrine pancreas. The senescence, considered a tumour suppression mechanism, was accompanied by the expression of biomarkers associated with early stages of malignant transformation. These findings inform how cancer may initiate when growth is compromised and provide new insights into cell-type specific consequences of protein synthesis insufficiency.
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Affiliation(s)
- Marina E. Tourlakis
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Siyi Zhang
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Heather L. Ball
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
| | - Rikesh Gandhi
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
| | - Hongrui Liu
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Jian Zhong
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
| | - Julie S. Yuan
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Department of Immunology, University of Toronto, Toronto, Canada
| | - Cynthia J. Guidos
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Department of Immunology, University of Toronto, Toronto, Canada
| | - Peter R. Durie
- Program in Physiology & Experimental Medicine, Research Institute, Division of Gastroenterology & Nutrition, The Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, Canada
| | - Johanna M. Rommens
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- * E-mail:
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16
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Miller MR, Soave D, Li W, Gong J, Pace RG, Boëlle PY, Cutting GR, Drumm ML, Knowles MR, Sun L, Rommens JM, Accurso F, Durie PR, Corvol H, Levy H, Sontag MK, Strug LJ. Variants in Solute Carrier SLC26A9 Modify Prenatal Exocrine Pancreatic Damage in Cystic Fibrosis. J Pediatr 2015; 166:1152-1157.e6. [PMID: 25771386 PMCID: PMC4530786 DOI: 10.1016/j.jpeds.2015.01.044] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 12/12/2014] [Accepted: 01/23/2015] [Indexed: 11/27/2022]
Abstract
OBJECTIVES To test the hypothesis that multiple constituents of the apical plasma membrane residing alongside the causal cystic fibrosis (CF) transmembrane conductance regulator protein, including known CF modifiers SLC26A9, SLC6A14, and SLC9A3, would be associated with prenatal exocrine pancreatic damage as measured by newborn screened (NBS) immunoreactive trypsinogen (IRT) levels. STUDY DESIGN NBS IRT measures and genome-wide genotype data were available on 111 subjects from Colorado, 37 subjects from Wisconsin, and 80 subjects from France. Multiple linear regression was used to determine whether any of 8 single nucleotide polymorphisms (SNPs) in SLC26A9, SLC6A14, and SLC9A3 were associated with IRT and whether other constituents of the apical plasma membrane contributed to IRT. RESULTS In the Colorado sample, 3 SLC26A9 SNPs were associated with NBS IRT (min P=1.16×10(-3); rs7512462), but no SLC6A14 or SLC9A3 SNPs were associated (P>.05). The rs7512462 association replicated in the Wisconsin sample (P=.03) but not in the French sample (P=.76). Furthermore, rs7512462 was the top-ranked apical membrane constituent in the combined Colorado and Wisconsin sample. CONCLUSIONS NBS IRT is a biomarker of prenatal exocrine pancreatic disease in patients with CF, and a SNP in SLC26A9 accounts for significant IRT variability. This work suggests SLC26A9 as a potential therapeutic target to ameliorate exocrine pancreatic disease.
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Affiliation(s)
- Melissa R. Miller
- Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, Ontario, Canada
| | - David Soave
- Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, Ontario, Canada,Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Weili Li
- Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, Ontario, Canada,Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Jiafen Gong
- Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rhonda G. Pace
- Cystic Fibrosis-Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Pierre-Yves Boëlle
- Pierre et Marie Curie University-Paris 6, Paris, France,Biostatistics Department, St Antoine Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP); Institut National de la Santé et la Researche Médicale (INSERM), UMR-S 1136, Paris, France
| | - Garry R. Cutting
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mitchell L. Drumm
- Departments of Pediatrics and Genetics, Case Western Reserve University, Cleveland, Ohio, USA
| | - Michael R. Knowles
- Cystic Fibrosis-Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lei Sun
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada,Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Johanna M. Rommens
- Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, Ontario, Canada,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Frank Accurso
- Department of Pediatrics, University of Colorado Denver School of Medicine, Aurora, Colorado, USA,Department of Pediatrics, Children’s Hospital of Colorado, Aurora, Colorado, USA
| | - Peter R. Durie
- Program in Physiology and Experimental Medicine, the Hospital for Sick Children, Toronto, Ontario, Canada,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Harriet Corvol
- Pierre et Marie Curie University-Paris 6, Paris, France,Pediatric Pulmonology Department, Trousseau Hospital, AP-HP, Inserm U938, Paris, France
| | - Hara Levy
- Department of Pediatrics, Section of Pulmonary and Sleep Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA,Children’s Research Institute, Children’s Hospital of Wisconsin, Milwaukee, Wisconsin, USA
| | - Marci K. Sontag
- Department of Pediatrics, Children’s Hospital of Colorado, Aurora, Colorado, USA,Department of Epidemiology, Colorado School of Public Health University of Colorado Denver, Aurora, Colorado, USA
| | - Lisa J. Strug
- Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, Ontario, Canada,Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
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Soave D, Miller MR, Keenan K, Li W, Gong J, Ip W, Accurso F, Sun L, Rommens JM, Sontag M, Durie PR, Strug LJ. Evidence for a causal relationship between early exocrine pancreatic disease and cystic fibrosis-related diabetes: a Mendelian randomization study. Diabetes 2014; 63:2114-9. [PMID: 24550193 PMCID: PMC4030111 DOI: 10.2337/db13-1464] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 02/13/2014] [Indexed: 01/20/2023]
Abstract
Circulating immunoreactive trypsinogen (IRT), a biomarker of exocrine pancreatic disease in cystic fibrosis (CF), is elevated in most CF newborns. In those with severe CF transmembrane conductance regulator (CFTR) genotypes, IRT declines rapidly in the first years of life, reflecting progressive pancreatic damage. Consistent with this progression, a less elevated newborn IRT measure would reflect more severe pancreatic disease, including compromised islet compartments, and potentially increased risk of CF-related diabetes (CFRD). We show in two independent CF populations that a lower newborn IRT estimate is associated with higher CFRD risk among individuals with severe CFTR genotypes, and we provide evidence to support a causal relationship. Increased loge(IRT) at birth was associated with decreased CFRD risk in Canadian and Colorado samples (hazard ratio 0.30 [95% CI 0.15-0.61] and 0.39 [0.18-0.81], respectively). Using Mendelian randomization with the SLC26A9 rs7512462 genotype as an instrumental variable since it is known to be associated with IRT birth levels in the CF population, we provide evidence to support a causal contribution of exocrine pancreatic status on CFRD risk. Our findings suggest CFRD risk could be predicted in early life and that maintained ductal fluid flow in the exocrine pancreas could delay the onset of CFRD.
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Affiliation(s)
- David Soave
- Program in Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Ontario, CanadaDivision of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Melissa R Miller
- Program in Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Katherine Keenan
- Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Weili Li
- Program in Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Ontario, CanadaDivision of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Jiafen Gong
- Program in Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wan Ip
- Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Frank Accurso
- Department of Pediatrics, University of Colorado Denver School of Medicine, Denver, CO
| | - Lei Sun
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, CanadaDepartment of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Johanna M Rommens
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, CanadaDepartment of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Marci Sontag
- Department of Epidemiology, Colorado School of Public Health and University of Colorado Denver, Aurora, CO
| | - Peter R Durie
- Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Toronto, Ontario, CanadaDepartment of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Lisa J Strug
- Program in Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Ontario, CanadaDivision of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
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Blackman SM, Commander CW, Watson C, Arcara KM, Strug LJ, Stonebraker JR, Wright FA, Rommens JM, Sun L, Pace RG, Norris SA, Durie PR, Drumm ML, Knowles MR, Cutting GR. Genetic modifiers of cystic fibrosis-related diabetes. Diabetes 2013; 62:3627-35. [PMID: 23670970 PMCID: PMC3781476 DOI: 10.2337/db13-0510] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Diabetes is a common age-dependent complication of cystic fibrosis (CF) that is strongly influenced by modifier genes. We conducted a genome-wide association study in 3,059 individuals with CF (644 with CF-related diabetes [CFRD]) and identified single nucleotide polymorphisms (SNPs) within and 5' to the SLC26A9 gene that associated with CFRD (hazard ratio [HR] 1.38; P = 3.6 × 10(-8)). Replication was demonstrated in 694 individuals (124 with CFRD) (HR, 1.47; P = 0.007), with combined analysis significant at P = 9.8 × 10(-10). SLC26A9 is an epithelial chloride/bicarbonate channel that can interact with the CF transmembrane regulator (CFTR), the protein mutated in CF. We also hypothesized that common SNPs associated with type 2 diabetes also might affect risk for CFRD. A previous association of CFRD with SNPs in TCF7L2 was replicated in this study (P = 0.004; combined analysis P = 3.8 × 10(-6)), and type 2 diabetes SNPs at or near CDKAL1, CDKN2A/B, and IGF2BP2 were associated with CFRD (P < 0.004). These five loci accounted for 8.3% of the phenotypic variance in CFRD onset and had a combined population-attributable risk of 68%. Diabetes is a highly prevalent complication of CF, for which susceptibility is determined in part by variants at SLC26A9 (which mediates processes proximate to the CF disease-causing gene) and at four susceptibility loci for type 2 diabetes in the general population.
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Affiliation(s)
- Scott M. Blackman
- Division of Pediatric Endocrinology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Corresponding author: Scott M. Blackman,
| | - Clayton W. Commander
- Cystic Fibrosis–Pulmonary Research and Treatment Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Christopher Watson
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kristin M. Arcara
- Division of Pediatric Endocrinology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lisa J. Strug
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Program in Child Health Evaluative Sciences, the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jaclyn R. Stonebraker
- Cystic Fibrosis–Pulmonary Research and Treatment Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Fred A. Wright
- Cystic Fibrosis–Pulmonary Research and Treatment Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Johanna M. Rommens
- Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Lei Sun
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Rhonda G. Pace
- Cystic Fibrosis–Pulmonary Research and Treatment Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Sarah A. Norris
- Cystic Fibrosis–Pulmonary Research and Treatment Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Peter R. Durie
- Program in Physiology and Experimental Medicine, the Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Mitchell L. Drumm
- Departments of Pediatrics and Genetics, Case Western Reserve University, Cleveland, Ohio
| | - Michael R. Knowles
- Cystic Fibrosis–Pulmonary Research and Treatment Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Garry R. Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Singh SA, Vlachos A, Morgenstern NJ, Ouansafi I, Ip W, Rommens JM, Durie P, Shimamura A, Lipton JM. Breast cancer in a case of Shwachman Diamond syndrome. Pediatr Blood Cancer 2012; 59:945-6. [PMID: 22213587 DOI: 10.1002/pbc.24052] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 11/22/2011] [Indexed: 12/19/2022]
Abstract
Shwachman Diamond syndrome (SDS) is a rare inherited bone marrow failure syndrome (IBMFS) characterized by neutropenia, exocrine pancreatic dysfunction, and cancer predisposition. Patients are at risk for myelodysplastic syndrome (MDS) and acute myelogenous leukemia (AML) but, unlike other IBMFS, there have been no reported cases of solid tumors. We report a novel case of a solid tumor in a patient with SDS and biallelic mutations in the Shwachman Bodian Diamond Syndrome gene (SBDS). Whether the development of breast cancer in this patient is due to SDS or an isolated case due to unknown factors requires further study.
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Affiliation(s)
- Sharon A Singh
- Division of Hematology/Oncology and Stem Cell Transplantation, Steven and Alexandra Cohen Children's Medical Center of New York, New Hyde Park, New York 11040, USA.
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20
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Tourlakis ME, Zhong J, Gandhi R, Zhang S, Chen L, Durie PR, Rommens JM. Deficiency of Sbds in the mouse pancreas leads to features of Shwachman-Diamond syndrome, with loss of zymogen granules. Gastroenterology 2012; 143:481-92. [PMID: 22510201 DOI: 10.1053/j.gastro.2012.04.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2011] [Revised: 04/01/2012] [Accepted: 04/10/2012] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Shwachman-Diamond syndrome (SDS) is the second leading cause of hereditary exocrine pancreatic dysfunction. More than 90% of patients with SDS have biallelic loss-of-function mutations in the Shwachman-Bodian Diamond syndrome (SBDS) gene, which encodes a factor involved in ribosome function. We investigated whether mutations in Sbds lead to similar pancreatic defects in mice. METHODS Pancreas-specific knock-out mice were generated using a floxed Sbds allele and bred with mice carrying a null or disease-associated missense Sbds allele. Cre recombinase, regulated by the pancreatic transcription factor 1a promoter, was used to disrupt Sbds specifically in the pancreas. Models were assessed for pancreatic dysfunction and growth impairment. RESULTS Disruption of Sbds in the mouse pancreas was sufficient to recapitulate SDS phenotypes. Pancreata of mice with Sbds mutations had decreased mass, fat infiltration, but general preservation of ductal and endocrine compartments. Pancreatic extracts from mutant mice had defects in formation of the 80S ribosomal complex. The exocrine compartment of mutant mice was hypoplastic and individual acini produced few zymogen granules. The null Sbds allele resulted in an earlier onset of phenotypes as well as endocrine impairment. Mutant mice had reduced serum levels of digestive enzymes and overall growth impairment. CONCLUSIONS We developed a mouse model of SDS with pancreatic phenotypes similar to those of the human disease. This model could be used to investigate organ-specific consequences of Sbds-associated ribosomopathy. Sbds genotypes correlated with phenotypes. Defects developed specifically in the pancreata of mice, reducing growth of mice and production of digestive enzymes. SBDS therefore appears to be required for normal pancreatic development and function.
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Affiliation(s)
- Marina E Tourlakis
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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21
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Sun L, Rommens JM, Corvol H, Li W, Li X, Chiang TA, Lin F, Dorfman R, Busson PF, Parekh RV, Zelenika D, Blackman SM, Corey M, Doshi VK, Henderson L, Naughton KM, O'Neal WK, Pace RG, Stonebraker JR, Wood SD, Wright FA, Zielenski J, Clement A, Drumm ML, Boëlle PY, Cutting GR, Knowles MR, Durie PR, Strug LJ. Multiple apical plasma membrane constituents are associated with susceptibility to meconium ileus in individuals with cystic fibrosis. Nat Genet 2012; 44:562-9. [PMID: 22466613 PMCID: PMC3371103 DOI: 10.1038/ng.2221] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 02/24/2012] [Indexed: 01/18/2023]
Abstract
Variants associated with meconium ileus in cystic fibrosis were identified in 3,763 affected individuals by genome-wide association study (GWAS). Five SNPs at two loci near SLC6A14 at Xq23-24 (minimum P = 1.28 × 10(-12) at rs3788766) and SLC26A9 at 1q32.1 (minimum P = 9.88 × 10(-9) at rs4077468) accounted for ~5% of phenotypic variability and were replicated in an independent sample of affected individuals (n = 2,372; P = 0.001 and 0.0001, respectively). By incorporating the knowledge that disease-causing mutations in CFTR alter electrolyte and fluid flux across surface epithelium into a hypothesis-driven GWAS (GWAS-HD), we identified associations with the same SNPs in SLC6A14 and SLC26A9 and established evidence for the involvement of SNPs in a third solute carrier gene, SLC9A3. In addition, GWAS-HD provided evidence of association between meconium ileus and multiple genes encoding constituents of the apical plasma membrane where CFTR resides (P = 0.0002; testing of 155 apical membrane genes jointly and in replication, P = 0.022). These findings suggest that modulating activities of apical membrane constituents could complement current therapeutic paradigms for cystic fibrosis.
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Affiliation(s)
- Lei Sun
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
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Greenwood CMT, Paterson AD, Linton L, Andrulis IL, Apicella C, Dimitromanolakis A, Kriukov V, Martin LJ, Salleh A, Samiltchuk E, Parekh RV, Southey MC, John EM, Hopper JL, Boyd NF, Rommens JM. A genome-wide linkage study of mammographic density, a risk factor for breast cancer. Breast Cancer Res 2011; 13:R132. [PMID: 22188651 PMCID: PMC3326574 DOI: 10.1186/bcr3078] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 10/16/2011] [Accepted: 12/21/2011] [Indexed: 02/07/2023] Open
Abstract
Introduction Mammographic breast density is a highly heritable (h2 > 0.6) and strong risk factor for breast cancer. We conducted a genome-wide linkage study to identify loci influencing mammographic breast density (MD). Methods Epidemiological data were assembled on 1,415 families from the Australia, Northern California and Ontario sites of the Breast Cancer Family Registry, and additional families recruited in Australia and Ontario. Families consisted of sister pairs with age-matched mammograms and data on factors known to influence MD. Single nucleotide polymorphism (SNP) genotyping was performed on 3,952 individuals using the Illumina Infinium 6K linkage panel. Results Using a variance components method, genome-wide linkage analysis was performed using quantitative traits obtained by adjusting MD measurements for known covariates. Our primary trait was formed by fitting a linear model to the square root of the percentage of the breast area that was dense (PMD), adjusting for age at mammogram, number of live births, menopausal status, weight, height, weight squared, and menopausal hormone therapy. The maximum logarithm of odds (LOD) score from the genome-wide scan was on chromosome 7p14.1-p13 (LOD = 2.69; 63.5 cM) for covariate-adjusted PMD, with a 1-LOD interval spanning 8.6 cM. A similar signal was seen for the covariate adjusted area of the breast that was dense (DA) phenotype. Simulations showed that the complete sample had adequate power to detect LOD scores of 3 or 3.5 for a locus accounting for 20% of phenotypic variance. A modest peak initially seen on chromosome 7q32.3-q34 increased in strength when only the 513 families with at least two sisters below 50 years of age were included in the analysis (LOD 3.2; 140.7 cM, 1-LOD interval spanning 9.6 cM). In a subgroup analysis, we also found a LOD score of 3.3 for DA phenotype on chromosome 12.11.22-q13.11 (60.8 cM, 1-LOD interval spanning 9.3 cM), overlapping a region identified in a previous study. Conclusions The suggestive peaks and the larger linkage signal seen in the subset of pedigrees with younger participants highlight regions of interest for further study to identify genes that determine MD, with the goal of understanding mammographic density and its involvement in susceptibility to breast cancer.
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Affiliation(s)
- Celia M T Greenwood
- Program in Genetics & Genome Biology, The Hospital for Sick Children, 101 College Street, East Tower, Toronto, ON M5G 1L7, Canada
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23
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Wright FA, Strug LJ, Doshi VK, Commander CW, Blackman SM, Sun L, Berthiaume Y, Cutler D, Cojocaru A, Collaco JM, Corey M, Dorfman R, Goddard K, Green D, Kent JW, Lange EM, Lee S, Li W, Luo J, Mayhew GM, Naughton KM, Pace RG, Paré P, Rommens JM, Sandford A, Stonebraker JR, Sun W, Taylor C, Vanscoy LL, Zou F, Blangero J, Zielenski J, O'Neal WK, Drumm ML, Durie PR, Knowles MR, Cutting GR. Genome-wide association and linkage identify modifier loci of lung disease severity in cystic fibrosis at 11p13 and 20q13.2. Nat Genet 2011; 43:539-46. [PMID: 21602797 PMCID: PMC3296486 DOI: 10.1038/ng.838] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 04/22/2011] [Indexed: 12/17/2022]
Abstract
A combined genome-wide association and linkage study was used to identify loci causing variation in cystic fibrosis lung disease severity. We identified a significant association (P = 3.34 × 10(-8)) near EHF and APIP (chr11p13) in p.Phe508del homozygotes (n = 1,978). The association replicated in p.Phe508del homozygotes (P = 0.006) from a separate family based study (n = 557), with P = 1.49 × 10(-9) for the three-study joint meta-analysis. Linkage analysis of 486 sibling pairs from the family based study identified a significant quantitative trait locus on chromosome 20q13.2 (log(10) odds = 5.03). Our findings provide insight into the causes of variation in lung disease severity in cystic fibrosis and suggest new therapeutic targets for this life-limiting disorder.
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Affiliation(s)
- Fred A Wright
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Raaijmakers MHGP, Mukherjee S, Guo S, Zhang S, Kobayashi T, Schoonmaker JA, Ebert BL, Al-Shahrour F, Hasserjian RP, Scadden EO, Aung Z, Matza M, Merkenschlager M, Lin C, Rommens JM, Scadden DT. Bone progenitor dysfunction induces myelodysplasia and secondary leukaemia. Nature 2010; 464:852-7. [PMID: 20305640 PMCID: PMC3422863 DOI: 10.1038/nature08851] [Citation(s) in RCA: 811] [Impact Index Per Article: 57.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Accepted: 01/19/2010] [Indexed: 12/17/2022]
Abstract
Mesenchymal cells contribute to the 'stroma' of most normal and malignant tissues, with specific mesenchymal cells participating in the regulatory niches of stem cells. By examining how mesenchymal osteolineage cells modulate haematopoiesis, here we show that deletion of Dicer1 specifically in mouse osteoprogenitors, but not in mature osteoblasts, disrupts the integrity of haematopoiesis. Myelodysplasia resulted and acute myelogenous leukaemia emerged that had acquired several genetic abnormalities while having intact Dicer1. Examining gene expression altered in osteoprogenitors as a result of Dicer1 deletion showed reduced expression of Sbds, the gene mutated in Schwachman-Bodian-Diamond syndrome-a human bone marrow failure and leukaemia pre-disposition condition. Deletion of Sbds in mouse osteoprogenitors induced bone marrow dysfunction with myelodysplasia. Therefore, perturbation of specific mesenchymal subsets of stromal cells can disorder differentiation, proliferation and apoptosis of heterologous cells, and disrupt tissue homeostasis. Furthermore, primary stromal dysfunction can result in secondary neoplastic disease, supporting the concept of niche-induced oncogenesis.
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Affiliation(s)
- Marc H G P Raaijmakers
- Center for Regenerative Medicine, Massachusetts General Hospital and Harvard Medical School CPZN, USA.
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25
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Kerr EN, Ellis L, Dupuis A, Rommens JM, Durie PR. The behavioral phenotype of school-age children with shwachman diamond syndrome indicates neurocognitive dysfunction with loss of Shwachman-Bodian-Diamond syndrome gene function. J Pediatr 2010; 156:433-8. [PMID: 19906387 DOI: 10.1016/j.jpeds.2009.09.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Revised: 07/22/2009] [Accepted: 09/04/2009] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To investigate the cognitive, behavioral and adaptive functioning of children with Shwachman-Diamond syndrome (SDS). STUDY DESIGN Thirty-two children with SDS (6-17 years) were evaluated by use of standardized neuropsychological tests. Results were compared with normative data, unaffected siblings (n = 13), and age-and sex-matched children with cystic fibrosis (CF; n = 20). RESULTS Although intragroup variability in performance was evident, children with SDS displayed weaker overall intellectual reasoning, higher-order language skills, perceptual reasoning, visual-motor processing speed, visual motor- integration, visual executive problem-solving, attention, and aspects of academic achievement, as well as lower functional level of independence relative to the general population. Significant issues with behavior were also identified, including prior formal diagnoses and social problems. Lower abilities were found relative to sibling and CF control subjects and were not associated with secondary complications of SDS, age, or sex. CONCLUSION Neurocognitive deficits in subjects with SDS are largely independent of family environment and having a chronic illness and are likely the consequences of Shwachman-Bodian-Diamond syndrome gene dysfunction. There is a need for a broad-based approach to the assessment of cognitive function and appropriate remediation of individuals with SDS.
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Affiliation(s)
- Elizabeth N Kerr
- Department of Psychology, Hospital for Sick Children, Toronto, Ontario, Canada.
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Ball HL, Zhang B, Riches JJ, Gandhi R, Li J, Rommens JM, Myers JS. Shwachman-Bodian Diamond syndrome is a multi-functional protein implicated in cellular stress responses. Hum Mol Genet 2009; 18:3684-95. [PMID: 19602484 DOI: 10.1093/hmg/ddp316] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Shwachman-Diamond syndrome (SDS; OMIM 260400) results from loss-of-function mutations in the Shwachman-Bodian Diamond syndrome (SBDS) gene. It is a multi-system disorder with clinical features of exocrine pancreatic dysfunction, skeletal abnormalities, bone marrow failure and predisposition to leukemic transformation. Although the cellular functions of SBDS are still unclear, its yeast ortholog has been implicated in ribosome biogenesis. Using affinity capture and mass spectrometry, we have developed an SBDS-interactome and report SBDS binding partners with diverse molecular functions, notably components of the large ribosomal subunit and proteins involved in DNA metabolism. Reciprocal co-immunoprecipitation confirmed the interaction of SBDS with the large ribosomal subunit protein RPL4 and with DNA-PK and RPA70, two proteins with critical roles in DNA repair. Function for SBDS in response to cellular stresses was implicated by demonstrating that SBDS-depleted HEK293 cells are hypersensitive to multiple types of DNA damage as well as chemically induced endoplasmic reticulum stress. Furthermore, using multiple routes to impair translation and mimic the effect of SBDS-depletion, we show that SBDS-dependent hypersensitivity of HEK293 cells to UV irradiation can be distinguished from a role of SBDS in translation. These results indicate functions of SBDS beyond ribosome biogenesis and may provide insight into the poorly understood cancer predisposition of SDS patients.
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Affiliation(s)
- Heather L Ball
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
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Rommens JM. PIONNIERS CANADIENS : Lap-Chee Tsui. Genome 2008. [DOI: 10.1139/g08-903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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28
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Rommens JM. CANADIAN PIONEERS: Lap-Chee Tsui. Genome 2008. [DOI: 10.1139/g08-905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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29
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Aznarez I, Barash Y, Shai O, He D, Zielenski J, Tsui LC, Parkinson J, Frey BJ, Rommens JM, Blencowe BJ. A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation. Genome Res 2008; 18:1247-58. [PMID: 18456862 DOI: 10.1101/gr.073155.107] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
To identify human intronic sequences associated with 5' splice site recognition, we performed a systematic search for motifs enriched in introns downstream of both constitutive and alternative cassette exons. Significant enrichment was observed for U-rich motifs within 100 nucleotides downstream of 5' splice sites of both classes of exons, with the highest enrichment between positions +6 and +30. Exons adjacent to U-rich intronic motifs contain lower frequencies of exonic splicing enhancers and higher frequencies of exonic splicing silencers, compared with exons not followed by U-rich intronic motifs. These findings motivated us to explore the possibility of a widespread role for U-rich motifs in promoting exon inclusion. Since cytotoxic granule-associated RNA binding protein (TIA1) and TIA1-like 1 (TIAL1; also known as TIAR) were previously shown in vitro to bind to U-rich motifs downstream of 5' splice sites, and to facilitate 5' splice site recognition in vitro and in vivo, we investigated whether these factors function more generally in the regulation of splicing of exons followed by U-rich intronic motifs. Simultaneous knockdown of TIA1 and TIAL1 resulted in increased skipping of 36/41 (88%) of alternatively spliced exons associated with U-rich motifs, but did not affect 32/33 (97%) alternatively spliced exons that are not associated with U-rich motifs. The increase in exon skipping correlated with the proximity of the first U-rich motif and the overall "U-richness" of the adjacent intronic region. The majority of the alternative splicing events regulated by TIA1/TIAL1 are conserved in mouse, and the corresponding genes are associated with diverse cellular functions. Based on our results, we estimate that approximately 15% of alternative cassette exons are regulated by TIA1/TIAL1 via U-rich intronic elements.
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Affiliation(s)
- Isabel Aznarez
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
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30
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Aznarez I, Zielenski J, Rommens JM, Blencowe BJ, Tsui LC. Exon skipping through the creation of a putative exonic splicing silencer as a consequence of the cystic fibrosis mutation R553X. J Med Genet 2007; 44:341-6. [PMID: 17475917 PMCID: PMC2597982 DOI: 10.1136/jmg.2006.045880] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Nonsense mutations that occur more than 50 bases upstream of terminal spliced junctions are generally thought to lead to degradation of the corresponding transcripts by the process of nonsense-mediated mRNA decay. It has also been proposed that some nonsense mutations may affect splicing by the process of nonsense-associated altered splicing (NAS), or by the disruption of a splicing regulatory element. In this study, the effect of the R553X mutation on the splicing of exon 11 of the cystic fibrosis transmembrane conductance regulator gene was investigated. Evidence that R553X causes exon 11 to skip through the creation of a putative exonic splicing silencer (ESS) was provided. The putative ESS appears to be active when located immediately upstream of a 5' splice site. These findings argue against the possibility that R553X-associated exon 11 skipping is caused by NAS. The study further suggests that aminoglycoside antibiotic treatment would not be effective for patients with the R553X mutation, owing to the skipping of exon 11, and further emphasises the need for detailed mechanistic characterisation of the consequences of nonsense disease mutations.
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31
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Zhang S, Shi M, Hui CC, Rommens JM. Loss of the mouse ortholog of the shwachman-diamond syndrome gene (Sbds) results in early embryonic lethality. Mol Cell Biol 2006; 26:6656-63. [PMID: 16914746 PMCID: PMC1592835 DOI: 10.1128/mcb.00091-06] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mutations in SBDS are responsible for Shwachman-Diamond syndrome (SDS), a disorder with clinical features of exocrine pancreatic insufficiency, bone marrow failure, and skeletal abnormalities. SBDS is a highly conserved protein whose function remains largely unknown. We identified and investigated the expression pattern of the murine ortholog. Variation in levels was observed, but Sbds was found to be expressed in all embryonic stages and most adult tissues. Higher expression levels were associated with rapid proliferation. A targeted disruption of Sbds was generated in order to understand the consequences of its loss in an in vivo model. Consistent with recessive disease inheritance for SDS, Sbds(+/-) mice have normal phenotypes, indistinguishable from those of their wild-type littermates. However, the development of Sbds(-/-) embryos arrests prior to embryonic day 6.5, with muted epiblast formation leading to early lethality. This finding is consistent with the absence of patients who are homozygous for early truncating mutations. Sbds is an essential gene for early mammalian development, with an expression pattern consistent with a critical role in cell proliferation.
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Affiliation(s)
- Siyi Zhang
- Research Institute, Program in Genetics and Genomic Biology, Room 15-313 TMDT, 101 College Street, East Tower, Toronto, Ontario M5G 1L7, Canada
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Oh RS, Bai X, Rommens JM. Human homologs of Ubc6p ubiquitin-conjugating enzyme and phosphorylation of HsUbc6e in response to endoplasmic reticulum stress. J Biol Chem 2006; 281:21480-21490. [PMID: 16720581 DOI: 10.1074/jbc.m601843200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ubiquitin-conjugating enzyme Ubc6p is a tail-anchored protein that is localized to the cytoplasmic face of the endoplasmic reticulum (ER) membrane and has been implicated in the degradation of many misfolded membrane proteins in yeast. We have undertaken characterization studies of two human homologs, hsUbc6 and hsUbc6e. Both possess tail-anchored protein motifs, display high conservation in their catalytic domains, and are functional ubiquitin-conjugating enzymes as determined by in vitro thiol-ester assay. Both also display induction by the unfolded protein response, a feature of many ER-associated degradation (ERAD) components. Post-translational modification involving phosphorylation of hsUbc6e was observed to be ER-stress-related and dependent on signaling of the PRK-like ER kinase (PERK). The phosphorylation site was mapped to Ser-184, which resides within the uncharacterized region linking the highly conserved catalytic core and the C-terminal transmembrane domain. Phosphorylation of hsUbc6e also did not alter stability, subcellular localization, or interaction with a partner ubiquitin-protein isopeptide ligase. Assays of hsUbc6e(S184D) and hsUbc6e(S184E), which mimic the phosphorylated state, suggest that phosphorylation may reduce capacity for forming ubiquitin-enzyme thiol-esters. The occurrence of two distinct Ubc6p homologs in vertebrates, including one with phosphorylation modification in response to ER stress, emphasizes diversity in function between these Ub-conjugating enzymes during ERAD processes.
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Affiliation(s)
- Ray S Oh
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario M5S 1A8; Program in Genetics & Genomic Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
| | - Xinli Bai
- Program in Genetics & Genomic Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
| | - Johanna M Rommens
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario M5S 1A8; Program in Genetics & Genomic Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada.
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Boocock GRB, Marit MR, Rommens JM. Phylogeny, sequence conservation, and functional complementation of the SBDS protein family. Genomics 2006; 87:758-71. [PMID: 16529906 DOI: 10.1016/j.ygeno.2006.01.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2005] [Revised: 01/16/2006] [Accepted: 01/31/2006] [Indexed: 11/16/2022]
Abstract
The Shwachman-Bodian-Diamond syndrome (SBDS) protein family occurs widely in nature, although its function has not been determined. Comprehensive database searches revealed SBDS homologues from 159 species, including examples from all sequenced archaeal and eukaryotic genomes and all eukaryotic kingdoms. Sequence alignment with ClustalX and MUSCLE algorithms led to the identification of conserved residues that occurred predominantly in the amino-terminal FYSH domain where they appeared to contribute to protein folding or stability. Only SBDS residue Gly91 was invariant in all species. Four distantly related protists were found to have two divergent SBDS genes in their genomes. In each case, phylogenetic analyses and the identification of shared sequence features suggested that one gene was derived from lateral gene transfer. We also identified a shared C-terminal zinc finger domain fusion in flowering plants and chromalveolates that may shed light on the function of the protein family and the evolutionary histories of these kingdoms. To assess the extent of SBDS functional conservation, we carried out complementation studies of SBDS homologues and interspecies chimeras in Saccharomyces cerevisiae. We determined that the FYSH domain was widely interchangeable among eukaryotes, while domain 2 imparted species specificity to protein function. Domain 3 was largely dispensable for function in our yeast complementation assay. Overall, the phylogeny of SBDS was shared with a group of proteins that were markedly enriched for RNA metabolism and/or ribosome-associated functions. These findings link Shwachman-Diamond syndrome to other bone marrow failure syndromes with defects in nucleolus-associated processes, including Diamond-Blackfan anemia, cartilage-hair hypoplasia, and dyskeratosis congenita.
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Affiliation(s)
- G R B Boocock
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, 101 College Street, East Tower, Toronto, Canada ON M5G 1L7
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Lerner-Ellis JP, Tirone JC, Pawelek PD, Doré C, Atkinson JL, Watkins D, Morel CF, Fujiwara TM, Moras E, Hosack AR, Dunbar GV, Antonicka H, Forgetta V, Dobson CM, Leclerc D, Gravel RA, Shoubridge EA, Coulton JW, Lepage P, Rommens JM, Morgan K, Rosenblatt DS. Identification of the gene responsible for methylmalonic aciduria and homocystinuria, cblC type. Nat Genet 2005; 38:93-100. [PMID: 16311595 DOI: 10.1038/ng1683] [Citation(s) in RCA: 271] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2005] [Accepted: 09/23/2005] [Indexed: 01/17/2023]
Abstract
Methylmalonic aciduria and homocystinuria, cblC type (OMIM 277400), is the most common inborn error of vitamin B(12) (cobalamin) metabolism, with about 250 known cases. Affected individuals have developmental, hematological, neurological, metabolic, ophthalmologic and dermatologic clinical findings. Although considered a disease of infancy or childhood, some individuals develop symptoms in adulthood. The cblC locus was mapped to chromosome region 1p by linkage analysis. We refined the chromosomal interval using homozygosity mapping and haplotype analyses and identified the MMACHC gene. In 204 individuals, 42 different mutations were identified, many consistent with a loss of function of the protein product. One mutation, 271dupA, accounted for 40% of all disease alleles. Transduction of wild-type MMACHC into immortalized cblC fibroblast cell lines corrected the cellular phenotype. Molecular modeling predicts that the C-terminal region of the gene product folds similarly to TonB, a bacterial protein involved in energy transduction for cobalamin uptake.
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Abstract
The amount of radiologically dense breast-tissue appearing on a mammogram varies between women because of differences in the composition of breast tissue, and is referred to here as mammographic density. This review presents evidence that mammographic density is a strong risk factor for breast cancer, and that risk of breast cancer is four to five times greater in women with density in more than 75% of the breast than in women with little or no density in the breast. Density in more than 50% of the breast could account for about a third of breast cancers. The epidemiology of mammographic density is consistent with its being a marker of susceptibility to breast cancer. Twin studies have shown that the proportion of the breast occupied by density, at a given age, is highly heritable, and inherited factors explain 63% of the variance. Mammographic breast density has the characteristics of a quantitative trait and might be determined by genes that are easier to identify than those for breast cancer itself. The genes that determine breast density might also be associated with risk of breast cancer, and their identification is also likely to provide insights into the biology of the breast and identify potential targets for preventive strategies.
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Affiliation(s)
- Norman F Boyd
- Campbell Family Institute for Breast Cancer Research, Ontario Cancer Institute, Toronto, Canada.
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36
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Savchenko A, Krogan N, Cort JR, Evdokimova E, Lew JM, Yee AA, Sánchez-Pulido L, Andrade MA, Bochkarev A, Watson JD, Kennedy MA, Greenblatt J, Hughes T, Arrowsmith CH, Rommens JM, Edwards AM. The Shwachman-Bodian-Diamond Syndrome Protein Family Is Involved in RNA Metabolism. J Biol Chem 2005; 280:19213-20. [PMID: 15701634 DOI: 10.1074/jbc.m414421200] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A combination of structural, biochemical, and genetic studies in model organisms was used to infer a cellular role for the human protein (SBDS) responsible for Shwachman-Bodian-Diamond syndrome. The crystal structure of the SBDS homologue in Archaeoglobus fulgidus, AF0491, revealed a three domain protein. The N-terminal domain, which harbors the majority of disease-linked mutations, has a novel three-dimensional fold. The central domain has the common winged helix-turn-helix motif, and the C-terminal domain shares structural homology with known RNA-binding domains. Proteomic analysis of the SBDS sequence homologue in Saccharomyces cerevisiae, YLR022C, revealed an association with over 20 proteins involved in ribosome biosynthesis. NMR structural genomics revealed another yeast protein, YHR087W, to be a structural homologue of the AF0491 N-terminal domain. Sequence analysis confirmed them as distant sequence homologues, therefore related by divergent evolution. Synthetic genetic array analysis of YHR087W revealed genetic interactions with proteins involved in RNA and rRNA processing including Mdm20/Nat3, Nsr1, and Npl3. Our observations, taken together with previous reports, support the conclusion that SBDS and its homologues play a role in RNA metabolism.
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Affiliation(s)
- Alexei Savchenko
- Ontario Center for Structural Proteomics, University of Toronto, Canada
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37
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Shammas C, Menne TF, Hilcenko C, Michell SR, Goyenechea B, Boocock GRB, Durie PR, Rommens JM, Warren AJ. Structural and Mutational Analysis of the SBDS Protein Family. J Biol Chem 2005; 280:19221-9. [PMID: 15701631 DOI: 10.1074/jbc.m414656200] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Shwachman-Diamond Syndrome (SDS) is an autosomal recessive disorder characterized by bone marrow failure with significant predisposition to the development of poor prognosis myelodysplasia and leukemia, exocrine pancreatic failure and metaphyseal chondrodysplasia. Although the SBDS gene mutated in this disorder is highly conserved in Archaea and all eukaryotes, the function is unknown. To interpret the molecular consequences of SDS-associated mutations, we have solved the crystal structure of the Archaeoglobus fulgidus SBDS protein orthologue at a resolution of 1.9 angstroms, revealing a three domain architecture. The N-terminal (FYSH) domain is the most frequent target for disease mutations and contains a novel mixed alpha/beta-fold identical to the single domain yeast protein Yhr087wp that is implicated in RNA metabolism. The central domain consists of a three-helical bundle, whereas the C-terminal domain has a ferredoxin-like fold. By genetic complementation analysis of the essential Saccharomyces cerevisiae SBDS orthologue YLR022C, we demonstrate an essential role in vivo for the FYSH domain and the central three-helical bundle. We further show that the common SDS-related K62X truncation is non-functional. Most SDS-related missense mutations that alter surface epitopes do not impair YLR022C function, but mutations affecting residues buried in the hydrophobic core of the FYSH domain severely impair or abrogate complementation. These data are consistent with absence of homozygosity for the common K62X truncation mutation in individuals with SDS, indicating that the SDS disease phenotype is a consequence of expression of hypomorphic SBDS alleles and that complete loss of SBDS function is likely to be lethal.
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Affiliation(s)
- Camille Shammas
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 2QH, United Kingdom
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Mäkitie O, Ellis L, Durie PR, Morrison JA, Sochett EB, Rommens JM, Cole WG. Skeletal phenotype in patients with Shwachman-Diamond syndrome and mutations in SBDS. Clin Genet 2004; 65:101-12. [PMID: 14984468 DOI: 10.1111/j.0009-9163.2004.00198.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Pancreatic exocrine and bone marrow dysfunctions are considered to be universal features of Shwachman-Diamond syndrome (SDS) whereas the associated skeletal dysplasia is variable and not consistently observed. The genetic defect in SDS has recently been identified; causative mutations have been shown in the SBDS gene. The aims of this study were to characterize the nature, frequency, and age-related changes of radiographic skeletal abnormalities in patients with SBDS mutations and to assess genotype-phenotype correlation. Fifteen patients (mean age 9.7 years) with a clinical diagnosis of SDS and documented SBDS gene mutations were included. Review of their skeletal radiographs showed abnormalities in all patients. The skeletal changes were variable, even in patients with identical genotypes. The typical features were (1) delayed appearance of secondary ossification centers, (2) variable widening and irregularity of the metaphyses in early childhood, followed by progressive thickening and irregularity of the growth plates, and (3) generalized osteopenia. There was a tendency towards normalization of the epiphyseal maturation defect and progression of the metaphyseal changes with age. The results suggest that the characteristic skeletal changes are present in all patients with SDS and SBDS mutations, but their severity and localization varies with age. No phenotype-genotype correlation was observed.
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Affiliation(s)
- O Mäkitie
- Programmes in Genetics & Genomic Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada.
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Scherer SW, Cheung J, MacDonald JR, Osborne LR, Nakabayashi K, Herbrick JA, Carson AR, Parker-Katiraee L, Skaug J, Khaja R, Zhang J, Hudek AK, Li M, Haddad M, Duggan GE, Fernandez BA, Kanematsu E, Gentles S, Christopoulos CC, Choufani S, Kwasnicka D, Zheng XH, Lai Z, Nusskern D, Zhang Q, Gu Z, Lu F, Zeesman S, Nowaczyk MJ, Teshima I, Chitayat D, Shuman C, Weksberg R, Zackai EH, Grebe TA, Cox SR, Kirkpatrick SJ, Rahman N, Friedman JM, Heng HHQ, Pelicci PG, Lo-Coco F, Belloni E, Shaffer LG, Pober B, Morton CC, Gusella JF, Bruns GAP, Korf BR, Quade BJ, Ligon AH, Ferguson H, Higgins AW, Leach NT, Herrick SR, Lemyre E, Farra CG, Kim HG, Summers AM, Gripp KW, Roberts W, Szatmari P, Winsor EJT, Grzeschik KH, Teebi A, Minassian BA, Kere J, Armengol L, Pujana MA, Estivill X, Wilson MD, Koop BF, Tosi S, Moore GE, Boright AP, Zlotorynski E, Kerem B, Kroisel PM, Petek E, Oscier DG, Mould SJ, Döhner H, Döhner K, Rommens JM, Vincent JB, Venter JC, Li PW, Mural RJ, Adams MD, Tsui LC. Human chromosome 7: DNA sequence and biology. Science 2003; 300:767-72. [PMID: 12690205 PMCID: PMC2882961 DOI: 10.1126/science.1083423] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. This approach enabled the discovery of candidate genes for developmental diseases including autism.
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Affiliation(s)
- Stephen W Scherer
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8.
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Boocock GRB, Morrison JA, Popovic M, Richards N, Ellis L, Durie PR, Rommens JM. Mutations in SBDS are associated with Shwachman-Diamond syndrome. Nat Genet 2003; 33:97-101. [PMID: 12496757 DOI: 10.1038/ng1062] [Citation(s) in RCA: 506] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2002] [Accepted: 11/14/2002] [Indexed: 11/09/2022]
Abstract
Shwachman-Diamond syndrome (SDS; OMIM 260400) is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, hematological dysfunction and skeletal abnormalities. Here, we report identification of disease-associated mutations in an uncharacterized gene, SBDS, in the interval of 1.9 cM at 7q11 previously shown to be associated with the disease. We report that SBDS has a 1.6-kb transcript and encodes a predicted protein of 250 amino acids. A pseudogene copy (SBDSP) with 97% nucleotide sequence identity resides in a locally duplicated genomic segment of 305 kb. We found recurring mutations resulting from gene conversion in 89% of unrelated individuals with SDS (141 of 158), with 60% (95 of 158) carrying two converted alleles. Converted segments consistently included at least one of two pseudogene-like sequence changes that result in protein truncation. SDBS is a member of a highly conserved protein family of unknown function with putative orthologs in diverse species including archaea and eukaryotes. Archaeal orthologs are located within highly conserved operons that include homologs of RNA-processing genes, suggesting that SDS may be caused by a deficiency in an aspect of RNA metabolism that is essential for development of the exocrine pancreas, hematopoiesis and chrondrogenesis.
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Affiliation(s)
- Graeme R B Boocock
- Program in Genetics and Genomic Biology, Room 11-109A, Elm Wing Annex, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
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Ip WF, Dupuis A, Ellis L, Beharry S, Morrison J, Stormon MO, Corey M, Rommens JM, Durie PR. Serum pancreatic enzymes define the pancreatic phenotype in patients with Shwachman-Diamond syndrome. J Pediatr 2002; 141:259-65. [PMID: 12183724 DOI: 10.1067/mpd.2002.125849] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
OBJECTIVE To evaluate the role of serum enzymes for defining the pancreatic phenotype in Shwachman-Diamond syndrome (SDS), an inherited multisystem condition. STUDY DESIGN Serum pancreatic trypsinogen and isoamylase were measured in 164 patients known or presumed to have SDS. The diagnosis was confirmed in 90 patients. Among 74 unconfirmed cases, 35 ("probable SDS") had hematologic dysfunction but lacked documented pancreatic dysfunction, whereas 39 patients ("improbable SDS") lacked both documented pancreatic and hematologic dysfunction. Classification and regression tree (CART) analysis was performed in 90 patients with SDS and 134 control patients to establish a rule for defining the pancreatic phenotype of SDS; the rule was then applied to the patients with unconfirmed diagnosis. RESULTS In the control patients, serum trypsinogen showed little variation with age, whereas serum isoamylase values rose from birth on, attaining adult values by 3 years. For patients with SDS, serum trypsinogen values were low in young patients and tended to increase with age, whereas serum isoamylase values remained low at all ages. The CART rule combined results from both enzymes and classified the pancreatic phenotype in all but one SDS patient, who was <3 years of age. Excluding patients <3 years of age, CART identified the pancreatic phenotype in 82% and 7% of the "probable SDS" and "improbable SDS" cases, respectively. CONCLUSIONS Serum pancreatic enzymes are useful for determining the pancreatic phenotype and confirming the diagnosis of SDS.
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Affiliation(s)
- Wan F Ip
- Department of Pediatrics, University of Toronto, Ontario, Canada
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Gyömörey K, Garami E, Galley K, Rommens JM, Bear CE. Non-CFTR chloride channels likely contribute to secretion in the murine small intestine. Pflugers Arch 2002; 443 Suppl 1:S103-6. [PMID: 11845313 DOI: 10.1007/s004240100654] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
While most cystic fibrosis (CF) transmembrane conductance regulator (CFTR)-knockout animals die due to intestinal obstruction before or at the time of weaning, a subpopulation of these animals are long living and exhibit a milder phenotype. The decreased severity of intestinal disease in these mildly affected CF mice is related to the expression of non-CFTR genetic modifiers. The identity of these genetic modifiers is not known, but we hypothesize that they may complement CFTR function as a chloride channel in this tissue. To assess the contribution of non-CFTR chloride channels to chloride secretion across the small intestine of CF mice with mild disease, we measured the basal transepithelial potential difference across this tissue as well as the secretory response to agonists of the cAMP and the calcium-mediated signaling pathways. Chloride secretion across the small intestine of mildly affected CF mice was not stimulated by forskolin or by carbachol. The absence of CFTR is thus not compensated by the activity of a distinct, cAMP- or calcium-activated chloride channel at the apical surface of the intestinal epithelium. On the other hand, a basal chloride secretion across the intestinal epithelium was present in these animals, and we hypothesize that this activity may be linked to improved survival of these animals.
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Affiliation(s)
- K Gyömörey
- Department of Structural Biology and Biochemistry, The Hospital for Sick Children, 55 University Ave., Toronto, M5G 1X8, Ontario, Canada
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43
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Popovic M, Goobie S, Morrison J, Ellis L, Ehtesham N, Richards N, Boocock G, Durie PR, Rommens JM. Fine mapping of the locus for Shwachman-Diamond syndrome at 7q11, identification of shared disease haplotypes, and exclusion of TPST1 as a candidate gene. Eur J Hum Genet 2002; 10:250-8. [PMID: 12032733 DOI: 10.1038/sj.ejhg.5200798] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2001] [Revised: 01/31/2002] [Accepted: 02/19/2002] [Indexed: 11/09/2022] Open
Abstract
Shwachman-Diamond syndrome (SDS) is an autosomal recessive disorder characterised by exocrine pancreatic dysfunction, haematological and skeletal abnormalities. We have previously defined the SDS locus as a 2.7 cM interval spanning the centromere of chromosome 7. To facilitate additional analysis of this complex and poorly characterised region, a framework of ordered genetic markers at 7p11-q11, including six newly identified, has been constructed using somatic cell, radiation hybrid and STS-content mapping. We have identified shared disease haplotypes, that recur in unrelated families of common ethnic origin, and extend across the SDS locus. Detection of ancestral and intrafamilial recombination events in patients refined the SDS locus to a 1.9 cM interval at 7q11, which contains the tyrosylprotein sulfotransferase 1 (TPST1) gene. Patients with SDS were screened for mutations in TPST1 by sequencing of exons and intron-exon junctions. Two single nucleotide polymorphisms, but no disease-causing mutations, were identified. In addition, Southern blot analysis yielded no evidence of large-scale mutations, and RT-PCR analysis failed to detect alterations in expression. These results exclude TPST1 as the causative gene for SDS. The established map of the refined SDS locus will assist in the identification and characterisation of other candidate genes for SDS.
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Affiliation(s)
- Maja Popovic
- Program in Genetics and Genomic Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
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Goobie S, Popovic M, Morrison J, Ellis L, Ginzberg H, Boocock GRB, Ehtesham N, Bétard C, Brewer CG, Roslin NM, Hudson TJ, Morgan K, Fujiwara TM, Durie PR, Rommens JM. Shwachman-Diamond syndrome with exocrine pancreatic dysfunction and bone marrow failure maps to the centromeric region of chromosome 7. Am J Hum Genet 2001; 68:1048-54. [PMID: 11254457 PMCID: PMC1275624 DOI: 10.1086/319505] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2000] [Accepted: 01/18/2001] [Indexed: 11/03/2022] Open
Abstract
Shwachman-Diamond syndrome (SDS) is an autosomal recessive disorder characterized by exocrine pancreatic insufficiency and hematologic and skeletal abnormalities. A genomewide scan of families with SDS was terminated at approximately 50% completion, with the identification of chromosome 7 markers that showed linkage with the disease. Finer mapping revealed significant linkage across a broad interval that included the centromere. The maximum two-point LOD score was 8.7, with D7S473, at a recombination fraction of 0. The maximum multipoint LOD score was 10, in the interval between D7S499 and D7S482 (5.4 cM on the female map and 0 cM on the male map), a region delimited by recombinant events detected in affected children. Evidence from all 15 of the multiplex families analyzed provided support for the linkage, consistent with a single locus for SDS. However, the presence of several different mutations is suggested by the heterogeneity of disease-associated haplotypes in the candidate region.
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Affiliation(s)
- Sharan Goobie
- Programs in Genetics and Genomic Biology and Integrative Biology, Research Institute, and Division of Gastroenterology and Nutrition, The Hospital for Sick Children, and Departments of Molecular and Medical Genetics and Paediatrics, University of Toronto, Toronto; and Montreal Genome Centre, McGill University Health Centre Research Institute, and Departments of Human Genetics and Medicine, McGill University, Montreal
| | - Maja Popovic
- Programs in Genetics and Genomic Biology and Integrative Biology, Research Institute, and Division of Gastroenterology and Nutrition, The Hospital for Sick Children, and Departments of Molecular and Medical Genetics and Paediatrics, University of Toronto, Toronto; and Montreal Genome Centre, McGill University Health Centre Research Institute, and Departments of Human Genetics and Medicine, McGill University, Montreal
| | - Jodi Morrison
- Programs in Genetics and Genomic Biology and Integrative Biology, Research Institute, and Division of Gastroenterology and Nutrition, The Hospital for Sick Children, and Departments of Molecular and Medical Genetics and Paediatrics, University of Toronto, Toronto; and Montreal Genome Centre, McGill University Health Centre Research Institute, and Departments of Human Genetics and Medicine, McGill University, Montreal
| | - Lynda Ellis
- Programs in Genetics and Genomic Biology and Integrative Biology, Research Institute, and Division of Gastroenterology and Nutrition, The Hospital for Sick Children, and Departments of Molecular and Medical Genetics and Paediatrics, University of Toronto, Toronto; and Montreal Genome Centre, McGill University Health Centre Research Institute, and Departments of Human Genetics and Medicine, McGill University, Montreal
| | - Hedy Ginzberg
- Programs in Genetics and Genomic Biology and Integrative Biology, Research Institute, and Division of Gastroenterology and Nutrition, The Hospital for Sick Children, and Departments of Molecular and Medical Genetics and Paediatrics, University of Toronto, Toronto; and Montreal Genome Centre, McGill University Health Centre Research Institute, and Departments of Human Genetics and Medicine, McGill University, Montreal
| | - Graeme R. B. Boocock
- Programs in Genetics and Genomic Biology and Integrative Biology, Research Institute, and Division of Gastroenterology and Nutrition, The Hospital for Sick Children, and Departments of Molecular and Medical Genetics and Paediatrics, University of Toronto, Toronto; and Montreal Genome Centre, McGill University Health Centre Research Institute, and Departments of Human Genetics and Medicine, McGill University, Montreal
| | - Nadia Ehtesham
- Programs in Genetics and Genomic Biology and Integrative Biology, Research Institute, and Division of Gastroenterology and Nutrition, The Hospital for Sick Children, and Departments of Molecular and Medical Genetics and Paediatrics, University of Toronto, Toronto; and Montreal Genome Centre, McGill University Health Centre Research Institute, and Departments of Human Genetics and Medicine, McGill University, Montreal
| | - Christine Bétard
- Programs in Genetics and Genomic Biology and Integrative Biology, Research Institute, and Division of Gastroenterology and Nutrition, The Hospital for Sick Children, and Departments of Molecular and Medical Genetics and Paediatrics, University of Toronto, Toronto; and Montreal Genome Centre, McGill University Health Centre Research Institute, and Departments of Human Genetics and Medicine, McGill University, Montreal
| | - Carl G. Brewer
- Programs in Genetics and Genomic Biology and Integrative Biology, Research Institute, and Division of Gastroenterology and Nutrition, The Hospital for Sick Children, and Departments of Molecular and Medical Genetics and Paediatrics, University of Toronto, Toronto; and Montreal Genome Centre, McGill University Health Centre Research Institute, and Departments of Human Genetics and Medicine, McGill University, Montreal
| | - Nicole M. Roslin
- Programs in Genetics and Genomic Biology and Integrative Biology, Research Institute, and Division of Gastroenterology and Nutrition, The Hospital for Sick Children, and Departments of Molecular and Medical Genetics and Paediatrics, University of Toronto, Toronto; and Montreal Genome Centre, McGill University Health Centre Research Institute, and Departments of Human Genetics and Medicine, McGill University, Montreal
| | - Thomas J. Hudson
- Programs in Genetics and Genomic Biology and Integrative Biology, Research Institute, and Division of Gastroenterology and Nutrition, The Hospital for Sick Children, and Departments of Molecular and Medical Genetics and Paediatrics, University of Toronto, Toronto; and Montreal Genome Centre, McGill University Health Centre Research Institute, and Departments of Human Genetics and Medicine, McGill University, Montreal
| | - Kenneth Morgan
- Programs in Genetics and Genomic Biology and Integrative Biology, Research Institute, and Division of Gastroenterology and Nutrition, The Hospital for Sick Children, and Departments of Molecular and Medical Genetics and Paediatrics, University of Toronto, Toronto; and Montreal Genome Centre, McGill University Health Centre Research Institute, and Departments of Human Genetics and Medicine, McGill University, Montreal
| | - T. Mary Fujiwara
- Programs in Genetics and Genomic Biology and Integrative Biology, Research Institute, and Division of Gastroenterology and Nutrition, The Hospital for Sick Children, and Departments of Molecular and Medical Genetics and Paediatrics, University of Toronto, Toronto; and Montreal Genome Centre, McGill University Health Centre Research Institute, and Departments of Human Genetics and Medicine, McGill University, Montreal
| | - Peter R. Durie
- Programs in Genetics and Genomic Biology and Integrative Biology, Research Institute, and Division of Gastroenterology and Nutrition, The Hospital for Sick Children, and Departments of Molecular and Medical Genetics and Paediatrics, University of Toronto, Toronto; and Montreal Genome Centre, McGill University Health Centre Research Institute, and Departments of Human Genetics and Medicine, McGill University, Montreal
| | - Johanna M. Rommens
- Programs in Genetics and Genomic Biology and Integrative Biology, Research Institute, and Division of Gastroenterology and Nutrition, The Hospital for Sick Children, and Departments of Molecular and Medical Genetics and Paediatrics, University of Toronto, Toronto; and Montreal Genome Centre, McGill University Health Centre Research Institute, and Departments of Human Genetics and Medicine, McGill University, Montreal
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Lechardeur D, Drzymala L, Sharma M, Zylka D, Kinach R, Pacia J, Hicks C, Usmani N, Rommens JM, Lukacs GL. Determinants of the nuclear localization of the heterodimeric DNA fragmentation factor (ICAD/CAD). J Cell Biol 2000; 150:321-34. [PMID: 10908575 PMCID: PMC2180231 DOI: 10.1083/jcb.150.2.321] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Programmed cell death or apoptosis leads to the activation of the caspase-activated DNase (CAD), which degrades chromosomal DNA into nucleosomal fragments. Biochemical studies revealed that CAD forms an inactive heterodimer with the inhibitor of caspase-activated DNase (ICAD), or its alternatively spliced variant, ICAD-S, in the cytoplasm. It was initially proposed that proteolytic cleavage of ICAD by activated caspases causes the dissociation of the ICAD/CAD heterodimer and the translocation of active CAD into the nucleus in apoptotic cells. Here, we show that endogenous and heterologously expressed ICAD and CAD reside predominantly in the nucleus in nonapoptotic cells. Deletional mutagenesis and GFP fusion proteins identified a bipartite nuclear localization signal (NLS) in ICAD and verified the function of the NLS in CAD. The two NLSs have an additive effect on the nuclear targeting of the CAD-ICAD complex, whereas ICAD-S, lacking its NLS, appears to have a modulatory role in the nuclear localization of CAD. Staurosporine-induced apoptosis evoked the proteolysis and disappearance of endogenous and exogenous ICAD from the nuclei of HeLa cells, as monitored by immunoblotting and immunofluorescence microscopy. Similar phenomenon was observed in the caspase-3-deficient MCF7 cells upon expressing procaspase-3 transiently. We conclude that a complex mechanism, involving the recognition of the NLSs of both ICAD and CAD, accounts for the constitutive accumulation of CAD/ICAD in the nucleus, where caspase-3-dependent regulation of CAD activity takes place.
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Affiliation(s)
- Delphine Lechardeur
- Program in Cell and Lung Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada M5G 1X8
| | - Luke Drzymala
- Program in Cell and Lung Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada M5G 1X8
| | - Manu Sharma
- Program in Cell and Lung Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada M5G 1X8
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada M5G 1X8
| | - Danuta Zylka
- Program in Cell and Lung Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada M5G 1X8
| | - Robert Kinach
- Program in Cell and Lung Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada M5G 1X8
| | - Joanna Pacia
- Program in Cell and Lung Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada M5G 1X8
| | - Christopher Hicks
- Program in Cell and Lung Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada M5G 1X8
| | - Nawaid Usmani
- Program in Cell and Lung Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada M5G 1X8
| | - Johanna M. Rommens
- Program in Genetics and Genomics Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada M5G 1X8
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada M5G 1X8
| | - Gergely L. Lukacs
- Program in Cell and Lung Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada M5G 1X8
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada M5G 1X8
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Van Oene M, Lukacs GL, Rommens JM. Cystic fibrosis mutations lead to carboxyl-terminal fragments that highlight an early biogenesis step of the cystic fibrosis transmembrane conductance regulator. J Biol Chem 2000; 275:19577-84. [PMID: 10764788 DOI: 10.1074/jbc.m002186200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Inefficient delivery of the cystic fibrosis transmembrane conductance regulator (CFTR) to the surface of cells contributes to disease in the majority of cystic fibrosis patients. Analysis of cystic fibrosis-associated missense mutations in the first nucleotide binding domain (NBD1), including A455E, S549R, Y563N, and P574H, revealed reduced levels of mature CFTR with elevated levels of carboxyl-terminal polypeptide fragments of 105 and 90 kDa. These fragments appear early in biogenesis and degrade rapidly in four distinct cell types tested including the bronchial epithelial IB3-1 cell line. They were detected at highest levels with CFTRA455E where the 105-kDa fragment accounted for 40% of newly synthesized polypeptide but for only 20 and 7% of nascent wild type and mutant DeltaF508 proteins, respectively. The bands represent core- and unglycosylated forms of the same CFTR fragment supporting that precursor forms are correctly inserted into the membrane of the endoplasmic reticulum. Proteolytic cleavage would be predicted to occur on the cytosolic face of the endoplasmic reticulum within the NBD1-R domain segment, but pharmacological testing did not support involvement of the 26 S proteasome. The examined missense mutations in NBD1 manifest differently than the major mutant, DeltaF508, and highlight a critical conformational aspect of biogenesis of CFTR.
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Affiliation(s)
- M Van Oene
- Department of Molecular and Medical Genetics, Program in Genetics & Genomic Biology, University of Toronto, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
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47
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Ginzberg H, Shin J, Ellis L, Goobie S, Morrison J, Corey M, Durie PR, Rommens JM. Segregation analysis in Shwachman-Diamond syndrome: evidence for recessive inheritance. Am J Hum Genet 2000; 66:1413-6. [PMID: 10739765 PMCID: PMC1288206 DOI: 10.1086/302856] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/1999] [Accepted: 02/02/2000] [Indexed: 11/03/2022] Open
Abstract
Shwachman-Diamond syndrome is a rare disorder of unknown cause. Reports have indicated the occurrence of affected siblings, but formal segregation analysis has not been performed. In families collected for genetic studies, the mean paternal age and mean difference in parental ages were found to be consistent with the general population. We determined estimates of segregation proportion in a cohort of 84 patients with complete sibship data under the assumption of complete ascertainment, using the Li and Mantel estimator, and of single ascertainment with the Davie modification. A third estimate was also computed with the expectation-maximization (EM) algorithm. All three estimates supported an autosomal recessive mode of inheritance, but complete ascertainment was found to be unlikely. Although there are no overt signs of disease in adult carriers (parents), the use of serum trypsinogen levels to indicate exocrine pancreatic dysfunction was evaluated as a potential measure for heterozygote expression. No consistent differences were found in levels between parents and a normal control population. Although genetic heterogeneity cannot be excluded, our results indicate that simulation and genetic analyses of Shwachman-Diamond syndrome should consider a recessive model of inheritance.
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Affiliation(s)
- H Ginzberg
- Division of Gastroenterology and Nutrition, Hospital for Sick Children, Toronto, Canada
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48
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Goobie S, Morrison J, Ginzberg H, Ellis L, Corey M, Masuno M, Imaizumi K, Kuroki Y, Fujiwara TM, Morgan K, Durie PR, Rommens JM. Exclusion of linkage of Shwachman-Diamond syndrome to chromosome regions 6q and 12q implicated by a de novo translocation. Am J Med Genet 1999; 85:171-4. [PMID: 10406671 DOI: 10.1002/(sici)1096-8628(19990716)85:2<171::aid-ajmg12>3.0.co;2-k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Shwachman-Diamond syndrome is a rare genetic disorder of unknown pathogenesis involving exocrine pancreatic insufficiency and hematological and skeletal abnormalities. There is broad clinical variability; the extent of heterogeneity is unknown but comparisons within a large cohort of patients show no striking differences between patients of families with single or multiple affected offspring. Segregation analysis of a cohort of 69 families has suggested an autosomal recessive mode of inheritance. A single constitutional de novo chromosome rearrangement was reported in a Japanese patient involving a balanced translocation, t(6;12)(q16.2;q21.2), thereby suggesting possible loci for a genetic defect. Evenly spaced microsatellite markers spanning 26-32 cM intervals from D6S1056 to D6S304 and D12S375 to D12S346 were analyzed for linkage in members of 13 Shwachman-Diamond syndrome families with two or three affected children. Two-point lod scores were calculated for each marker under assumptions of recessive inheritance and complete penetrance. Negative lod scores indicated exclusion of both chromosome regions. Further, affected sibs were discordant for inheritance of chromosomes in most families based on constructed haplotypes. The cytogenetic abnormality is not associated with most cases of Shwachman-Diamond syndrome.
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Affiliation(s)
- S Goobie
- Research Institute, The Hospital for Sick Children, Department of Molecular & Medical Genetics, University of Toronto, Ontario, Canada
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Ginzberg H, Shin J, Ellis L, Morrison J, Ip W, Dror Y, Freedman M, Heitlinger LA, Belt MA, Corey M, Rommens JM, Durie PR. Shwachman syndrome: phenotypic manifestations of sibling sets and isolated cases in a large patient cohort are similar. J Pediatr 1999; 135:81-8. [PMID: 10393609 DOI: 10.1016/s0022-3476(99)70332-x] [Citation(s) in RCA: 180] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVES With the use of clinical data from a large international cohort, we evaluated and compared affected siblings and isolated cases. STUDY DESIGN Data from 116 families were collected, and patients conforming to our predetermined diagnostic criteria were analyzed. Phenotypic manifestations of affected siblings and singletons were compared with the use of t tests, Wilcoxon scores, and chi2 analysis. RESULTS Eighty-eight patients (33 female, 55 male; median age 5.20 years) fulfilled our predetermined diagnostic criteria for Shwachman syndrome; 63 patients were isolated cases, and 25 affected siblings were from 12 multiplex families. Steatorrhea was present in 86% (57 of 66), and 91% (78 of 86) displayed a low serum trypsinogen concentration. Patients older than 4 years more often had pancreatic sufficiency. Neutropenia occurred in 98%, anemia in 42%, and thrombocytopenia in 34%. Myelodysplasia or cytogenetic abnormalities were reported in 7 patients. Short stature with normal nutritional status was a prominent feature. CONCLUSIONS Clinical features among patients with Shwachman syndrome varied between patients and with age. Similarities in phenotype between isolated cases and affected sibling sets support the hypothesis that Shwachman syndrome is a single disease entity.
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Affiliation(s)
- H Ginzberg
- Department of Pediatrics, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada
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Heus HC, Hing A, van Baren MJ, Joosse M, Breedveld GJ, Wang JC, Burgess A, Donnis-Keller H, Berglund C, Zguricas J, Scherer SW, Rommens JM, Oostra BA, Heutink P. A physical and transcriptional map of the preaxial polydactyly locus on chromosome 7q36. Genomics 1999; 57:342-51. [PMID: 10329000 DOI: 10.1006/geno.1999.5796] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Preaxial polydactyly is a congenital hand malformation that includes duplicated thumbs, various forms of triphalangeal thumbs, and duplications of the index finger. A locus for preaxial polydactyly has been mapped to a region of 1.9 cM on chromosome 7q36 between polymorphic markers D7S550 and D7S2423. We constructed a detailed physical map of the preaxial polydactyly candidate region. With a combination of methods we identified and positioned 11 transcripts within this map. By recombination analysis on families with preaxial polydactyly, using newly developed polymorphic markers, we were able to reduce the candidate region to approximately 450 kb. The homeobox gene HLXB9, a putative receptor C7orf2, and two transcripts of unknown function, C7orf3 and C7orf4, map in the refined candidate region and have been subjected to mutation analysis in individuals with preaxial polydactyly.
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Affiliation(s)
- H C Heus
- Department of Clinical Genetics, Erasmus University Rotterdam, Rotterdam, 3000 DR, The Netherlands
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