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Liu Q, Zhou Y, Cogan JD, Mitchell DB, Sheng Q, Zhao S, Bai Y, Ciombor KK, Sabusap CM, Malabanan MM, Markin CR, Douglas K, Ding G, Banovich NE, Nickerson DA, Blue EE, Bamshad MJ, Brown KK, Schwartz DA, Phillips JA, Martinez-Barricarte R, Salisbury ML, Shyr Y, Loyd JE, Kropski JA, Blackwell TS. The Genetic Landscape of Familial Pulmonary Fibrosis. Am J Respir Crit Care Med 2023; 207:1345-1357. [PMID: 36622818 PMCID: PMC10595451 DOI: 10.1164/rccm.202204-0781oc] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 04/24/2022] [Accepted: 01/09/2023] [Indexed: 01/10/2023] Open
Abstract
Rationale and Objectives: Up to 20% of idiopathic interstitial lung disease is familial, referred to as familial pulmonary fibrosis (FPF). An integrated analysis of FPF genetic risk was performed by comprehensively evaluating for genetic rare variants (RVs) in a large cohort of FPF kindreds. Methods: Whole-exome sequencing and/or candidate gene sequencing from affected individuals in 569 FPF kindreds was performed, followed by cosegregation analysis in large kindreds, gene burden analysis, gene-based risk scoring, cell-type enrichment analysis, and coexpression network construction. Measurements and Main Results: It was found that 14.9-23.4% of genetic risk in kindreds could be explained by RVs in genes previously linked to FPF, predominantly telomere-related genes. New candidate genes were identified in a small number of families-including SYDE1, SERPINB8, GPR87, and NETO1-and tools were developed for evaluation and prioritization of RV-containing genes across kindreds. Several pathways were enriched for RV-containing genes in FPF, including focal adhesion and mitochondrial complex I assembly. By combining single-cell transcriptomics with prioritized candidate genes, expression of RV-containing genes was discovered to be enriched in smooth muscle cells, type II alveolar epithelial cells, and endothelial cells. Conclusions: In the most comprehensive FPF genetic study to date, the prevalence of RVs in known FPF-related genes was defined, and new candidate genes and pathways relevant to FPF were identified. However, new RV-containing genes shared across multiple kindreds were not identified, thereby suggesting that heterogeneous genetic variants involving a variety of genes and pathways mediate genetic risk in most FPF kindreds.
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Affiliation(s)
- Qi Liu
- Department of Biostatistics
| | | | - Joy D. Cogan
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics
| | | | | | | | | | | | | | | | | | | | - Guixiao Ding
- Division of Allergy, Pulmonary and Critical Care Medicine
| | | | | | | | - Michael J. Bamshad
- Department of Genome Sciences
- Brotman-Baty Institute, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle, Washington
| | | | - David A. Schwartz
- Department of Medicine, School of Medicine, University of Colorado Denver, Denver, Colorado; and
| | - John A. Phillips
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics
| | | | | | | | - James E. Loyd
- Division of Allergy, Pulmonary and Critical Care Medicine
| | - Jonathan A. Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
| | - Timothy S. Blackwell
- Division of Allergy, Pulmonary and Critical Care Medicine
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
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2
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Cabral‐Miranda F, Tamburini G, Martinez G, Ardiles AO, Medinas DB, Gerakis Y, Hung MD, Vidal R, Fuentealba M, Miedema T, Duran‐Aniotz C, Diaz J, Ibaceta‐Gonzalez C, Sabusap CM, Bermedo‐Garcia F, Mujica P, Adamson S, Vitangcol K, Huerta H, Zhang X, Nakamura T, Sardi SP, Lipton SA, Kennedy BK, Henriquez JP, Cárdenas JC, Plate L, Palacios AG, Hetz C. Unfolded protein response IRE1/XBP1 signaling is required for healthy mammalian brain aging. EMBO J 2022; 41:e111952. [PMID: 36314651 PMCID: PMC9670206 DOI: 10.15252/embj.2022111952] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 06/22/2022] [Revised: 09/09/2022] [Accepted: 09/16/2022] [Indexed: 11/18/2022] Open
Abstract
Aging is a major risk factor to develop neurodegenerative diseases and is associated with decreased buffering capacity of the proteostasis network. We investigated the significance of the unfolded protein response (UPR), a major signaling pathway activated to cope with endoplasmic reticulum (ER) stress, in the functional deterioration of the mammalian brain during aging. We report that genetic disruption of the ER stress sensor IRE1 accelerated age-related cognitive decline. In mouse models, overexpressing an active form of the UPR transcription factor XBP1 restored synaptic and cognitive function, in addition to reducing cell senescence. Proteomic profiling of hippocampal tissue showed that XBP1 expression significantly restore changes associated with aging, including factors involved in synaptic function and pathways linked to neurodegenerative diseases. The genes modified by XBP1 in the aged hippocampus where also altered. Collectively, our results demonstrate that strategies to manipulate the UPR in mammals may help sustain healthy brain aging.
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Affiliation(s)
- Felipe Cabral‐Miranda
- Center for GeroscienceBrain Health and MetabolismSantiagoChile
- Biomedical Neuroscience Institute, Faculty of MedicineUniversity of ChileSantiagoChile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, Faculty of MedicineUniversity of ChileSantiagoChile
- Instituto de Ciências BiomédicasUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Giovanni Tamburini
- Center for GeroscienceBrain Health and MetabolismSantiagoChile
- Biomedical Neuroscience Institute, Faculty of MedicineUniversity of ChileSantiagoChile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, Faculty of MedicineUniversity of ChileSantiagoChile
| | - Gabriela Martinez
- Center for GeroscienceBrain Health and MetabolismSantiagoChile
- Biomedical Neuroscience Institute, Faculty of MedicineUniversity of ChileSantiagoChile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, Faculty of MedicineUniversity of ChileSantiagoChile
| | - Alvaro O Ardiles
- Centro Interdisciplinario de Neurociencia de ValparaísoUniversidad de ValparaisoValparaisoChile
- Centro de Neurología Traslacional, Escuela de MedicinaUniversidad de ValparaísoValparaisoChile
| | - Danilo B Medinas
- Center for GeroscienceBrain Health and MetabolismSantiagoChile
- Biomedical Neuroscience Institute, Faculty of MedicineUniversity of ChileSantiagoChile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, Faculty of MedicineUniversity of ChileSantiagoChile
| | - Yannis Gerakis
- Center for GeroscienceBrain Health and MetabolismSantiagoChile
- Biomedical Neuroscience Institute, Faculty of MedicineUniversity of ChileSantiagoChile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, Faculty of MedicineUniversity of ChileSantiagoChile
| | - Mei‐Li Diaz Hung
- Center for GeroscienceBrain Health and MetabolismSantiagoChile
- Biomedical Neuroscience Institute, Faculty of MedicineUniversity of ChileSantiagoChile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, Faculty of MedicineUniversity of ChileSantiagoChile
| | - René Vidal
- Center for GeroscienceBrain Health and MetabolismSantiagoChile
- Biomedical Neuroscience Institute, Faculty of MedicineUniversity of ChileSantiagoChile
- Center for Integrative BiologyUniversidad MayorSantiagoChile
| | - Matias Fuentealba
- Center for GeroscienceBrain Health and MetabolismSantiagoChile
- Biomedical Neuroscience Institute, Faculty of MedicineUniversity of ChileSantiagoChile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, Faculty of MedicineUniversity of ChileSantiagoChile
| | - Tim Miedema
- Center for GeroscienceBrain Health and MetabolismSantiagoChile
- Biomedical Neuroscience Institute, Faculty of MedicineUniversity of ChileSantiagoChile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, Faculty of MedicineUniversity of ChileSantiagoChile
| | - Claudia Duran‐Aniotz
- Center for GeroscienceBrain Health and MetabolismSantiagoChile
- Biomedical Neuroscience Institute, Faculty of MedicineUniversity of ChileSantiagoChile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, Faculty of MedicineUniversity of ChileSantiagoChile
| | - Javier Diaz
- Center for GeroscienceBrain Health and MetabolismSantiagoChile
- Biomedical Neuroscience Institute, Faculty of MedicineUniversity of ChileSantiagoChile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, Faculty of MedicineUniversity of ChileSantiagoChile
| | | | - Carleen M Sabusap
- Departments of Chemistry and Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | - Francisca Bermedo‐Garcia
- Department of Cell Biology, Center for Advanced Microscopy (CMA BioBio)Universidad de ConcepciónConcepciónChile
| | - Paula Mujica
- Centro de Neurología Traslacional, Escuela de MedicinaUniversidad de ValparaísoValparaisoChile
| | | | | | - Hernan Huerta
- Center for Integrative BiologyUniversidad MayorSantiagoChile
| | - Xu Zhang
- Department of Molecular Medicine and Neurodegeneration New Medicines CenterThe Scripps Research InstituteLa JollaCAUSA
| | - Tomohiro Nakamura
- Department of Molecular Medicine and Neurodegeneration New Medicines CenterThe Scripps Research InstituteLa JollaCAUSA
| | | | - Stuart A Lipton
- Department of Molecular Medicine and Neurodegeneration New Medicines CenterThe Scripps Research InstituteLa JollaCAUSA
- Department of Neurosciences, School of MedicineUniversity of California, San DiegoLa JollaCAUSA
| | - Brian K Kennedy
- Buck Institute for Research on AgingNovatoCAUSA
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore; Centre for Healthy Longevity, National University Health System; Departments of Biochemistry and Physiology, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
| | - Juan Pablo Henriquez
- Department of Cell Biology, Center for Advanced Microscopy (CMA BioBio)Universidad de ConcepciónConcepciónChile
| | - J Cesar Cárdenas
- Center for GeroscienceBrain Health and MetabolismSantiagoChile
- Center for Integrative BiologyUniversidad MayorSantiagoChile
- Buck Institute for Research on AgingNovatoCAUSA
| | - Lars Plate
- Departments of Chemistry and Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | - Adrian G Palacios
- Centro Interdisciplinario de Neurociencia de ValparaísoUniversidad de ValparaisoValparaisoChile
| | - Claudio Hetz
- Center for GeroscienceBrain Health and MetabolismSantiagoChile
- Biomedical Neuroscience Institute, Faculty of MedicineUniversity of ChileSantiagoChile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, Faculty of MedicineUniversity of ChileSantiagoChile
- Buck Institute for Research on AgingNovatoCAUSA
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Oliver KE, Rauscher R, Mijnders M, Wang W, Wolpert MJ, Maya J, Sabusap CM, Kesterson RA, Kirk KL, Rab A, Braakman I, Hong JS, Hartman JL, Ignatova Z, Sorscher EJ. Slowing ribosome velocity restores folding and function of mutant CFTR. J Clin Invest 2020; 129:5236-5253. [PMID: 31657788 DOI: 10.1172/jci124282] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 08/28/2019] [Indexed: 12/19/2022] Open
Abstract
Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR), with approximately 90% of patients harboring at least one copy of the disease-associated variant F508del. We utilized a yeast phenomic system to identify genetic modifiers of F508del-CFTR biogenesis, from which ribosomal protein L12 (RPL12/uL11) emerged as a molecular target. In the present study, we investigated mechanism(s) by which suppression of RPL12 rescues F508del protein synthesis and activity. Using ribosome profiling, we found that rates of translation initiation and elongation were markedly slowed by RPL12 silencing. However, proteolytic stability and patch-clamp assays revealed RPL12 depletion significantly increased F508del-CFTR steady-state expression, interdomain assembly, and baseline open-channel probability. We next evaluated whether Rpl12-corrected F508del-CFTR could be further enhanced with concomitant pharmacologic repair (e.g., using clinically approved modulators lumacaftor and tezacaftor) and demonstrated additivity of these treatments. Rpl12 knockdown also partially restored maturation of specific CFTR variants in addition to F508del, and WT Cftr biogenesis was enhanced in the pancreas, colon, and ileum of Rpl12 haplosufficient mice. Modulation of ribosome velocity therefore represents a robust method for understanding both CF pathogenesis and therapeutic response.
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Affiliation(s)
| | - Robert Rauscher
- Institute for Biochemistry & Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Marjolein Mijnders
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Wei Wang
- Gregory Fleming James Cystic Fibrosis Research Center and
| | | | - Jessica Maya
- Gregory Fleming James Cystic Fibrosis Research Center and
| | | | - Robert A Kesterson
- Department of Genetics, University of Alabama at Birmingham (UAB), Birmingham, Alabama, USA
| | - Kevin L Kirk
- Gregory Fleming James Cystic Fibrosis Research Center and
| | - Andras Rab
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ineke Braakman
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Jeong S Hong
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - John L Hartman
- Gregory Fleming James Cystic Fibrosis Research Center and.,Department of Genetics, University of Alabama at Birmingham (UAB), Birmingham, Alabama, USA
| | - Zoya Ignatova
- Institute for Biochemistry & Molecular Biology, University of Hamburg, Hamburg, Germany
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Sabusap CM, Wang W, McNicholas CM, Chung WJ, Fu L, Wen H, Mazur M, Kirk KL, Collawn JF, Hong JS, Sorscher EJ. Analysis of cystic fibrosis-associated P67L CFTR illustrates barriers to personalized therapeutics for orphan diseases. JCI Insight 2016; 1. [PMID: 27660821 DOI: 10.1172/jci.insight.86581] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Emerging knowledge indicates the difficulty in categorizing unusual cystic fibrosis (CF) mutations, with regard to both pathogenic mechanism and theratype. As case in point, we present data concerning P67L mutation of the cystic fibrosis transmembrane conductance regulator (CFTR), a defect carried by a small number of individuals with CF and sometimes attributed to a channel conductance abnormality. Findings from our laboratory and others establish that P67L causes protein misfolding, disrupts maturation, confers gating defects, is thermally stable, and exhibits near normal conductance. These results provide one framework by which rare CF alleles such as P67L can be more comprehensively profiled vis-à-vis molecular pathogenesis. We also demonstrate that emerging CF treatments - ivacaftor and lumacaftor - can mediate pronounced pharmacologic activation of P67L CFTR. Infrequent CF alleles are often improperly characterized, in part, due to the small numbers of patients involved. Moreover, access to new personalized treatments among patients with ultra-orphan genotypes has been limited by difficulty arranging phase III clinical trials, and off-label prescribing has been impaired by high drug cost and difficulty arranging third party reimbursement. Rare CFTR mutations such as P67L are emblematic of the challenges to "precision" medicine, including use of the best available mechanistic knowledge to treat patients with unusual forms of disease.
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Affiliation(s)
- Carleen M Sabusap
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama, Birmingham, Alabama, USA
| | - Wei Wang
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama, Birmingham, Alabama, USA
| | - Carmel M McNicholas
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama, Birmingham, Alabama, USA
| | - W Joon Chung
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama, Birmingham, Alabama, USA
| | - Lianwu Fu
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama, Birmingham, Alabama, USA
| | - Hui Wen
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama, Birmingham, Alabama, USA
| | - Marina Mazur
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama, Birmingham, Alabama, USA
| | - Kevin L Kirk
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama, Birmingham, Alabama, USA
| | - James F Collawn
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama, Birmingham, Alabama, USA
| | - Jeong S Hong
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama, Birmingham, Alabama, USA
| | - Eric J Sorscher
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama, Birmingham, Alabama, USA.; Emory University, Atlanta, Georgia, USA
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