51
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Basilicata MF, Keller Valsecchi CI. The good, the bad, and the ugly: Evolutionary and pathological aspects of gene dosage alterations. PLoS Genet 2021; 17:e1009906. [PMID: 34882671 PMCID: PMC8659298 DOI: 10.1371/journal.pgen.1009906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Diploid organisms contain a maternal and a paternal genome complement that is thought to provide robustness and allow developmental progression despite genetic perturbations that occur in heterozygosity. However, changes affecting gene dosage from the chromosome down to the individual gene level possess a significant pathological potential and can lead to developmental disorders (DDs). This indicates that expression from a balanced gene complement is highly relevant for proper cellular and organismal function in eukaryotes. Paradoxically, gene and whole chromosome duplications are a principal driver of evolution, while heteromorphic sex chromosomes (XY and ZW) are naturally occurring aneuploidies important for sex determination. Here, we provide an overview of the biology of gene dosage at the crossroads between evolutionary benefit and pathogenicity during disease. We describe the buffering mechanisms and cellular responses to alterations, which could provide a common ground for the understanding of DDs caused by copy number alterations.
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52
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Targa A, Larrimore KE, Wong CK, Chong YL, Fung R, Lee J, Choi H, Rancati G. Non-genetic and genetic rewiring underlie adaptation to hypomorphic alleles of an essential gene. EMBO J 2021; 40:e107839. [PMID: 34528284 PMCID: PMC8561638 DOI: 10.15252/embj.2021107839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 08/05/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022] Open
Abstract
Adaptive evolution to cellular stress is a process implicated in a wide range of biological and clinical phenomena. Two major routes of adaptation have been identified: non-genetic changes, which allow expression of different phenotypes in novel environments, and genetic variation achieved by selection of fitter phenotypes. While these processes are broadly accepted, their temporal and epistatic features in the context of cellular evolution and emerging drug resistance are contentious. In this manuscript, we generated hypomorphic alleles of the essential nuclear pore complex (NPC) gene NUP58. By dissecting early and long-term mechanisms of adaptation in independent clones, we observed that early physiological adaptation correlated with transcriptome rewiring and upregulation of genes known to interact with the NPC; long-term adaptation and fitness recovery instead occurred via focal amplification of NUP58 and restoration of mutant protein expression. These data support the concept that early phenotypic plasticity allows later acquisition of genetic adaptations to a specific impairment. We propose this approach as a genetic model to mimic targeted drug therapy in human cells and to dissect mechanisms of adaptation.
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Affiliation(s)
- Altea Targa
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Skin Research Institute of Singapore (SRIS)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Katherine E Larrimore
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Skin Research Institute of Singapore (SRIS)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Cheng Kit Wong
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Yu Lin Chong
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Skin Research Institute of Singapore (SRIS)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Ronald Fung
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Joseph Lee
- Department of MedicineYong Loo Lin School of MedicineNUS and National University Health SystemSingaporeSingapore
| | - Hyungwon Choi
- Department of MedicineYong Loo Lin School of MedicineNUS and National University Health SystemSingaporeSingapore
| | - Giulia Rancati
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Skin Research Institute of Singapore (SRIS)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
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53
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Ramensky VE, Ershova AI, Zaicenoka M, Kiseleva AV, Zharikova AA, Vyatkin YV, Sotnikova EA, Efimova IA, Divashuk MG, Kurilova OV, Skirko OP, Muromtseva GA, Belova OA, Rachkova SA, Pokrovskaya MS, Shalnova SA, Meshkov AN, Drapkina OM. Targeted Sequencing of 242 Clinically Important Genes in the Russian Population From the Ivanovo Region. Front Genet 2021; 12:709419. [PMID: 34691145 PMCID: PMC8529250 DOI: 10.3389/fgene.2021.709419] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/31/2021] [Indexed: 12/16/2022] Open
Abstract
We performed a targeted sequencing of 242 clinically important genes mostly associated with cardiovascular diseases in a representative population sample of 1,658 individuals from the Ivanovo region northeast of Moscow. Approximately 11% of 11,876 detected variants were not found in the Single Nucleotide Polymorphism Database (dbSNP) or reported earlier in the Russian population. Most novel variants were singletons and doubletons in our sample, and virtually no novel alleles presumably specific for the Russian population were able to reach the frequencies above 0.1-0.2%. The overwhelming majority (99.3%) of variants detected in this study in three or more copies were shared with other populations. We found two dominant and seven recessive known pathogenic variants with allele frequencies significantly increased compared to those in the gnomAD non-Finnish Europeans. Of the 242 targeted genes, 28 were in the list of 59 genes for which the American College of Medical Genetics and Genomics (ACMG) recommended the reporting of incidental findings. Based on the number of variants detected in the sequenced subset of ACMG59 genes, we approximated the prevalence of known pathogenic and novel or rare protein-truncating variants in the complete set of ACMG59 genes in the Ivanovo population at 1.4 and 2.8%, respectively. We analyzed the available clinical data and observed the incomplete penetrance of known pathogenic variants in the 28 ACMG59 genes: only 1 individual out of 12 with such variants had the phenotype most likely related to the variant. When known pathogenic and novel or rare protein-truncating variants were considered together, the overall rate of confirmed phenotypes was about 19%, with maximum in the subset of novel protein-truncating variants. We report three novel protein truncating variants in APOB and one in MYH7 observed in individuals with hypobetalipoproteinemia and hypertrophic cardiomyopathy, respectively. Our results provide a valuable reference for the clinical interpretation of gene sequencing in Russian and other populations.
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Affiliation(s)
- Vasily E Ramensky
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Alexandra I Ershova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Marija Zaicenoka
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russia
| | - Anna V Kiseleva
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Anastasia A Zharikova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Yuri V Vyatkin
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Evgeniia A Sotnikova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Irina A Efimova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Mikhail G Divashuk
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia.,All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Olga V Kurilova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Olga P Skirko
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Galina A Muromtseva
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | | | | | - Maria S Pokrovskaya
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Svetlana A Shalnova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Alexey N Meshkov
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Oxana M Drapkina
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
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54
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Singh RS. Decoding 'Unnecessary Complexity': A Law of Complexity and a Concept of Hidden Variation Behind "Missing Heritability" in Precision Medicine. J Mol Evol 2021; 89:513-526. [PMID: 34341835 PMCID: PMC8327892 DOI: 10.1007/s00239-021-10023-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/20/2021] [Indexed: 01/06/2023]
Abstract
The high hopes for the Human Genome Project and personalized medicine were not met because the relationship between genotypes and phenotypes turned out to be more complex than expected. In a previous study we laid the foundation of a theory of complexity and showed that because of the blind nature of evolution, and molecular and historical contingency, cells have accumulated unnecessary complexity, complexity beyond what is necessary and sufficient to describe an organism. Here we provide empirical evidence and show that unnecessary complexity has become integrated into the genome in the form of redundancy and is relevant to molecular evolution of phenotypic complexity. Unnecessary complexity creates uncertainty between molecular and phenotypic complexity, such that phenotypic complexity (CP) is higher than molecular complexity (CM), which is higher than DNA complexity (CD). The qualitative inequality in complexity is based on the following hierarchy: CP > CM > CD. This law-like relationship holds true for all complex traits, including complex diseases. We present a hypothesis of two types of variation, namely open and closed (hidden) systems, show that hidden variation provides a hitherto undiscovered "third source" of phenotypic variation, beside genotype and environment, and argue that "missing heritability" for some complex diseases is likely to be a case of "diluted heritability". There is a need for radically new ways of thinking about the principles of genotype-phenotype relationship. Understanding how cells use hidden, pathway variation to respond to stress can shed light on why two individuals who share the same risk factors may not develop the same disease, or how cancer cells escape death.
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Affiliation(s)
- Rama S Singh
- Department of Biology, and Origins Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S4K1, Canada.
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55
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Souza IA, Gandini MA, Zamponi GW. Splice-variant specific effects of a CACNA1H mutation associated with writer's cramp. Mol Brain 2021; 14:145. [PMID: 34544471 PMCID: PMC8451114 DOI: 10.1186/s13041-021-00861-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/14/2021] [Indexed: 11/25/2022] Open
Abstract
The CACNA1H gene encodes the α1 subunit of the low voltage-activated Cav3.2 T-type calcium channel, an important regulator of neuronal excitability. Alternative mRNA splicing can generate multiple channel variants with distinct biophysical properties and expression patterns. Two major splice variants, containing or lacking exon 26 (± 26) have been found in different human tissues. In this study, we report splice variant specific effects of a Cav3.2 mutation found in patients with autosomal dominant writer’s cramp, a specific type of focal dystonia. We had previously reported that the R481C missense mutation caused a gain of function effect when expressed in Cav3.2 (+ 26) by accelerating its recovery from inactivation. Here, we show that when the mutation is expressed in the short variant of the channel (− 26), we observe a significant increase in current density when compared to wild-type Cav3.2 (− 26) but the effect on the recovery from inactivation is lost. Our data add to growing evidence that the functional expression of calcium channel mutations depends on which splice variant is being examined.
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Affiliation(s)
- Ivana A Souza
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, Cumming School of Medicine, Alberta Children's Hospital Research Institute,, University of Calgary, Alberta, Calgary, Canada
| | - Maria A Gandini
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, Cumming School of Medicine, Alberta Children's Hospital Research Institute,, University of Calgary, Alberta, Calgary, Canada
| | - Gerald W Zamponi
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, Cumming School of Medicine, Alberta Children's Hospital Research Institute,, University of Calgary, Alberta, Calgary, Canada.
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56
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Shido K, Kojima K, Yoshida-Akai S, Kikuchi K, Hatamochi A, Aiba S, Yamasaki K. Ehlers-Danlos syndrome type IV with a novel COL3A1 exon 14 skipping variation confirmed by Tohoku Medical Megabank Organization genomic database. J Dermatol 2021; 48:1918-1922. [PMID: 34453356 DOI: 10.1111/1346-8138.16131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 11/29/2022]
Abstract
A novel COL3A1 variant was identified in a Japanese case of Ehlers-Danlos syndrome type IV (EDS-IV) with a characteristic "Madonna" face, fragile uterus, and easy bruising in addition to a history of cavernous sinus fistula. We confirmed variable diameters of collagen fibrils in the dermis and decrease in type 3 collagen production from cultured fibroblasts. Genomic DNA sequencing of the COL3A1 region and COL3A1 cDNA sequence expressing in cultured fibroblasts identified that a nucleotide variation at c.951+2T>G on intron 14 leads to skipping of exon 14 in COL3A1 cDNA. The novel variation in the splice site of COL3A1 region g.IVS14+2T>G was not listed in the EDS-IV pathogenic genetic databases including Human Gene Mutation Database, ClinVar, and Leiden Open Variation Database. Using the whole genome sequence database of 8380 Japanese individuals reported by the Tohoku Medical Megabank Organization (ToMMo) cohort study, we also confirmed that COL3A1 g.IVS14+2T>G was not a common single nucleotide variation in the Japanese population, although 13 EDS-related COL3A1 variants were identified in the ToMMo database of 8380 Japanese individuals. These results demonstrated that our case of EDS-IV was a result of the novel variation of COL3A1 g.IVS14+2T>G. These statistical genetics approaches with the combination of the ToMMo database of 8380 Japanese individuals and pathogenic genetic databases are a useful method to confirm the uniqueness of novel variation in Japanese.
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Affiliation(s)
- Kosuke Shido
- Department of Dermatology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.,Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Kaname Kojima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | | | - Katsuko Kikuchi
- Department of Dermatology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Atsushi Hatamochi
- Department of Dermatology, Dokkyo Medical University Graduate School of Medicine, Shimotsuga-gun, Tochigi, Japan
| | - Setsuya Aiba
- Department of Dermatology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Kenshi Yamasaki
- Department of Dermatology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
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57
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van Leeuwen J, Pons C, Tan G, Wang JZ, Hou J, Weile J, Gebbia M, Liang W, Shuteriqi E, Li Z, Lopes M, Ušaj M, Dos Santos Lopes A, van Lieshout N, Myers CL, Roth FP, Aloy P, Andrews BJ, Boone C. Systematic analysis of bypass suppression of essential genes. Mol Syst Biol 2021; 16:e9828. [PMID: 32939983 PMCID: PMC7507402 DOI: 10.15252/msb.20209828] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022] Open
Abstract
Essential genes tend to be highly conserved across eukaryotes, but, in some cases, their critical roles can be bypassed through genetic rewiring. From a systematic analysis of 728 different essential yeast genes, we discovered that 124 (17%) were dispensable essential genes. Through whole-genome sequencing and detailed genetic analysis, we investigated the genetic interactions and genome alterations underlying bypass suppression. Dispensable essential genes often had paralogs, were enriched for genes encoding membrane-associated proteins, and were depleted for members of protein complexes. Functionally related genes frequently drove the bypass suppression interactions. These gene properties were predictive of essential gene dispensability and of specific suppressors among hundreds of genes on aneuploid chromosomes. Our findings identify yeast's core essential gene set and reveal that the properties of dispensable essential genes are conserved from yeast to human cells, correlating with human genes that display cell line-specific essentiality in the Cancer Dependency Map (DepMap) project.
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Affiliation(s)
- Jolanda van Leeuwen
- Center for Integrative Genomics, Bâtiment Génopode, University of Lausanne, Lausanne, Switzerland.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Carles Pons
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Guihong Tan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Jason Zi Wang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jing Hou
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Jochen Weile
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Marinella Gebbia
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Wendy Liang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Ermira Shuteriqi
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Zhijian Li
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Maykel Lopes
- Center for Integrative Genomics, Bâtiment Génopode, University of Lausanne, Lausanne, Switzerland
| | - Matej Ušaj
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Andreia Dos Santos Lopes
- Center for Integrative Genomics, Bâtiment Génopode, University of Lausanne, Lausanne, Switzerland
| | - Natascha van Lieshout
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Frederick P Roth
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Brenda J Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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58
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Seaby EG, Ennis S. Challenges in the diagnosis and discovery of rare genetic disorders using contemporary sequencing technologies. Brief Funct Genomics 2021; 19:243-258. [PMID: 32393978 DOI: 10.1093/bfgp/elaa009] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Next generation sequencing (NGS) has revolutionised rare disease diagnostics. Concomitant with advancing technologies has been a rise in the number of new gene disorders discovered and diagnoses made for patients and their families. However, despite the trend towards whole exome and whole genome sequencing, diagnostic rates remain suboptimal. On average, only ~30% of patients receive a molecular diagnosis. National sequencing projects launched in the last 5 years are integrating clinical diagnostic testing with research avenues to widen the spectrum of known genetic disorders. Consequently, efforts to diagnose genetic disorders in a clinical setting are now often shared with efforts to prioritise candidate variants for the detection of new disease genes. Herein we discuss some of the biggest obstacles precluding molecular diagnosis and discovery of new gene disorders. We consider bioinformatic and analytical challenges faced when interpreting next generation sequencing data and showcase some of the newest tools available to mitigate these issues. We consider how incomplete penetrance, non-coding variation and structural variants are likely to impact diagnostic rates, and we further discuss methods for uplifting novel gene discovery by adopting a gene-to-patient-based approach.
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59
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Seaby EG, Rehm HL, O’Donnell-Luria A. Strategies to Uplift Novel Mendelian Gene Discovery for Improved Clinical Outcomes. Front Genet 2021; 12:674295. [PMID: 34220947 PMCID: PMC8248347 DOI: 10.3389/fgene.2021.674295] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/12/2021] [Indexed: 01/31/2023] Open
Abstract
Rare genetic disorders, while individually rare, are collectively common. They represent some of the most severe disorders affecting patients worldwide with significant morbidity and mortality. Over the last decade, advances in genomic methods have significantly uplifted diagnostic rates for patients and facilitated novel and targeted therapies. However, many patients with rare genetic disorders still remain undiagnosed as the genetic etiology of only a proportion of Mendelian conditions has been discovered to date. This article explores existing strategies to identify novel Mendelian genes and how these discoveries impact clinical care and therapeutics. We discuss the importance of data sharing, phenotype-driven approaches, patient-led approaches, utilization of large-scale genomic sequencing projects, constraint-based methods, integration of multi-omics data, and gene-to-patient methods. We further consider the health economic advantages of novel gene discovery and speculate on potential future methods for improved clinical outcomes.
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Affiliation(s)
- Eleanor G. Seaby
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Genomic Informatics Group, University Hospital Southampton, Southampton, United Kingdom
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, United States
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States
| | - Anne O’Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, United States
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, United States
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60
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Zhang P, Cobat A, Lee YS, Wu Y, Bayrak CS, Boccon-Gibod C, Matuozzo D, Lorenzo L, Jain A, Boucherit S, Vallée L, Stüve B, Chabrier S, Casanova JL, Abel L, Zhang SY, Itan Y. A computational approach for detecting physiological homogeneity in the midst of genetic heterogeneity. Am J Hum Genet 2021; 108:1012-1025. [PMID: 34015270 DOI: 10.1016/j.ajhg.2021.04.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023] Open
Abstract
The human genetic dissection of clinical phenotypes is complicated by genetic heterogeneity. Gene burden approaches that detect genetic signals in case-control studies are underpowered in genetically heterogeneous cohorts. We therefore developed a genome-wide computational method, network-based heterogeneity clustering (NHC), to detect physiological homogeneity in the midst of genetic heterogeneity. Simulation studies showed our method to be capable of systematically converging genes in biological proximity on the background biological interaction network, and capturing gene clusters harboring presumably deleterious variants, in an efficient and unbiased manner. We applied NHC to whole-exome sequencing data from a cohort of 122 individuals with herpes simplex encephalitis (HSE), including 13 individuals with previously published monogenic inborn errors of TLR3-dependent IFN-α/β immunity. The top gene cluster identified by our approach successfully detected and prioritized all causal variants of five TLR3 pathway genes in the 13 previously reported individuals. This approach also suggested candidate variants of three reported genes and four candidate genes from the same pathway in another ten previously unstudied individuals. TLR3 responsiveness was impaired in dermal fibroblasts from four of the five individuals tested, suggesting that the variants detected were causal for HSE. NHC is, therefore, an effective and unbiased approach for unraveling genetic heterogeneity by detecting physiological homogeneity.
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Affiliation(s)
- Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA.
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris 75015, France; University of Paris, Imagine Institute, Paris 75015, France
| | - Yoon-Seung Lee
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Yiming Wu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Cigdem Sevim Bayrak
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Clémentine Boccon-Gibod
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Daniela Matuozzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris 75015, France; University of Paris, Imagine Institute, Paris 75015, France
| | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris 75015, France; University of Paris, Imagine Institute, Paris 75015, France
| | - Aayushee Jain
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Soraya Boucherit
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris 75015, France; University of Paris, Imagine Institute, Paris 75015, France
| | - Louis Vallée
- Neuropediatric Department, Roger Salengro Hospital, Lille 59037, France
| | - Burkhard Stüve
- Clinics of the City of Cologne gGmbH, Cologne 53323, Germany
| | - Stéphane Chabrier
- CHU Saint-Étienne, French Centre for Pediatric Stroke, Saint-Étienne, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris 75015, France; University of Paris, Imagine Institute, Paris 75015, France; Howard Hughes Medical Institute, New York, NY 10065, USA.
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris 75015, France; University of Paris, Imagine Institute, Paris 75015, France
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris 75015, France; University of Paris, Imagine Institute, Paris 75015, France
| | - Yuval Itan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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How do non-geneticist physicians deal with genetic tests? A qualitative analysis. Eur J Hum Genet 2021; 30:320-331. [PMID: 33907318 PMCID: PMC8904857 DOI: 10.1038/s41431-021-00884-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 12/01/2022] Open
Abstract
Genetic testing is accepted to be a common practice in many medical specialties. These genetic tests raise issues such as respect for basic rights, how to handle results and uncertainty and how to balance concerns for medical confidentiality with the rights of third parties. Physicians need help to deal with the rapid development of genomic medicine as most of them have received no specific training on the medical, ethical, and social issues involved. Analyzing how these professionals integrate genetic testing into the patient-provider relationship is essential to paving the way for a better use of genomics by all. We conducted a qualitative study comprising a series of focus groups with 21 neurologists and endocrinologists about their genetic testing practices in the western part of France. The interviews were transcribed and analyzed for major themes. We identified an automated care management procedure of genetic testing that affects patient autonomy. The simple fact of having a written consent cannot justify a genetic test given the stakes associated with the results. We also suggest orienting practices toward a systemic approach using a multidisciplinary team or network to provide resources for dealing with uncertainties in interpreting results or situations that require additional technical or clinical skills and, if necessary, to allow for joint consultations with both a geneticist and a non-geneticist medical specialist.
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Pathogenic missense protein variants affect different functional pathways and proteomic features than healthy population variants. PLoS Biol 2021; 19:e3001207. [PMID: 33909605 PMCID: PMC8110273 DOI: 10.1371/journal.pbio.3001207] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 05/10/2021] [Accepted: 03/26/2021] [Indexed: 12/27/2022] Open
Abstract
Missense variants are present amongst the healthy population, but some of them are causative of human diseases. A classification of variants associated with “healthy” or “diseased” states is therefore not always straightforward. A deeper understanding of the nature of missense variants in health and disease, the cellular processes they may affect, and the general molecular principles which underlie these differences is essential to offer mechanistic explanations of the true impact of pathogenic variants. Here, we have formalised a statistical framework which enables robust probabilistic quantification of variant enrichment across full-length proteins, their domains, and 3D structure-defined regions. Using this framework, we validate and extend previously reported trends of variant enrichment in different protein structural regions (surface/core/interface). By examining the association of variant enrichment with available functional pathways and transcriptomic and proteomic (protein half-life, thermal stability, abundance) data, we have mined a rich set of molecular features which distinguish between pathogenic and population variants: Pathogenic variants mainly affect proteins involved in cell proliferation and nucleotide processing and are enriched in more abundant proteins. Additionally, rare population variants display features closer to common than pathogenic variants. We validate the association between these molecular features and variant pathogenicity by comparing against existing in silico variant impact annotations. This study provides molecular details into how different proteins exhibit resilience and/or sensitivity towards missense variants and provides the rationale to prioritise variant-enriched proteins and protein domains for therapeutic targeting and development. The ZoomVar database, which we created for this study, is available at fraternalilab.kcl.ac.uk/ZoomVar. It allows users to programmatically annotate missense variants with protein structural information and to calculate variant enrichment in different protein structural regions. How do can one improve the classification of genetic variants as harmful or harmless? This study uses a robust statistical analysis to exploit the interplay between protein structure, proteomic measurements and functional pathways to enable better discrimination between missense variants in health and disease.
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Tukker AM, Royal CD, Bowman AB, McAllister KA. The Impact of Environmental Factors on Monogenic Mendelian Diseases. Toxicol Sci 2021; 181:3-12. [PMID: 33677604 PMCID: PMC8599782 DOI: 10.1093/toxsci/kfab022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Environmental factors and gene-environment interactions modify the variable expressivity, progression, severity, and onset of some classic (monogenic) Mendelian-inherited genetic diseases. Cystic fibrosis, Huntington disease, Parkinson's disease, and sickle cell disease are examples of well-known Mendelian disorders that are influenced by exogenous exposures. Environmental factors may act by direct or indirect mechanisms to modify disease severity, timing, and presentation, including through epigenomic influences, protein misfolding, miRNA alterations, transporter activity, and mitochondrial effects. Because pathological features of early-onset Mendelian diseases can mimic later onset complex diseases, we propose that studies of environmental exposure vulnerabilities using monogenic model systems of rare Mendelian diseases have high potential to provide insight into complex disease phenotypes arising from multi-genetic/multi-toxicant interactions. Mendelian disorders can be modeled by homologous mutations in animal model systems with strong recapitulation of human disease etiology and natural history, providing an important advantage for study of these diseases. Monogenic high penetrant mutations are ideal for toxicant challenge studies with a wide variety of environmental stressors, because background genetic variability may be less able to alter the relatively strong phenotype driving disease-causing mutations. These models promote mechanistic understandings of gene-environment interactions and biological pathways relevant to both Mendelian and related sporadic complex disease outcomes by creating a sensitized background for relevant environmental risk factors. Additionally, rare disease communities are motivated research participants, creating the potential of strong research allies among rare Mendelian disease advocacy groups and disease registries and providing a variety of translational opportunities that are under-utilized in genetic or environmental health science.
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Affiliation(s)
- Anke M Tukker
- School of Health Sciences, Purdue University, West Lafayette, Indiana 47907-2051
| | - Charmaine D Royal
- Departments of African and African American Studies, Biology, Global Health, and Family Medicine and Community Health and Center on Genomics, Race, Identity, Difference, Duke University, Durham, North Carolina 27708
| | - Aaron B Bowman
- School of Health Sciences, Purdue University, West Lafayette, Indiana 47907-2051
| | - Kimberly A McAllister
- Genes Environment and Health Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
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Gaffke L, Pierzynowska K, Rintz E, Cyske Z, Giecewicz I, Węgrzyn G. Gene Expression-Related Changes in Morphologies of Organelles and Cellular Component Organization in Mucopolysaccharidoses. Int J Mol Sci 2021; 22:ijms22052766. [PMID: 33803318 PMCID: PMC7967209 DOI: 10.3390/ijms22052766] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/28/2021] [Accepted: 03/05/2021] [Indexed: 12/13/2022] Open
Abstract
Mucopolysaccharidoses (MPS) are inherited metabolic diseases characterized by accumulation of incompletely degraded glycosaminoglycans (GAGs) in lysosomes. Although primary causes of these diseases are mutations in genes coding for enzymes involved in lysosomal GAG degradation, it was demonstrated that storage of these complex carbohydrates provokes a cascade of secondary and tertiary changes affecting cellular functions. Potentially, this might lead to appearance of cellular disorders which could not be corrected even if the primary cause of the disease is removed. In this work, we studied changes in cellular organelles in MPS fibroblasts relative to control cells. All 11 types and subtypes of MPS were included into this study to obtain a complex picture of changes in organelles in this group of diseases. Two experimental approaches were employed, transcriptomic analyses and electron microscopic assessment of morphology of organelles. We analyzed levels of transcripts of genes grouped into two terms included into the QuickGO database, ‘Cellular component organization’ (GO:0016043) and ‘Cellular anatomical entity’ (GO:0110165), to find that number of transcripts with significantly changed levels in MPS fibroblasts vs. controls ranged from 109 to 322 (depending on MPS type) in GO:0016043, and from 70 to 208 in GO:0110165. This dysregulation of expression of genes crucial for proper structures and functions of various organelles was accompanied by severe changes in morphologies of lysosomes, nuclei, mitochondria, Golgi apparatus, and endoplasmic reticulum. Interestingly, some observed changes occurred in all/most MPS types while others were specific to particular disease types/subtypes. We suggest that severe changes in organelles in MPS cells might arise from dysregulation of expression of a battery of genes involved in organelles’ structures and functions. Intriguingly, normalization of GAG levels by using recombinant human enzymes specific to different MPS types corrected morphologies of some, but not all, organelles, while it failed to improve regulation of expression of selected genes. These results might suggest reasons for inability of enzyme replacement therapy to correct all MPS symptoms, particularly if initiated at advanced stages of the disease.
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Ferrer‐Avargues R, Castillejo MI, Dámaso E, Díez‐Obrero V, Garrigos N, Molina T, Codoñer‐Alejos A, Segura Á, Sánchez‐Heras AB, Castillejo A, Soto JL. Co-occurrence of germline pathogenic variants for different hereditary cancer syndromes in patients with Lynch syndrome. Cancer Commun (Lond) 2021; 41:218-228. [PMID: 33630411 PMCID: PMC7968885 DOI: 10.1002/cac2.12134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 01/05/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Lynch syndrome (LS) is a hereditary condition characterized by a high risk of colorectal cancer, endometrial cancer, and other neoplasia associated with germline alterations in DNA mismatch repair genes. The classical genetic diagnostic strategy for LS consists of the Sanger sequencing of genes associated with the suspected syndrome. Next-generation sequencing (NGS) enables the simultaneous sequencing of a large number of hereditary cancer genes. Here, we aimed to study whether other germline pathogenic variants of hereditary cancer genes are present in patients with LS. METHODS A cohort of 84 probands with a previous genetic diagnosis of LS by Sanger sequencing was reanalyzed using NGS via a commercial panel of 94 hereditary cancer genes by hybrid capture. The American College of Medical Genetics and Genomics criteria were used to classify the clinical significance of the variants. The findings of NGS were confirmed by Sanger sequencing. When possible, genetic analyses of the new findings in the proband's relatives were also performed by Sanger sequencing. RESULTS We identified five families (6%), out of 84, with at least two germline pathogenic variants conferring to high or moderate risk in different dominant cancer-predisposing genes: [MLH1-BRCA2-NBN], [MLH1-BRCA1], [MSH2-ATM], [MSH6-NF1], and [MLH1-FANCA]. Interestingly, only one out of these five families exhibited a clinical phenotype associated with the new pathogenic variants. The family with three pathogenic variants of the [MLH1-BRCA2-NBN] genes showed a high aggregation of tumors associated with LS and breast and ovarian cancer syndrome. CONCLUSIONS Our results showed that the co-occurrence of more than one pathogenic variant in cancer-predisposing genes was remarkable among cases of LS. In most cases, no clinicial manifestations were associated with the secondary pathogenic variants. Further studies are needed to confirm these findings and elucidate their clinical impact. Reanalysis of LS families should be considered only in families with mixed clinical phenotypes.
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Affiliation(s)
- Rosario Ferrer‐Avargues
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO)FISABIO‐ Elche Health DepartmentElche032303Spain
| | - María Isabel Castillejo
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO)FISABIO‐ Elche Health DepartmentElche032303Spain
- Molecular Genetics Unit. Elche University HospitalElche032303Spain
| | - Estela Dámaso
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO)FISABIO‐ Elche Health DepartmentElche032303Spain
- Molecular Genetics Unit. Elche University HospitalElche032303Spain
| | - Virginia Díez‐Obrero
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO)FISABIO‐ Elche Health DepartmentElche032303Spain
| | - Noemí Garrigos
- Department of Molecular BiopathologyImmunological Center of AlicanteSan Juan‐Alicante03550Spain
| | - Tatiana Molina
- Department of Molecular BiopathologyImmunological Center of AlicanteSan Juan‐Alicante03550Spain
| | - Alan Codoñer‐Alejos
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO)FISABIO‐ Elche Health DepartmentElche032303Spain
- Molecular Genetics Unit. Elche University HospitalElche032303Spain
| | - Ángel Segura
- Medical Oncology DepartmentCancer Genetic Counseling Unit. La Fe University HospitalValencia46026Spain
| | - Ana Beatriz Sánchez‐Heras
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO)FISABIO‐ Elche Health DepartmentElche032303Spain
- Medical Oncology DepartmentCancer Genetic Counseling Unit. Elche University HospitalElche03203Spain
| | - Adela Castillejo
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO)FISABIO‐ Elche Health DepartmentElche032303Spain
- Molecular Genetics Unit. Elche University HospitalElche032303Spain
| | - José Luis Soto
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO)FISABIO‐ Elche Health DepartmentElche032303Spain
- Molecular Genetics Unit. Elche University HospitalElche032303Spain
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Hess JL, Tylee DS, Mattheisen M, Børglum AD, Als TD, Grove J, Werge T, Mortensen PB, Mors O, Nordentoft M, Hougaard DM, Byberg-Grauholm J, Bækvad-Hansen M, Greenwood TA, Tsuang MT, Curtis D, Steinberg S, Sigurdsson E, Stefánsson H, Stefánsson K, Edenberg HJ, Holmans P, Faraone SV, Glatt SJ. A polygenic resilience score moderates the genetic risk for schizophrenia. Mol Psychiatry 2021; 26:800-815. [PMID: 31492941 PMCID: PMC7058518 DOI: 10.1038/s41380-019-0463-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/29/2019] [Accepted: 04/17/2019] [Indexed: 12/19/2022]
Abstract
Based on the discovery by the Resilience Project (Chen R. et al. Nat Biotechnol 34:531-538, 2016) of rare variants that confer resistance to Mendelian disease, and protective alleles for some complex diseases, we posited the existence of genetic variants that promote resilience to highly heritable polygenic disorders1,0 such as schizophrenia. Resilience has been traditionally viewed as a psychological construct, although our use of the term resilience refers to a different construct that directly relates to the Resilience Project, namely: heritable variation that promotes resistance to disease by reducing the penetrance of risk loci, wherein resilience and risk loci operate orthogonal to one another. In this study, we established a procedure to identify unaffected individuals with relatively high polygenic risk for schizophrenia, and contrasted them with risk-matched schizophrenia cases to generate the first known "polygenic resilience score" that represents the additive contributions to SZ resistance by variants that are distinct from risk loci. The resilience score was derived from data compiled by the Psychiatric Genomics Consortium, and replicated in three independent samples. This work establishes a generalizable framework for finding resilience variants for any complex, heritable disorder.
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Affiliation(s)
- Jonathan L Hess
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Daniel S Tylee
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
- Department of Psychiatry, Yale New Haven Hospital, New Haven, CT, USA
| | - Manuel Mattheisen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark
| | - Anders D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark
| | - Thomas D Als
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark
| | - Jakob Grove
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Preben Bo Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | - David M Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Jonas Byberg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Tiffany A Greenwood
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Ming T Tsuang
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - David Curtis
- University College London Genetics Institute, London, UK
- Centre for Psychiatry, Barts and the London School of Medicine and Dentistry, London, UK
| | | | - Engilbert Sigurdsson
- Department of Psychiatry, National University Hospital, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Kári Stefánsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Peter Holmans
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, UK
| | - Stephen V Faraone
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Stephen J Glatt
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab), Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA.
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA.
- Department of Public Health and Preventive Medicine, SUNY Upstate Medical University, Syracuse, NY, USA.
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Mn W, L J, Jw H, Ks R, J T, At H, Cf W. Use of SNP chips to detect rare pathogenic variants: retrospective, population based diagnostic evaluation. BMJ 2021; 372:n214. [PMID: 33589468 PMCID: PMC7879796 DOI: 10.1136/bmj.n214] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To determine whether the sensitivity and specificity of SNP chips are adequate for detecting rare pathogenic variants in a clinically unselected population. DESIGN Retrospective, population based diagnostic evaluation. PARTICIPANTS 49 908 people recruited to the UK Biobank with SNP chip and next generation sequencing data, and an additional 21 people who purchased consumer genetic tests and shared their data online via the Personal Genome Project. MAIN OUTCOME MEASURES Genotyping (that is, identification of the correct DNA base at a specific genomic location) using SNP chips versus sequencing, with results split by frequency of that genotype in the population. Rare pathogenic variants in the BRCA1 and BRCA2 genes were selected as an exemplar for detailed analysis of clinically actionable variants in the UK Biobank, and BRCA related cancers (breast, ovarian, prostate, and pancreatic) were assessed in participants through use of cancer registry data. RESULTS Overall, genotyping using SNP chips performed well compared with sequencing; sensitivity, specificity, positive predictive value, and negative predictive value were all above 99% for 108 574 common variants directly genotyped on the SNP chips and sequenced in the UK Biobank. However, the likelihood of a true positive result decreased dramatically with decreasing variant frequency; for variants that are very rare in the population, with a frequency below 0.001% in UK Biobank, the positive predictive value was very low and only 16% of 4757 heterozygous genotypes from the SNP chips were confirmed with sequencing data. Results were similar for SNP chip data from the Personal Genome Project, and 20/21 individuals analysed had at least one false positive rare pathogenic variant that had been incorrectly genotyped. For pathogenic variants in the BRCA1 and BRCA2 genes, which are individually very rare, the overall performance metrics for the SNP chips versus sequencing in the UK Biobank were: sensitivity 34.6%, specificity 98.3%, positive predictive value 4.2%, and negative predictive value 99.9%. Rates of BRCA related cancers in UK Biobank participants with a positive SNP chip result were similar to those for age matched controls (odds ratio 1.31, 95% confidence interval 0.99 to 1.71) because the vast majority of variants were false positives, whereas sequence positive participants had a significantly increased risk (odds ratio 4.05, 2.72 to 6.03). CONCLUSIONS SNP chips are extremely unreliable for genotyping very rare pathogenic variants and should not be used to guide health decisions without validation.
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Affiliation(s)
- Weedon Mn
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Jackson L
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Harrison Jw
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Ruth Ks
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Tyrrell J
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Hattersley At
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Wright Cf
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
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Slaught C, Berry EG, Bacik L, Skalet AH, Anadiotis G, Tuohy T, Leachman SA. Clinical challenges in interpreting multiple pathogenic mutations in single patients. Hered Cancer Clin Pract 2021; 19:15. [PMID: 33541411 PMCID: PMC7863461 DOI: 10.1186/s13053-021-00172-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 01/25/2021] [Indexed: 01/13/2023] Open
Abstract
Background In the past two decades, genetic testing for cancer risk assessment has entered mainstream clinical practice due to the availability of low-cost panels of multiple cancer-associated genes. However, the clinical value of multiple-gene panels for cancer susceptibility is not well established, especially in cases where panel testing identifies more than one pathogenic variant. The risk for specific malignancies as a result of a mutated gene is complex and likely influenced by superimposed modifier variants and/or environmental effects. Recent data suggests that the combination of multiple pathogenic variants may be fewer than reported by chance, suggesting that some mutation combinations may be detrimental. Management of patients with “incidentally” discovered mutations can be particularly challenging, especially when established guidelines call for radical procedures (e.g. total gastrectomy in CDH1) in patients and families without a classic clinical history concerning for that cancer predisposition syndrome. Case presentation We present two cases, one of an individual and one of a family, with multiple pathogenic mutations detected by multi-gene panel testing to highlight challenges practitioners face in counseling patients about pathogenic variants and determining preventive and therapeutic interventions. Conclusions Ongoing investigation is needed to improve our understanding of inherited susceptibility to disease in general and cancer predisposition syndromes, as this information has the potential to lead to the development of more precise and patient-specific counseling and surveillance strategies. The real-world adoption of new or improved technologies into clinical practice frequently requires medical decision-making in the absence of established understanding of gene-gene interactions. In the meantime, practitioners must be prepared to apply a rationale based on currently available knowledge to clinical decision-making. Current practice is evolving to rely heavily on clinical concordance with personal and family history in making specific therapeutic decisions. Supplementary Information The online version contains supplementary material available at 10.1186/s13053-021-00172-3.
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Affiliation(s)
- Christa Slaught
- Department of Dermatology, Oregon Health & Science University, 3303 SW Bond Ave, Suite 16D, Portland, OR, 97239, USA
| | - Elizabeth G Berry
- Department of Dermatology, Oregon Health & Science University, 3303 SW Bond Ave, Suite 16D, Portland, OR, 97239, USA.
| | - Lindsay Bacik
- Department of Dermatology, Penn State Health, Hershey, USA
| | - Alison H Skalet
- Department of Dermatology, Oregon Health & Science University, 3303 SW Bond Ave, Suite 16D, Portland, OR, 97239, USA.,Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, USA.,Knight Cancer Institute, Oregon Health & Science University, Portland, USA.,Department of Radiation Medicine, Oregon Health & Science University, Portland, USA
| | - George Anadiotis
- Legacy Cancer Institute, Cancer Genetics Services, Legacy Health Systems, Portland, USA
| | - Therese Tuohy
- Legacy Cancer Institute, Cancer Genetics Services, Legacy Health Systems, Portland, USA
| | - Sancy A Leachman
- Department of Dermatology, Oregon Health & Science University, 3303 SW Bond Ave, Suite 16D, Portland, OR, 97239, USA.,Knight Cancer Institute, Oregon Health & Science University, Portland, USA
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Aviel YB, Ofir A, Ben-Izhak O, Vlodavsky E, Karbian N, Brik R, Mevorach D, Magen D. A novel loss-of-function mutation in LACC1 underlies hereditary juvenile arthritis with extended intra-familial phenotypic heterogeneity. Rheumatology (Oxford) 2021; 60:4888-4898. [PMID: 33493343 DOI: 10.1093/rheumatology/keab017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 11/19/2020] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVE To investigate phenotypic and molecular characteristics of a consanguineous family with autosomal-recessive, polyarticular, juvenile idiopathic arthritis (JIA) with extra-articular manifestations, including renal amyloidosis and Crohn's disease, associated with a novel homozygous truncating variant in LACC1. METHODS Whole exome sequencing (WES) or targeted Sanger verification were performed in 15 participants. LACC1 expression and cytokine array were analyzed in patient-derived and CRISPR/Cas9-generated LACC1-knockout macrophages (Mϕ). RESULTS A homozygous truncating variant (p.Glu348Ter) in LACC1 was identified in three affected and one asymptomatic family member, and predicted harmful by causing premature stop of the LACC1 protein sequences, and by absence from ethnically-matched controls and public variation databases. Expression studies in patient-derived macrophages (Mϕ) showed no endogenous p. Glu348Ter-LACC1 RNA transcription or protein expression, compatible with nonsense-mediated mRNA decay. WES analysis in the asymptomatic homozygous subject for p. Glu348Ter-LACC1 detected an exclusive heterozygous variant (p.Arg928Gln) in complement component C5. Further complement activity analysis suggested a protective role for the p. Arg928Gln-C5 variant as a phenotypic modifier of LACC1-associated disease. Finally, cytokine profile analysis indicated increased levels of pro-inflammatory cytokines in LACC1-disrupted as compared with wild-type Mϕ. CONCLUSIONS Our findings reinforce the role of LACC1 disruption in autosomal-recessive JIA, extend the clinical spectrum and intra-familial heterogeneity of the disease-associated phenotype, indicate a modulatory effect of complement factor C5 on phenotypic severity, and suggest an inhibitory role for wild-type LACC1 on pro-inflammatory pathways.
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Affiliation(s)
- Yonatan Butbul Aviel
- Department of Pediatrics and Pediatric Rheumatology Service, Ruth Children's Hospital, Rambam Health Care Campus, Haifa, Israel.,Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ayala Ofir
- Laboratory of Molecular Medicine, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ofer Ben-Izhak
- Department of Pathology, Rambam Health Care Campus, Haifa, Israel.,Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Euvgeni Vlodavsky
- Department of Pathology, Rambam Health Care Campus, Haifa, Israel.,Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Netanel Karbian
- Rheumatology Research Center, Department of Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Riva Brik
- Department of Pediatrics and Pediatric Rheumatology Service, Ruth Children's Hospital, Rambam Health Care Campus, Haifa, Israel.,Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Dror Mevorach
- Rheumatology Research Center, Department of Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Daniella Magen
- Laboratory of Molecular Medicine, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.,Pediatric Nephrology Institute, Ruth Children's Hospital, Rambam Health Care Campus, Haifa, Israel
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70
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Ehrhart F, Jacobsen A, Rigau M, Bosio M, Kaliyaperumal R, Laros JFJ, Willighagen EL, Valencia A, Roos M, Capella-Gutierrez S, Curfs LMG, Evelo CT. A catalogue of 863 Rett-syndrome-causing MECP2 mutations and lessons learned from data integration. Sci Data 2021; 8:10. [PMID: 33452270 PMCID: PMC7810705 DOI: 10.1038/s41597-020-00794-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/30/2020] [Indexed: 11/09/2022] Open
Abstract
Rett syndrome (RTT) is a rare neurological disorder mostly caused by a genetic variation in MECP2. Making new MECP2 variants and the related phenotypes available provides data for better understanding of disease mechanisms and faster identification of variants for diagnosis. This is, however, currently hampered by the lack of interoperability between genotype-phenotype databases. Here, we demonstrate on the example of MECP2 in RTT that by making the genotype-phenotype data more Findable, Accessible, Interoperable, and Reusable (FAIR), we can facilitate prioritization and analysis of variants. In total, 10,968 MECP2 variants were successfully integrated. Among these variants 863 unique confirmed RTT causing and 209 unique confirmed benign variants were found. This dataset was used for comparison of pathogenicity predicting tools, protein consequences, and identification of ambiguous variants. Prediction tools generally recognised the RTT causing and benign variants, however, there was a broad range of overlap Nineteen variants were identified that were annotated as both disease-causing and benign, suggesting that there are additional factors in these cases contributing to disease development. Measurement(s) | Rett syndrome • phenotype • MECP2 Gene | Technology Type(s) | digital curation • network analysis | Sample Characteristic - Organism | Homo sapiens |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13359476
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Affiliation(s)
- Friederike Ehrhart
- Department of Bioinformatics - BiGCaT, NUTRIM School of Nutrition and Translational Research in Metabolism, MHeNS School of Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands. .,GKC - Rett Expertise Centre, Maastricht University Medical Center, Maastricht, The Netherlands.
| | - Annika Jacobsen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Maria Rigau
- Barcelona Supercomputing Centre (BSC), Barcelona, Spain
| | - Mattia Bosio
- Barcelona Supercomputing Centre (BSC), Barcelona, Spain
| | - Rajaram Kaliyaperumal
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen F J Laros
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Egon L Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM School of Nutrition and Translational Research in Metabolism, MHeNS School of Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Alfonso Valencia
- Barcelona Supercomputing Centre (BSC), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Marco Roos
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Leopold M G Curfs
- GKC - Rett Expertise Centre, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Chris T Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM School of Nutrition and Translational Research in Metabolism, MHeNS School of Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands.,GKC - Rett Expertise Centre, Maastricht University Medical Center, Maastricht, The Netherlands
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71
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Hagelkruys A, Wirnsberger G, Stadlmann J, Wöhner M, Horrer M, Vilagos B, Jonsson G, Kogler M, Tortola L, Novatchkova M, Bönelt P, Hoffmann D, Koglgruber R, Steffen U, Schett G, Busslinger M, Bergthaler A, Klein C, Penninger JM. A crucial role for Jagunal homolog 1 in humoral immunity and antibody glycosylation in mice and humans. J Exp Med 2021; 218:e20200559. [PMID: 32930709 PMCID: PMC7953624 DOI: 10.1084/jem.20200559] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/17/2020] [Accepted: 08/18/2020] [Indexed: 12/28/2022] Open
Abstract
Jagunal homolog 1 (JAGN1) has been identified as a critical regulator of neutrophil biology in mutant mice and rare-disease patients carrying JAGN1 mutations. Here, we report that Jagn1 deficiency results in alterations in the endoplasmic reticulum (ER) of antibody-producing cells as well as decreased antibody production and secretion. Consequently, mice lacking Jagn1 in B cells exhibit reduced serum immunoglobulin (Ig) levels at steady state and fail to mount an efficient humoral immune response upon immunization with specific antigens or when challenged with viral infections. We also demonstrate that Jagn1 deficiency in B cells results in aberrant IgG N-glycosylation leading to enhanced Fc receptor binding. Jagn1 deficiency in particular affects fucosylation of IgG subtypes in mice as well as rare-disease patients with loss-of-function mutations in JAGN1. Moreover, we show that ER stress affects antibody glycosylation. Our data uncover a novel and key role for JAGN1 and ER stress in antibody glycosylation and humoral immunity in mice and humans.
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Affiliation(s)
- Astrid Hagelkruys
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Gerald Wirnsberger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
- Apeiron Biologics AG, Vienna, Austria
| | - Johannes Stadlmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Biochemistry, University of Natural Resource and Life Sciences, Vienna, Austria
| | - Miriam Wöhner
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Marion Horrer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Bojan Vilagos
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gustav Jonsson
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Melanie Kogler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Luigi Tortola
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Maria Novatchkova
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Peter Bönelt
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - David Hoffmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Rubina Koglgruber
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Ulrike Steffen
- Department of Internal Medicine 3-Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Georg Schett
- Department of Internal Medicine 3-Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Meinrad Busslinger
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, Ludwig Maximilians University, Munich, Germany
| | - Josef M. Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
- Department of Medical Genetics, Life Science Institute, University of British Columbia, Vancouver, Canada
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72
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Goldstein I, Ehrenreich IM. The complex role of genetic background in shaping the effects of spontaneous and induced mutations. Yeast 2020; 38:187-196. [PMID: 33125810 PMCID: PMC7984271 DOI: 10.1002/yea.3530] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/09/2020] [Accepted: 10/24/2020] [Indexed: 12/27/2022] Open
Abstract
Spontaneous and induced mutations frequently show different phenotypic effects across genetically distinct individuals. It is generally appreciated that these background effects mainly result from genetic interactions between the mutations and segregating loci. However, the architectures and molecular bases of these genetic interactions are not well understood. Recent work in a number of model organisms has tried to advance knowledge of background effects both by using large‐scale screens to find mutations that exhibit this phenomenon and by identifying the specific loci that are involved. Here, we review this body of research, emphasizing in particular the insights it provides into both the prevalence of background effects across different mutations and the mechanisms that cause these background effects. A large fraction of mutations show different effects in distinct individuals. These background effects are mainly caused by epistasis with segregating loci. Mapping studies show a diversity of genetic architectures can be involved. Genetically complex changes in gene expression are often, but not always, causative.
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Affiliation(s)
- Ilan Goldstein
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089-2910, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089-2910, USA
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73
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Auslander N, Ramos DM, Zelaya I, Karathia H, Crawford TO, Schäffer AA, Sumner CJ, Ruppin E. The GENDULF algorithm: mining transcriptomics to uncover modifier genes for monogenic diseases. Mol Syst Biol 2020; 16:e9701. [PMID: 33438800 PMCID: PMC7754056 DOI: 10.15252/msb.20209701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/20/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022] Open
Abstract
Modifier genes are believed to account for the clinical variability observed in many Mendelian disorders, but their identification remains challenging due to the limited availability of genomics data from large patient cohorts. Here, we present GENDULF (GENetic moDULators identiFication), one of the first methods to facilitate prediction of disease modifiers using healthy and diseased tissue gene expression data. GENDULF is designed for monogenic diseases in which the mechanism is loss of function leading to reduced expression of the mutated gene. When applied to cystic fibrosis, GENDULF successfully identifies multiple, previously established disease modifiers, including EHF, SLC6A14, and CLCA1. It is then utilized in spinal muscular atrophy (SMA) and predicts U2AF1 as a modifier whose low expression correlates with higher SMN2 pre-mRNA exon 7 retention. Indeed, knockdown of U2AF1 in SMA patient-derived cells leads to increased full-length SMN2 transcript and SMN protein expression. Taking advantage of the increasing availability of transcriptomic data, GENDULF is a novel addition to existing strategies for prediction of genetic disease modifiers, providing insights into disease pathogenesis and uncovering novel therapeutic targets.
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Affiliation(s)
- Noam Auslander
- Cancer Data Science Laboratory (CDSL)National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
- National Center for Biotechnology InformationNational Library of MedicineNational Institutes of HealthBethesdaMDUSA
| | - Daniel M Ramos
- Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Ivette Zelaya
- Interdepartmental Program in BioinformaticsUniversity of California Los AngelesLos AngelesCAUSA
| | - Hiren Karathia
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer InstituteNational Institutes of HealthMDUSA
| | - Thomas O. Crawford
- Department of PediatricsJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory (CDSL)National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Charlotte J Sumner
- Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Eytan Ruppin
- Cancer Data Science Laboratory (CDSL)National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
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74
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Postema FAM, Oosterwijk JC, Hennekam RC. Genetic control of tumor development in malformation syndromes. Am J Med Genet A 2020; 185:324-335. [PMID: 33141500 DOI: 10.1002/ajmg.a.61947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 02/01/2023]
Abstract
One of the questions that arises frequently when caring for an individual with a malformation syndrome, is whether some form of tumor surveillance is indicated. In some syndromes there is a highly variable increased risk to develop tumors, while in others this is not the case. The risks can be hard to predict and difficult to explain to affected individuals and their families, and often also to caregivers. The queries arise especially if syndrome causing mutations are also known to occur in tumors. It needs insight in the mechanisms to understand and explain differences of tumor occurrence, and to offer optimal care to individuals with syndromes. Here we provide a short overview of the major mechanisms of the control for tumor occurrences in malformation syndromes.
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Affiliation(s)
- Floor A M Postema
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jan C Oosterwijk
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Raoul C Hennekam
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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75
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Diofano F, Weinmann K, Schneider I, Thiessen KD, Rottbauer W, Just S. Genetic compensation prevents myopathy and heart failure in an in vivo model of Bag3 deficiency. PLoS Genet 2020; 16:e1009088. [PMID: 33137814 PMCID: PMC7605898 DOI: 10.1371/journal.pgen.1009088] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/31/2020] [Indexed: 12/15/2022] Open
Abstract
Mutations in the molecular co-chaperone Bcl2-associated athanogene 3 (BAG3) are found to cause dilated cardiomyopathy (DCM), resulting in systolic dysfunction and heart failure, as well as myofibrillar myopathy (MFM), which is characterized by protein aggregation and myofibrillar disintegration in skeletal muscle cells. Here, we generated a CRISPR/Cas9-induced Bag3 knockout zebrafish line and found the complete preservation of heart and skeletal muscle structure and function during embryonic development, in contrast to morpholino-mediated knockdown of Bag3. Intriguingly, genetic compensation, a process of transcriptional adaptation which acts independent of protein feedback loops, was found to prevent heart and skeletal muscle damage in our Bag3 knockout model. Proteomic profiling and quantitative real-time PCR analyses identified Bag2, another member of the Bag protein family, significantly upregulated on a transcript and protein level in bag3-/- mutants. This implied that the decay of bag3 mutant mRNA in homozygous bag3-/- embryos caused the transcriptional upregulation of bag2 expression. We further demonstrated that morpholino-mediated knockdown of Bag2 in bag3-/- embryos evoked severe functional and structural heart and skeletal muscle defects, which are similar to Bag3 morphants. However, Bag2 knockdown in bag3+/+ or bag3+/- embryos did not result in (cardio-)myopathy. Finally, we found that inhibition of the nonsense-mediated mRNA decay (NMD) machinery by knockdown of upf1, an essential NMD factor, caused severe heart and skeletal muscle defects in bag3-/- mutants due to the blockade of transcriptional adaptation of bag2 expression. Our findings provide evidence that genetic compensation might vitally influence the penetrance of disease-causing bag3 mutations in vivo. One form of genetic compensation is described as transcriptional adaptation of gene expression triggered by deleterious gene mutations. Although the precise molecular mechanism that induces genetic compensation needs to be defined, it represents a powerful biological phenomenon that warrants genetic robustness. We find that antisense-mediated knockdown of Bag3 in zebrafish embryos causes heart failure and myopathy. By contrast, CRISPR/Cas9-induced depletion of Bag3 does not result in the abrogation of heart and skeletal muscle function in zebrafish embryos. We find here that transcriptional activation of the Bag family member bag2 is capable of restoring heart and skeletal muscle function in bag3 mutant embryos, whereas this compensatory mechanism is not present in the bag3 morphants. Furthermore, we show that nonsense-mediated decay of bag3 mRNA is the molecular trigger for the compensatory upregulation of bag2. Our study provides evidence that genetic compensation via transcriptional adaptation is a vital modulator of disease peculiarity and penetrance in bag3 mutant zebrafish and that this biological phenomenon might also be active in certain human BAG3 mutation carriers.
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MESH Headings
- Adaptor Proteins, Signal Transducing/deficiency
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Animals
- Apoptosis/genetics
- Apoptosis Regulatory Proteins/deficiency
- Apoptosis Regulatory Proteins/genetics
- Apoptosis Regulatory Proteins/metabolism
- Cardiomyopathies/genetics
- Cardiomyopathies/metabolism
- Cardiomyopathies/pathology
- Cardiomyopathy, Dilated/genetics
- Cardiomyopathy, Dilated/metabolism
- Cardiomyopathy, Dilated/pathology
- Disease Models, Animal
- Heart Failure/genetics
- Heart Failure/metabolism
- Heart Failure/pathology
- Molecular Chaperones/genetics
- Molecular Chaperones/metabolism
- Muscle Fibers, Skeletal/metabolism
- Muscular Diseases/genetics
- Muscular Diseases/metabolism
- Muscular Diseases/pathology
- Mutation
- Myocardium/metabolism
- Myopathies, Structural, Congenital/metabolism
- Phenotype
- Proteomics
- Zebrafish
- Zebrafish Proteins/deficiency
- Zebrafish Proteins/genetics
- Zebrafish Proteins/metabolism
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Affiliation(s)
- Federica Diofano
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Karolina Weinmann
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
- Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Isabelle Schneider
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Kevin D. Thiessen
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | | | - Steffen Just
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
- * E-mail:
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76
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Mollard E, Hatton-Bowers H, Tippens J. Finding Strength in Vulnerability: Ethical Approaches when Conducting Research with Vulnerable Populations. J Midwifery Womens Health 2020; 65:802-807. [PMID: 32881276 DOI: 10.1111/jmwh.13151] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/28/2020] [Accepted: 06/09/2020] [Indexed: 11/30/2022]
Abstract
Researchers who desire to make positive changes for vulnerable populations often conduct problem-focused studies. Although problem-focused research is important, when such studies are not carefully designed, their results can contribute to a deficit discourse. A deficit discourse is a narrative that describes the person through a myopic lens of negativity characterized only by illness, death, depression, failure, or the like. Deficit discourse negatively affects how health care providers and society interact with vulnerable people. This article discusses deficit discourse in health care and strengths-based research: an ethical approach to working with vulnerable individuals in research settings and a strategy to overcome deficit discourse. Strengths-based research approaches balance risks with countermeasures that include areas that are positive and amenable to growth or intervention. Strengths-based research can be conducted using qualitative, quantitative, or mixed-methods methodology. Strengths-based research should be culturally relevant and population-specific, often including the individuals of study throughout the process. By modifying the research approach, critical problems can be identified and addressed while also emphasizing positive ways to empower individuals and improve their lives. Additionally, these changes better the way researchers and health care providers view and care for people while also challenging deficit discourses in society at large.
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Affiliation(s)
- Elizabeth Mollard
- College of Nursing - Lincoln Division, University of Nebraska Medical Center, Lincoln, Nebraska
| | - Holly Hatton-Bowers
- College of Education and Human Sciences, University of Nebraska, Lincoln, Nebraska
| | - Julie Tippens
- College of Education and Human Sciences, University of Nebraska, Lincoln, Nebraska
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77
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Sztal TE, Stainier DYR. Transcriptional adaptation: a mechanism underlying genetic robustness. Development 2020; 147:147/15/dev186452. [PMID: 32816903 DOI: 10.1242/dev.186452] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Mutations play a crucial role in evolution as they provide the genetic variation that allows evolutionary change. Although some mutations in regulatory elements or coding regions can be beneficial, a large number of them disrupt gene function and reduce fitness. Organisms utilize several mechanisms to compensate for the damaging consequences of genetic perturbations. One such mechanism is the recently identified process of transcriptional adaptation (TA): during this event, mutations that cause mutant mRNA degradation trigger the transcriptional modulation of so-called adapting genes. In some cases, for example when one (or more) of the upregulated genes is functionally redundant with the mutated gene, this process compensates for the loss of the mutated gene's product. Notably, unlike other mechanisms underlying genetic robustness, TA is not triggered by the loss of protein function, an observation that has prompted studies into the machinery of TA and the contexts in which it functions. Here, we review the discovery and current understanding of TA, and discuss how its main features appear to be conserved across species. In light of these findings, we also speculate on the importance of TA in the context of human disease, and provide some recommendations for genome-editing strategies that should be more effective.
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Affiliation(s)
- Tamar E Sztal
- School of Biological Sciences, Monash University, Melbourne 3800, Australia
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Ludwigstrasse 43, Bad Nauheim 61231, Germany
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78
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Hennekam RCM. Pathophysiology of premature aging characteristics in Mendelian progeroid disorders. Eur J Med Genet 2020; 63:104028. [PMID: 32791128 DOI: 10.1016/j.ejmg.2020.104028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 12/15/2022]
Abstract
Aging is a physiological process that is in part genetically determined. Some of the signs and symptoms of aging also occur prematurely in Mendelian disorders. Such disorders are excellent sources of information of underlying mechanisms for these components of aging, and studying these may allow detection of pathways that have not yet considered in detail in physiological aging. Here I define the clinical characteristics that constitute aging and propose that at least 40% of aging signs and symptoms should be present before an entity should be tagged as progeroid. A literature search using these characteristics yields 17 entities that fulfill this definition: Hutchinson-Gilford progeria, mandibulo-acral dysplasia, Nestor-Guillermo progeria, Werner syndrome, Cockayne syndrome, cutis laxa progeroid, Penttinen progeroid syndrome, Mandibular underdevelopment, Deafness, Progeroid features, Lipodystrophy, Fontaine progeroid syndrome, SHORT syndrome, Wiedemann-Rautenstrauch syndrome, Mulvihill-Smith syndrome, dyskeratosis congenita, Marfan syndrome lipodystrophy type, Warburg-Cinotti syndrome, Lessel syndrome and Bloom syndrome. The presenting and main characteristics of these entities are indicated briefly. Their pathophysiology is not complete pathophysiology is reviewed but only the pathophysiology of the premature aging characteristics of this series of entities is compared to the known mechanisms ("Hallmarks") of physiological aging as summarized in the review paper by Lopez-Otin and colleagues. Although many causative genes have not been studied fully for all known aging mechanisms the comparison demonstrates that additional mechanisms must play a role to explain the aging characteristic in some of the progeroid entities of the progeroid entities, and possibly also in physiological aging.
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Affiliation(s)
- Raoul C M Hennekam
- Department of Paediatrics, Room H7-236, Amsterdam UMC - location AMC, Meibergdreef 9, 1105AZ, Amsterdam, the Netherlands.
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79
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Easteal S, Arkell RM, Balboa RF, Bellingham SA, Brown AD, Calma T, Cook MC, Davis M, Dawkins HJS, Dinger ME, Dobbie MS, Farlow A, Gwynne KG, Hermes A, Hoy WE, Jenkins MR, Jiang SH, Kaplan W, Leslie S, Llamas B, Mann GJ, McMorran BJ, McWhirter RE, Meldrum CJ, Nagaraj SH, Newman SJ, Nunn JS, Ormond-Parker L, Orr NJ, Paliwal D, Patel HR, Pearson G, Pratt GR, Rambaldini B, Russell LW, Savarirayan R, Silcocks M, Skinner JC, Souilmi Y, Vinuesa CG, Baynam G. Equitable Expanded Carrier Screening Needs Indigenous Clinical and Population Genomic Data. Am J Hum Genet 2020; 107:175-182. [PMID: 32763188 PMCID: PMC7413856 DOI: 10.1016/j.ajhg.2020.06.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Expanded carrier screening (ECS) for recessive monogenic diseases requires prior knowledge of genomic variation, including DNA variants that cause disease. The composition of pathogenic variants differs greatly among human populations, but historically, research about monogenic diseases has focused mainly on people with European ancestry. By comparison, less is known about pathogenic DNA variants in people from other parts of the world. Consequently, inclusion of currently underrepresented Indigenous and other minority population groups in genomic research is essential to enable equitable outcomes in ECS and other areas of genomic medicine. Here, we discuss this issue in relation to the implementation of ECS in Australia, which is currently being evaluated as part of the national Government's Genomics Health Futures Mission. We argue that significant effort is required to build an evidence base and genomic reference data so that ECS can bring significant clinical benefit for many Aboriginal and/or Torres Strait Islander Australians. These efforts are essential steps to achieving the Australian Government's objectives and its commitment "to leveraging the benefits of genomics in the health system for all Australians." They require culturally safe, community-led research and community involvement embedded within national health and medical genomics programs to ensure that new knowledge is integrated into medicine and health services in ways that address the specific and articulated cultural and health needs of Indigenous people. Until this occurs, people who do not have European ancestry are at risk of being, in relative terms, further disadvantaged.
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Affiliation(s)
- Simon Easteal
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia.
| | - Ruth M Arkell
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Renzo F Balboa
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia
| | - Shayne A Bellingham
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia
| | - Alex D Brown
- Aboriginal Health Equity, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia; Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Tom Calma
- Poche Centre for Indigenous Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Matthew C Cook
- Department of Immunology, Canberra Hospital, Canberra, ACT 2606, Australia
| | - Megan Davis
- UNSW Law, University of New South Wales, Sydney, NSW 2052, Australia
| | - Hugh J S Dawkins
- HBF Health Limited, Perth, WA 6000, Australia; School of Medicine, The University of Notre Dame Australia, Sydney, NSW 2010, Australia; Sir Walter Murdoch School of Policy and International Affairs, Murdoch University, Murdoch, WA 6150, Australia; Division of Genetics, School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6008, Australia; Centre for Population Health Research, Curtin University of Technology, Bentley, WA 6102, Australia
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Michael S Dobbie
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia; John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Ashley Farlow
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia; Melbourne Integrative Genomics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kylie G Gwynne
- Poche Centre for Indigenous Health, University of Sydney, Sydney, NSW 2006, Australia; Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2113, Australia
| | - Azure Hermes
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia
| | - Wendy E Hoy
- Faculty of Medicine, University of Queensland, Brisbane, QLD 4072, Australia
| | - Misty R Jenkins
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; La Trobe Institute of Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Simon H Jiang
- Department of Immunology, Canberra Hospital, Canberra, ACT 2606, Australia
| | - Warren Kaplan
- Informatics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Stephen Leslie
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia; Melbourne Integrative Genomics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Bastien Llamas
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia; Centre of Excellence in Australian Biodiversity and Heritage, School of Biological Sciences, The Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Graham J Mann
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Brendan J McMorran
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Rebekah E McWhirter
- Centre for Law and Genetics, Faculty of Law, University of Tasmania, Hobart, TAS 7001, Australia
| | | | - Shivashankar H Nagaraj
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Saul J Newman
- Biological Data Science Institute, Australian National University, Canberra, ACT 2600, Australia
| | - Jack S Nunn
- Public Health, La Trobe University, Melbourne, VIC 3086, Australia
| | - Lyndon Ormond-Parker
- Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Neil J Orr
- Poche Centre for Indigenous Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Devashi Paliwal
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia; John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Hardip R Patel
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia
| | - Glenn Pearson
- Aboriginal Health, Telethon Kids Institute, Perth, WA 6009, Australia
| | - Greg R Pratt
- Aboriginal and Torres Strait Islander Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Boe Rambaldini
- Poche Centre for Indigenous Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Lynette W Russell
- Centre of Excellence in Australian Biodiversity and Heritage, Monash Indigenous Studies Centre, Monash University, Melbourne, VIC 3800, Australia
| | - Ravi Savarirayan
- Victorian Clinical Genetic Services, Murdoch Children's Research Institute, and University of Melbourne, Parkville, VIC 3052, Australia
| | - Matthew Silcocks
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia; Melbourne Integrative Genomics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - John C Skinner
- Poche Centre for Indigenous Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Yassine Souilmi
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia; School of Biological Sciences, The Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Carola G Vinuesa
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Gareth Baynam
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA 6004, Australia; The Western Australian Register of Developmental Anomalies, Department of Health, Government of Western Australia, Perth, WA 6004, Australia; School of Medicine, Division of Paediatrics and Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia.
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80
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Du LL. Resurrection from lethal knockouts: Bypass of gene essentiality. Biochem Biophys Res Commun 2020; 528:405-412. [PMID: 32507598 DOI: 10.1016/j.bbrc.2020.05.207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 01/03/2023]
Abstract
Understanding genotype-phenotype relationships is a central pursuit in biology. Gene knockout generates a complete loss-of-function genotype and is a commonly used approach for probing gene functions. The most severe phenotypic consequence of gene knockout is lethality. Genes with a lethal knockout phenotype are called essential genes. Based on genome-wide knockout analyses in yeasts, up to approximately a quarter of genes in a genome can be essential. Like other genotype-phenotype relationships, gene essentiality is subject to background effects and can vary due to gene-gene interactions. In particular, for some essential genes, lethality caused by knockout can be rescued by extragenic suppressors. Such "bypass of essentiality" (BOE) gene-gene interactions have been an understudied type of genetic suppression. A recent systematic analysis revealed that, remarkably, the essentiality of nearly 30% of essential genes in the fission yeast Schizosaccharomyces pombe can be bypassed by BOE interactions. Here, I review the history and recent progress on uncovering and understanding the bypass of gene essentiality.
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Affiliation(s)
- Li-Lin Du
- National Institute of Biological Sciences, Beijing, 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China.
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81
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Leopold JA, Maron BA, Loscalzo J. The application of big data to cardiovascular disease: paths to precision medicine. J Clin Invest 2020; 130:29-38. [PMID: 31895052 DOI: 10.1172/jci129203] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Advanced phenotyping of cardiovascular diseases has evolved with the application of high-resolution omics screening to populations enrolled in large-scale observational and clinical trials. This strategy has revealed that considerable heterogeneity exists at the genotype, endophenotype, and clinical phenotype levels in cardiovascular diseases, a feature of the most common diseases that has not been elucidated by conventional reductionism. In this discussion, we address genomic context and (endo)phenotypic heterogeneity, and examine commonly encountered cardiovascular diseases to illustrate the genotypic underpinnings of (endo)phenotypic diversity. We highlight the existing challenges in cardiovascular disease genotyping and phenotyping that can be addressed by the integration of big data and interpreted using novel analytical methodologies (network analysis). Precision cardiovascular medicine will only be broadly applied to cardiovascular patients once this comprehensive data set is subjected to unique, integrative analytical strategies that accommodate molecular and clinical heterogeneity rather than ignore or reduce it.
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82
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Cody JD. The Consequences of Abnormal Gene Dosage: Lessons from Chromosome 18. Trends Genet 2020; 36:764-776. [PMID: 32660784 DOI: 10.1016/j.tig.2020.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/18/2022]
Abstract
Accurate interpretation of genomic copy number variation (CNV) remains a challenge and has important consequences for both congenital and late-onset disease. Hemizygosity dosage characterization of the genes on chromosome 18 reveals a spectrum of outcomes ranging from no clinical effect, to risk factors for disease, to both low- and high-penetrance disease. These data are important for accurate and predictive clinical management. Additionally, the potential mechanisms of reduced penetrance due to dosage compensation are discussed as a key to understanding avenues for potential treatment. This review describes the chromosome 18 findings, and discusses the molecular mechanisms that allow haploinsufficiency, reduced penetrance, and dosage compensation.
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Affiliation(s)
- Jannine DeMars Cody
- Department of Pediatrics, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Chromosome 18 Registry and Research Society, San Antonio, TX 78229, USA.
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83
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Genç Ö, An JY, Fetter RD, Kulik Y, Zunino G, Sanders SJ, Davis GW. Homeostatic plasticity fails at the intersection of autism-gene mutations and a novel class of common genetic modifiers. eLife 2020; 9:55775. [PMID: 32609087 PMCID: PMC7394548 DOI: 10.7554/elife.55775] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/07/2020] [Indexed: 01/08/2023] Open
Abstract
We identify a set of common phenotypic modifiers that interact with five independent autism gene orthologs (RIMS1, CHD8, CHD2, WDFY3, ASH1L) causing a common failure of presynaptic homeostatic plasticity (PHP) in Drosophila. Heterozygous null mutations in each autism gene are demonstrated to have normal baseline neurotransmission and PHP. However, PHP is sensitized and rendered prone to failure. A subsequent electrophysiology-based genetic screen identifies the first known heterozygous mutations that commonly genetically interact with multiple ASD gene orthologs, causing PHP to fail. Two phenotypic modifiers identified in the screen, PDPK1 and PPP2R5D, are characterized. Finally, transcriptomic, ultrastructural and electrophysiological analyses define one mechanism by which PHP fails; an unexpected, maladaptive up-regulation of CREG, a conserved, neuronally expressed, stress response gene and a novel repressor of PHP. Thus, we define a novel genetic landscape by which diverse, unrelated autism risk genes may converge to commonly affect the robustness of synaptic transmission.
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Affiliation(s)
- Özgür Genç
- Department of Biochemistry and Biophysics Kavli Institute for Fundamental Neuroscience University of California, San Francisco, San Francisco, United States
| | - Joon-Yong An
- Department of Psychiatry UCSF Weill Institute for Neurosciences University of California, San Francisco, San Francisco, United States.,School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Republic of Korea
| | - Richard D Fetter
- Department of Biochemistry and Biophysics Kavli Institute for Fundamental Neuroscience University of California, San Francisco, San Francisco, United States
| | - Yelena Kulik
- Department of Biochemistry and Biophysics Kavli Institute for Fundamental Neuroscience University of California, San Francisco, San Francisco, United States
| | - Giulia Zunino
- Department of Biochemistry and Biophysics Kavli Institute for Fundamental Neuroscience University of California, San Francisco, San Francisco, United States
| | - Stephan J Sanders
- Department of Psychiatry UCSF Weill Institute for Neurosciences University of California, San Francisco, San Francisco, United States
| | - Graeme W Davis
- Department of Biochemistry and Biophysics Kavli Institute for Fundamental Neuroscience University of California, San Francisco, San Francisco, United States
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84
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Chami N, Preuss M, Walker RW, Moscati A, Loos RJF. The role of polygenic susceptibility to obesity among carriers of pathogenic mutations in MC4R in the UK Biobank population. PLoS Med 2020; 17:e1003196. [PMID: 32692746 PMCID: PMC7373259 DOI: 10.1371/journal.pmed.1003196] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 06/16/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Melanocortin 4 receptor (MC4R) deficiency, caused by mutations in MC4R, is the most common cause of monogenic forms of obesity. However, these mutations have often been identified in small-scale, case-focused studies. Here, we assess the penetrance of previously reported MC4R mutations at a population level. Furthermore, we examine why some carriers of pathogenic mutations remain of normal weight, to gain insight into the mechanisms that control body weight. METHODS AND FINDINGS We identified 59 known obesity-increasing mutations in MC4R from the Human Gene Mutation Database (HGMD) and Clinvar. We assessed their penetrance and effect on obesity (body mass index [BMI] ≥ 30 kg/m2) in >450,000 individuals (age 40-69 years) of the UK Biobank, a population-based cohort study. Of these 59 mutations, only 11 had moderate-to-high penetrance and increased the odds of obesity by more than 2-fold. We subsequently focused on these 11 mutations and examined differences between carriers of normal weight and carriers with obesity. Twenty-eight of the 182 carriers of these 11 mutations were of normal weight. Body composition of carriers of normal weight was similar to noncarriers of normal weight, whereas among individuals with obesity, carriers had a somewhat higher BMI than noncarriers (1.44 ± 0.07 standard deviation scores [SDSs] ± standard error [SE] versus 1.29 ± 0.001, P = 0.03), because of greater lean mass (1.44 ± 0.09 versus 1.15 ± 0.002, P = 0.002). Carriers of normal weight more often reported that, already at age 10 years, their body size was below average or average (72%) compared with carriers with obesity (48%) (P = 0.01). To assess the polygenic contribution to body weight in carriers of normal weight and carriers with obesity, we calculated a genome-wide polygenic risk score for BMI (PRSBMI). The PRSBMI of carriers of normal weight (PRSBMI = -0.64 ± 0.18) was significantly lower than of carriers with obesity (0.40 ± 0.11; P = 1.7 × 10-6), and tended to be lower than that of noncarriers of normal weight (-0.29 ± 0.003; P = 0.05). Among carriers, those with a low PRSBMI (bottom quartile) have an approximately 5-kg/m2 lower BMI (approximately 14 kg of body weight for a 1.7-m-tall person) than those with a high PRS (top quartile). Because the UK Biobank population is healthier than the general population in the United Kingdom, penetrance may have been somewhat underestimated. CONCLUSIONS We showed that large-scale data are needed to validate the impact of mutations observed in small-scale and case-focused studies. Furthermore, we observed that despite the key role of MC4R in obesity, the effects of pathogenic MC4R mutations may be countered, at least in part, by a low polygenic risk potentially representing other innate mechanisms implicated in body weight regulation.
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Affiliation(s)
- Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Michael Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ryan W. Walker
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Arden Moscati
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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85
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Qu B, Wu S, Jiao G, Zou X, Li Z, Guo L, Sun X, Huang C, Sun Z, Zhang Y, Li H, Zhou Q, Sui R, Li W. Treating Bietti crystalline dystrophy in a high-fat diet-exacerbated murine model using gene therapy. Gene Ther 2020; 27:370-382. [PMID: 32483213 DOI: 10.1038/s41434-020-0159-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/12/2020] [Accepted: 05/19/2020] [Indexed: 11/09/2022]
Abstract
Lipid metabolic deficiencies are associated with many genetic disorders. Bietti crystalline dystrophy (BCD), a blindness-causing inherited disorder with changed lipid profiles, is more common in Chinese and Japanese than other populations. Our results reveal that mouse models lacking Cyp4v3 have less physiological and functional changes than those of BCD patients with this gene defect. After the administration of a high-fat diet (HFD), the occurrence of retinal lesions were both accelerated and aggregated in the Cyp4v3-/- mouse models, implying that changed lipid levels were not only associated factors but also risk factors to BCD patients. Facilitated by the results, we found that the reduced electroretinography waveforms and retinal thickness observed in the HFD-induced mouse models were effectively recovered after subretinal delivery of a human CYP4V2 gene carried by an adeno-associated virus vector, which demonstrates the potential curability of BCD by gene therapy.
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Affiliation(s)
- Bin Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shijing Wu
- Department of Ophthalmology, Peking Union Medical College Hospital, Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.,Key Laboratory of Ocular Fundus Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Guanyi Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuan Zou
- Department of Ophthalmology, Peking Union Medical College Hospital, Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.,Key Laboratory of Ocular Fundus Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Zhikun Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lu Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuehan Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng Huang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zixi Sun
- Department of Ophthalmology, Peking Union Medical College Hospital, Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.,Key Laboratory of Ocular Fundus Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hui Li
- Department of Ophthalmology, Peking Union Medical College Hospital, Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.,Key Laboratory of Ocular Fundus Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China. .,Key Laboratory of Ocular Fundus Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
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86
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Kroncke BM, Smith DK, Zuo Y, Glazer AM, Roden DM, Blume JD. A Bayesian method to estimate variant-induced disease penetrance. PLoS Genet 2020; 16:e1008862. [PMID: 32569262 PMCID: PMC7347235 DOI: 10.1371/journal.pgen.1008862] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 07/09/2020] [Accepted: 05/14/2020] [Indexed: 01/09/2023] Open
Abstract
A major challenge emerging in genomic medicine is how to assess best disease risk from rare or novel variants found in disease-related genes. The expanding volume of data generated by very large phenotyping efforts coupled to DNA sequence data presents an opportunity to reinterpret genetic liability of disease risk. Here we propose a framework to estimate the probability of disease given the presence of a genetic variant conditioned on features of that variant. We refer to this as the penetrance, the fraction of all variant heterozygotes that will present with disease. We demonstrate this methodology using a well-established disease-gene pair, the cardiac sodium channel gene SCN5A and the heart arrhythmia Brugada syndrome. From a review of 756 publications, we developed a pattern mixture algorithm, based on a Bayesian Beta-Binomial model, to generate SCN5A penetrance probabilities for the Brugada syndrome conditioned on variant-specific attributes. These probabilities are determined from variant-specific features (e.g. function, structural context, and sequence conservation) and from observations of affected and unaffected heterozygotes. Variant functional perturbation and structural context prove most predictive of Brugada syndrome penetrance.
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Affiliation(s)
- Brett M. Kroncke
- Department of Medicine Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Pharmacology Vanderbilt University, Nashville, Tennessee, United States of America
| | - Derek K. Smith
- Department of Biostatistics Vanderbilt University, Nashville, Tennessee, United States of America
| | - Yi Zuo
- Department of Biostatistics Vanderbilt University, Nashville, Tennessee, United States of America
| | - Andrew M. Glazer
- Department of Medicine Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Dan M. Roden
- Department of Medicine Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Pharmacology Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biomedical Informatics Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jeffrey D. Blume
- Department of Biostatistics Vanderbilt University, Nashville, Tennessee, United States of America
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87
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Presynaptic Homeostasis Opposes Disease Progression in Mouse Models of ALS-Like Degeneration: Evidence for Homeostatic Neuroprotection. Neuron 2020; 107:95-111.e6. [PMID: 32380032 DOI: 10.1016/j.neuron.2020.04.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/06/2020] [Accepted: 04/06/2020] [Indexed: 12/11/2022]
Abstract
Progressive synapse loss is an inevitable and insidious part of age-related neurodegenerative disease. Typically, synapse loss precedes symptoms of cognitive and motor decline. This suggests the existence of compensatory mechanisms that can temporarily counteract the effects of ongoing neurodegeneration. Here, we demonstrate that presynaptic homeostatic plasticity (PHP) is induced at degenerating neuromuscular junctions, mediated by an evolutionarily conserved activity of presynaptic ENaC channels in both Drosophila and mouse. To assess the consequence of eliminating PHP in a mouse model of ALS-like degeneration, we generated a motoneuron-specific deletion of Scnn1a, encoding the ENaC channel alpha subunit. We show that Scnn1a is essential for PHP without adversely affecting baseline neural function or lifespan. However, Scnn1a knockout in a degeneration-causing mutant background accelerated motoneuron loss and disease progression to twice the rate observed in littermate controls with intact PHP. We propose a model of neuroprotective homeostatic plasticity, extending organismal lifespan and health span.
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88
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Ohnmacht J, May P, Sinkkonen L, Krüger R. Missing heritability in Parkinson's disease: the emerging role of non-coding genetic variation. J Neural Transm (Vienna) 2020; 127:729-748. [PMID: 32248367 PMCID: PMC7242266 DOI: 10.1007/s00702-020-02184-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/24/2020] [Indexed: 02/01/2023]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder caused by a complex interplay of genetic and environmental factors. For the stratification of PD patients and the development of advanced clinical trials, including causative treatments, a better understanding of the underlying genetic architecture of PD is required. Despite substantial efforts, genome-wide association studies have not been able to explain most of the observed heritability. The majority of PD-associated genetic variants are located in non-coding regions of the genome. A systematic assessment of their functional role is hampered by our incomplete understanding of genotype-phenotype correlations, for example through differential regulation of gene expression. Here, the recent progress and remaining challenges for the elucidation of the role of non-coding genetic variants is reviewed with a focus on PD as a complex disease with multifactorial origins. The function of gene regulatory elements and the impact of non-coding variants on them, and the means to map these elements on a genome-wide level, will be delineated. Moreover, examples of how the integration of functional genomic annotations can serve to identify disease-associated pathways and to prioritize disease- and cell type-specific regulatory variants will be given. Finally, strategies for functional validation and considerations for suitable model systems are outlined. Together this emphasizes the contribution of rare and common genetic variants to the complex pathogenesis of PD and points to remaining challenges for the dissection of genetic complexity that may allow for better stratification, improved diagnostics and more targeted treatments for PD in the future.
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Affiliation(s)
- Jochen Ohnmacht
- LCSB, University of Luxembourg, Belvaux, Luxembourg
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Patrick May
- LCSB, University of Luxembourg, Belvaux, Luxembourg
| | - Lasse Sinkkonen
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Rejko Krüger
- LCSB, University of Luxembourg, Belvaux, Luxembourg.
- Luxembourg Institute of Health (LIH), Transversal Translational Medicine, Strassen, Luxembourg.
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg.
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89
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Turner H, Jackson L. Evidence for penetrance in patients without a family history of disease: a systematic review. Eur J Hum Genet 2020; 28:539-550. [PMID: 31937893 PMCID: PMC7170932 DOI: 10.1038/s41431-019-0556-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 10/08/2019] [Accepted: 11/26/2019] [Indexed: 01/21/2023] Open
Abstract
Family-based penetrance is frequently cited as a major challenge for translating penetrance estimates from familial populations to asymptomatic populations. A systematic review was performed to assess the literature evidencing penetrance estimates in patients without a family history of disease, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) framework. Initially 1592 papers were identified, which were filtered to a final nine, through application of inclusion and exclusion criteria. Fundamental differences in the identified papers prevented combination of papers using meta-analysis, so thematic analysis to produce a narrative synthesis was performed. Key themes included disease risk modifiers, evidence, study limitations and bias. A methodological appraisal too was used to assess quality of included studies. It is evident from the findings that the evidence base for penetrance estimates in individuals without a family history of disease is limited. Future work is needed to refine design of penetrance studies and the impact of incorrect estimates.
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Affiliation(s)
- Heather Turner
- University of Exeter Medical School, 4.07 RILD, Royal Devon & Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK
| | - Leigh Jackson
- University of Exeter Medical School, 4.07 RILD, Royal Devon & Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK.
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90
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Mutai H, Wasano K, Momozawa Y, Kamatani Y, Miya F, Masuda S, Morimoto N, Nara K, Takahashi S, Tsunoda T, Homma K, Kubo M, Matsunaga T. Variants encoding a restricted carboxy-terminal domain of SLC12A2 cause hereditary hearing loss in humans. PLoS Genet 2020; 16:e1008643. [PMID: 32294086 PMCID: PMC7159186 DOI: 10.1371/journal.pgen.1008643] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 01/31/2020] [Indexed: 02/07/2023] Open
Abstract
Hereditary hearing loss is challenging to diagnose because of the heterogeneity of the causative genes. Further, some genes involved in hereditary hearing loss have yet to be identified. Using whole-exome analysis of three families with congenital, severe-to-profound hearing loss, we identified a missense variant of SLC12A2 in five affected members of one family showing a dominant inheritance mode, along with de novo splice-site and missense variants of SLC12A2 in two sporadic cases, as promising candidates associated with hearing loss. Furthermore, we detected another de novo missense variant of SLC12A2 in a sporadic case. SLC12A2 encodes Na+, K+, 2Cl− cotransporter (NKCC) 1 and plays critical roles in the homeostasis of K+-enriched endolymph. Slc12a2-deficient mice have congenital, profound deafness; however, no human variant of SLC12A2 has been reported as associated with hearing loss. All identified SLC12A2 variants mapped to exon 21 or its 3’-splice site. In vitro analysis indicated that the splice-site variant generates an exon 21-skipped SLC12A2 mRNA transcript expressed at much lower levels than the exon 21-included transcript in the cochlea, suggesting a tissue-specific role for the exon 21-encoded region in the carboy-terminal domain. In vitro functional analysis demonstrated that Cl− influx was significantly decreased in all SLC12A2 variants studied. Immunohistochemistry revealed that SLC12A2 is located on the plasma membrane of several types of cells in the cochlea, including the strial marginal cells, which are critical for endolymph homeostasis. Overall, this study suggests that variants affecting exon 21 of the SLC12A2 transcript are responsible for hereditary hearing loss in humans. Sounds are perceived by auditory sensory cells, owing to tissues surrounding them, including the cochlear lateral wall. Part of the cochlear lateral wall, the stria vascularis, is critical for production and maintenance of inner-ear fluid with a high potassium concentration, and for generating the positive voltage in the inner ear, important for sound perception, by stimulating secretion of potassium from marginal cells. The gene SLC12A2 encodes a protein involved in sodium, potassium, and chloride transport essential for proper function of specific cells in the stria vascularis; however, human variants of SLC12A2 have not previously been associated with hearing loss. By comprehensive genetic analysis of protein-coding sequences, we identified four candidate changes in SLC12A2 in four families with congenital, severe-to-profound hearing loss. Intriguingly, all four genetic variants were either within or at the 3’-splice site of the exon 21 which encodes a part of the carboxy terminal intracellular domain of SLC12A2. Experiments in cultured cells showed that skipping or mutation of exon 21 significantly decreased chloride influx mediated by the SLC12A2 protein. Overall, our results strongly indicate that mutations influencing exon 21 of SLC12A2 represent a novel mechanism underlying deafness in humans.
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Affiliation(s)
- Hideki Mutai
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Meguro, Tokyo, Japan
| | - Koichiro Wasano
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Meguro, Tokyo, Japan
- Department of Otolaryngology-Head and Neck Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshidakonoecho, Kyoto, Japan
| | - Fuyuki Miya
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Sawako Masuda
- Department of Otorhinolaryngology, National Hospital Organization Mie National Hospital, Tsu, Mie, Japan
| | - Noriko Morimoto
- Department of Otorhinolaryngology, National Center for Child Health and Development, Setagaya, Tokyo, Japan
| | - Kiyomitsu Nara
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Meguro, Tokyo, Japan
| | - Satoe Takahashi
- Department of Otolaryngology-Head and Neck Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Tatsuhiko Tsunoda
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
- Laboratory for Medical Science Mathematics, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Kazuaki Homma
- Department of Otolaryngology-Head and Neck Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- The Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders, Northwestern University, Evanston, Illinois, United States of America
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Tatsuo Matsunaga
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Meguro, Tokyo, Japan
- Medical Genetics Center, National Hospital Organization Tokyo Medical Center, Meguro, Tokyo, Japan
- * E-mail:
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91
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Dillard KJ, Ochs M, Niskanen JE, Arumilli M, Donner J, Kyöstilä K, Hytönen MK, Anttila M, Lohi H. Recessive missense LAMP3 variant associated with defect in lamellar body biogenesis and fatal neonatal interstitial lung disease in dogs. PLoS Genet 2020; 16:e1008651. [PMID: 32150563 PMCID: PMC7082050 DOI: 10.1371/journal.pgen.1008651] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 03/19/2020] [Accepted: 02/04/2020] [Indexed: 01/06/2023] Open
Abstract
Neonatal interstitial lung diseases due to abnormal surfactant biogenesis are rare in humans and have never been reported as a spontaneous disorder in animals. We describe here a novel lung disorder in Airedale Terrier (AT) dogs with clinical symptoms and pathology similar to the most severe neonatal forms of human surfactant deficiency. Lethal hypoxic respiratory distress and failure occurred within the first days or weeks of life in the affected puppies. Transmission electron microscopy of the affected lungs revealed maturation arrest in the formation of lamellar bodies (LBs) in the alveolar epithelial type II (AECII) cells. The secretory organelles were small and contained fewer lamellae, often in combination with small vesicles surrounded by an occasionally disrupted common limiting membrane. A combined approach of genome-wide association study and whole exome sequencing identified a recessive variant, c.1159G>A, p.(E387K), in LAMP3, a limiting membrane protein of the cytoplasmic surfactant organelles in AECII cells. The substitution resides in the LAMP domain adjacent to a conserved disulfide bond. In summary, this study describes a novel interstitial lung disease in dogs, identifies a new candidate gene for human surfactant dysfunction and brings important insights into the essential role of LAMP3 in the process of the LB formation.
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Affiliation(s)
- Kati J. Dillard
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Veterinary Bacteriology and Pathology Research Unit, Finnish Food Authority, Helsinki, Finland
| | - Matthias Ochs
- Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany
- Institute of Functional Anatomy, Charité - Universitaetsmedizin Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Berlin, Germany
| | - Julia E. Niskanen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Meharji Arumilli
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Jonas Donner
- Genoscoper Laboratories Ltd (Wisdom Health), Helsinki, Finland
| | - Kaisa Kyöstilä
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Marjo K. Hytönen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Marjukka Anttila
- Veterinary Bacteriology and Pathology Research Unit, Finnish Food Authority, Helsinki, Finland
| | - Hannes Lohi
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
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92
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Chia CY, Madrigal P, Denil SLIJ, Martinez I, Garcia-Bernardo J, El-Khairi R, Chhatriwala M, Shepherd MH, Hattersley AT, Dunn NR, Vallier L. GATA6 Cooperates with EOMES/SMAD2/3 to Deploy the Gene Regulatory Network Governing Human Definitive Endoderm and Pancreas Formation. Stem Cell Reports 2020; 12:57-70. [PMID: 30629940 PMCID: PMC6335596 DOI: 10.1016/j.stemcr.2018.12.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/09/2018] [Accepted: 12/10/2018] [Indexed: 12/17/2022] Open
Abstract
Heterozygous de novo mutations in GATA6 are the most frequent cause of pancreatic agenesis in humans. In mice, however, a similar phenotype requires the biallelic loss of Gata6 and its paralog Gata4. To elaborate the human-specific requirements for GATA6, we chose to model GATA6 loss in vitro by combining both gene-edited and patient-derived pluripotent stem cells (hPSCs) and directed differentiation toward β-like cells. We find that GATA6 heterozygous hPSCs show a modest reduction in definitive endoderm (DE) formation, while GATA6-null hPSCs fail to enter the DE lineage. Consistent with these results, genome-wide studies show that GATA6 binds and cooperates with EOMES/SMAD2/3 to regulate the expression of cardinal endoderm genes. The early deficit in DE is accompanied by a significant reduction in PDX1+ pancreatic progenitors and C-PEPTIDE+ β-like cells. Taken together, our data position GATA6 as a gatekeeper to early human, but not murine, pancreatic ontogeny.
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Affiliation(s)
- Crystal Y Chia
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK; Institute of Medical Biology, A(∗)STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Pedro Madrigal
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory for Regenerative Medicine, University of Cambridge, Cambridge, UK, and Department of Surgery, University of Cambridge, Cambridge, UK
| | - Simon L I J Denil
- Institute of Medical Biology, A(∗)STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Iker Martinez
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | | | | | - Maggie H Shepherd
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Level 3 RILD Building, Barrack Road, Exeter EX25DW, UK
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Level 3 RILD Building, Barrack Road, Exeter EX25DW, UK
| | - N Ray Dunn
- Institute of Medical Biology, A(∗)STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.
| | - Ludovic Vallier
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK; Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory for Regenerative Medicine, University of Cambridge, Cambridge, UK, and Department of Surgery, University of Cambridge, Cambridge, UK.
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93
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Rahit KMTH, Tarailo-Graovac M. Genetic Modifiers and Rare Mendelian Disease. Genes (Basel) 2020; 11:E239. [PMID: 32106447 PMCID: PMC7140819 DOI: 10.3390/genes11030239] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 02/21/2020] [Indexed: 12/11/2022] Open
Abstract
Despite advances in high-throughput sequencing that have revolutionized the discovery of gene defects in rare Mendelian diseases, there are still gaps in translating individual genome variation to observed phenotypic outcomes. While we continue to improve genomics approaches to identify primary disease-causing variants, it is evident that no genetic variant acts alone. In other words, some other variants in the genome (genetic modifiers) may alleviate (suppress) or exacerbate (enhance) the severity of the disease, resulting in the variability of phenotypic outcomes. Thus, to truly understand the disease, we need to consider how the disease-causing variants interact with the rest of the genome in an individual. Here, we review the current state-of-the-field in the identification of genetic modifiers in rare Mendelian diseases and discuss the potential for future approaches that could bridge the existing gap.
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Affiliation(s)
- K. M. Tahsin Hassan Rahit
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Maja Tarailo-Graovac
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
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94
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Comiskey DF, He H, Liyanarachchi S, Sheikh MS, Genutis LK, Hendrickson IV, Yu L, Brock PL, de la Chapelle A. Variants in LRRC34 reveal distinct mechanisms for predisposition to papillary thyroid carcinoma. J Med Genet 2020; 57:519-527. [PMID: 32051256 DOI: 10.1136/jmedgenet-2019-106554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/25/2019] [Accepted: 12/11/2019] [Indexed: 11/04/2022]
Abstract
BACKGROUND Papillary thyroid carcinoma (PTC) demonstrates high heritability and a low somatic mutation burden relative to other cancers. Therefore, the genetic risk predisposing to PTC is likely due to a combination of low penetrance variants. A recent genome-wide association study revealed the association of PTC with a missense variant, rs6793295, at 3q26 in a gene called Leucine Repeat Rich Containing 34 (LRRC34). METHODS We report the mechanisms of PTC risk at 3q26 using a combination of overexpression, mass spectroscopy, knockdown, transcriptome profiling, migration assays and genetic analysis. RESULTS We observed differential binding of wild-type and missense LRRC34 to RANBP1. Overexpression of missense LRRC34 reduced RanGTP levels and increased apoptosis. We also identified a second linkage disequilibrium (LD) block upstream of LRRC34 containing regulatory variants with allele-specific expression. Transcriptome profiling of LRRC34 knockdown cells showed changes in genes involved with cellular movement. LRRC34 knockdown reduced the migration of thyroid cancer cell lines. Lastly, we assessed the relative contribution of PTC risk from each locus using haplotype analysis. CONCLUSIONS Our study demonstrates two separate mechanisms, one in G protein signalling and the other in transcriptional control, dictating PTC risk at 3q26 using both biochemical and genetic techniques.
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Affiliation(s)
- Daniel Forrest Comiskey
- Cancer Biology and Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Huiling He
- Cancer Biology and Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Sandya Liyanarachchi
- Cancer Biology and Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Mehek S Sheikh
- Cancer Biology and Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Luke K Genutis
- Cancer Biology and Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Isabella V Hendrickson
- Cancer Biology and Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Lianbo Yu
- Center for Biostatistics, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Pamela L Brock
- Internal Medicine, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Albert de la Chapelle
- Cancer Biology and Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
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95
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Smith-Lemli-Opitz syndrome: what is the actual risk for couples carriers of the DHCR7:c.964-1G>C variant? Eur J Hum Genet 2020; 28:938-942. [PMID: 32055014 DOI: 10.1038/s41431-020-0577-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 11/28/2019] [Accepted: 01/22/2020] [Indexed: 11/09/2022] Open
Abstract
The founder variant DHCR7:c.964-1G>C causing autosomal recessive Smith-Lemli-Opitz (SLOS) was introduced into the Israeli preconception carrier program for Ashkenazi Jews in 2017 because of the high carrier frequency in this population (2.3%). Other disease-causing variants in DHCR7 are relatively rare in Israeli population. Discrepancy between the carrier frequency and disease prevalence raises the question of the actual risks for affected offspring for couples detected by the screening program. We performed a literature review of all relevant publications regarding homozygous DHCR7:c.964-1G>C fetuses/patients. We also collected clinical data about couples identified in the national screening program, including reproductive history. Out of 32 homozygous fetuses, six died in utero, 11 pregnancies were terminated during second trimester, and 15 children were born. All died between first days of life till 3 months of age. Reproductive history of SLOS-at-risk couples showed that after correction for ascertainment bias, out of 61 pregnancies, there was an absence of affected fetuses/children and an excess of miscarriages even if assumed that all the homozygous fetuses were miscarried. Out of these, eight families were Israelis, they had a total of one sick child, 21 healthy children, and 21 miscarriages. Our observations support the previous knowledge that homozygosity for c.964-1G>C in DHCR7 leads to a severe phenotype or early miscarriage. An unexpected observation was the excess of early miscarriages. This phenomenon is unclear and awaits further studies.
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96
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Underestimated Aspect of Mucopolysaccharidosis Pathogenesis: Global Changes in Cellular Processes Revealed by Transcriptomic Studies. Int J Mol Sci 2020; 21:ijms21041204. [PMID: 32054071 PMCID: PMC7072725 DOI: 10.3390/ijms21041204] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/31/2020] [Accepted: 02/07/2020] [Indexed: 12/13/2022] Open
Abstract
Mucopolysaccharidoses (MPS), a group of inherited metabolic disorders caused by deficiency in enzymes involved in degradation of glycosaminoglycans (GAGs), are examples (and models) of monogenic diseases. Accumulation of undegraded GAGs in lysosomes was supposed to be the major cause of MPS symptoms; however, their complexity and variability between particular types of the disease can be hardly explained by such a simple storage mechanism. Here we show that transcriptomic (RNA-seq) analysis of the material derived from fibroblasts of patients suffering from all types and subtypes of MPS, supported by RT-qPCR results, revealed surprisingly large changes in expression of genes involved in various cellular processes, indicating complex mechanisms of MPS. Although each MPS type and subtype was characterized by specific changes in gene expression profile, there were genes with significantly changed expression relative to wild-type cells that could be classified as common for various MPS types, suggesting similar disturbances in cellular processes. Therefore, both common features of all MPS types, and differences between them, might be potentially explained on the basis of changes in certain cellular processes arising from disturbed regulations of genes’ expression. These results may shed a new light on the mechanisms of genetic diseases, indicating how a single mutation can result in complex pathomechanism, due to perturbations in the network of cellular reactions. Moreover, they should be considered in studies on development of novel therapies, suggesting also why currently available treatment methods fail to correct all/most symptoms of MPS. We propose a hypothesis that disturbances in some cellular processes cannot be corrected by simple reduction of GAG levels; thus, combined therapies are necessary which may require improvement of these processes.
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97
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Green DJ, Sallah SR, Ellingford JM, Lovell SC, Sergouniotis PI. Variability in Gene Expression is Associated with Incomplete Penetrance in Inherited Eye Disorders. Genes (Basel) 2020; 11:genes11020179. [PMID: 32050448 PMCID: PMC7074066 DOI: 10.3390/genes11020179] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/29/2020] [Accepted: 02/06/2020] [Indexed: 12/21/2022] Open
Abstract
Inherited eye disorders (IED) are a heterogeneous group of Mendelian conditions that are associated with visual impairment. Although these disorders often exhibit incomplete penetrance and variable expressivity, the scale and mechanisms of these phenomena remain largely unknown. Here, we utilize publicly-available genomic and transcriptomic datasets to gain insights into variable penetrance in IED. Variants in a curated set of 340 IED-implicated genes were extracted from the Human Gene Mutation Database (HGMD) 2019.1 and cross-checked with the Genome Aggregation Database (gnomAD) 2.1 control-only dataset. Genes for which >1 variants were encountered in both HGMD and gnomAD were considered to be associated with variable penetrance (n = 56). Variability in gene expression levels was then estimated for the subset of these genes that was found to be adequately expressed in two relevant resources: the Genotype-Tissue Expression (GTEx) and Eye Genotype Expression (EyeGEx) datasets. We found that genes suspected to be associated with variable penetrance tended to have significantly more variability in gene expression levels in the general population (p = 0.0000015); this finding was consistent across tissue types. The results of this study point to the possible influence of cis and/or trans-acting elements on the expressivity of variants causing Mendelian disorders. They also highlight the potential utility of quantifying gene expression as part of the investigation of families showing evidence of variable penetrance.
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Affiliation(s)
- David J. Green
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester M13 9PT, UK; (D.J.G.); (S.R.S.); (J.M.E.); (S.C.L.)
| | - Shalaw R. Sallah
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester M13 9PT, UK; (D.J.G.); (S.R.S.); (J.M.E.); (S.C.L.)
| | - Jamie M. Ellingford
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester M13 9PT, UK; (D.J.G.); (S.R.S.); (J.M.E.); (S.C.L.)
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK
| | - Simon C. Lovell
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester M13 9PT, UK; (D.J.G.); (S.R.S.); (J.M.E.); (S.C.L.)
| | - Panagiotis I. Sergouniotis
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester M13 9PT, UK; (D.J.G.); (S.R.S.); (J.M.E.); (S.C.L.)
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK
- Correspondence: ; Tel.: +44-(0)161-27-55748
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Najafi A, Caspar SM, Meienberg J, Rohrbach M, Steinmann B, Matyas G. Variant filtering, digenic variants, and other challenges in clinical sequencing: a lesson from fibrillinopathies. Clin Genet 2020; 97:235-245. [PMID: 31506931 PMCID: PMC7004123 DOI: 10.1111/cge.13640] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/04/2019] [Accepted: 09/07/2019] [Indexed: 12/23/2022]
Abstract
Genome-scale high-throughput sequencing enables the detection of unprecedented numbers of sequence variants. Variant filtering and interpretation are facilitated by mutation databases, in silico tools, and population-based reference datasets such as ExAC/gnomAD, while variants are classified using the ACMG/AMP guidelines. These methods, however, pose clinically relevant challenges. We queried the gnomAD dataset for (likely) pathogenic variants in genes causing autosomal-dominant disorders. Furthermore, focusing on the fibrillinopathies Marfan syndrome (MFS) and congenital contractural arachnodactyly (CCA), we screened 500 genomes of our patients for co-occurring variants in FBN1 and FBN2. In gnomAD, we detected 2653 (likely) pathogenic variants in 253 genes associated with autosomal-dominant disorders, enabling the estimation of variant-filtering thresholds and disease predisposition/prevalence rates. In our database, we discovered two families with hitherto unreported co-occurrence of FBN1/FBN2 variants causing phenotypes with mixed or modified MFS/CCA clinical features. We show that (likely) pathogenic gnomAD variants may be more frequent than expected and are challenging to classify according to the ACMG/AMP guidelines as well as that fibrillinopathies are likely underdiagnosed and may co-occur. Consequently, selection of appropriate frequency cutoffs, recognition of digenic variants, and variant classification represent considerable challenges in variant interpretation. Neglecting these challenges may lead to incomplete or missed diagnoses.
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Affiliation(s)
- Arash Najafi
- Center for Cardiovascular Genetics and Gene DiagnosticsFoundation for People with Rare DiseasesSchlieren‐ZurichSwitzerland
- Cantonal Hospital WinterthurInstitute of Radiology and Nuclear MedicineWinterthurSwitzerland
| | - Sylvan M. Caspar
- Center for Cardiovascular Genetics and Gene DiagnosticsFoundation for People with Rare DiseasesSchlieren‐ZurichSwitzerland
| | - Janine Meienberg
- Center for Cardiovascular Genetics and Gene DiagnosticsFoundation for People with Rare DiseasesSchlieren‐ZurichSwitzerland
| | - Marianne Rohrbach
- Division of Metabolism and Children's Research CenterUniversity Children's Hospital Zurich Eleonore FoundationZurichSwitzerland
| | - Beat Steinmann
- Division of Metabolism and Children's Research CenterUniversity Children's Hospital Zurich Eleonore FoundationZurichSwitzerland
| | - Gabor Matyas
- Center for Cardiovascular Genetics and Gene DiagnosticsFoundation for People with Rare DiseasesSchlieren‐ZurichSwitzerland
- Zurich Center for Integrative Human PhysiologyUniversity of ZurichZurichSwitzerland
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99
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Pinese M, Lacaze P, Rath EM, Stone A, Brion MJ, Ameur A, Nagpal S, Puttick C, Husson S, Degrave D, Cristina TN, Kahl VFS, Statham AL, Woods RL, McNeil JJ, Riaz M, Barr M, Nelson MR, Reid CM, Murray AM, Shah RC, Wolfe R, Atkins JR, Fitzsimmons C, Cairns HM, Green MJ, Carr VJ, Cowley MJ, Pickett HA, James PA, Powell JE, Kaplan W, Gibson G, Gyllensten U, Cairns MJ, McNamara M, Dinger ME, Thomas DM. The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly. Nat Commun 2020; 11:435. [PMID: 31974348 PMCID: PMC6978518 DOI: 10.1038/s41467-019-14079-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 12/13/2019] [Indexed: 01/24/2023] Open
Abstract
Population health research is increasingly focused on the genetic determinants of healthy ageing, but there is no public resource of whole genome sequences and phenotype data from healthy elderly individuals. Here we describe the first release of the Medical Genome Reference Bank (MGRB), comprising whole genome sequence and phenotype of 2570 elderly Australians depleted for cancer, cardiovascular disease, and dementia. We analyse the MGRB for single-nucleotide, indel and structural variation in the nuclear and mitochondrial genomes. MGRB individuals have fewer disease-associated common and rare germline variants, relative to both cancer cases and the gnomAD and UK Biobank cohorts, consistent with risk depletion. Age-related somatic changes are correlated with grip strength in men, suggesting blood-derived whole genomes may also provide a biologic measure of age-related functional deterioration. The MGRB provides a broadly applicable reference cohort for clinical genetics and genomic association studies, and for understanding the genetics of healthy ageing. Healthspan and healthy aging are areas of research with potential socioeconomic impact. Here, the authors present the Medical Genome Reference Bank (MGRB) which consist of over 4,000 individuals aged 70 years and older without a history of the major age-related diseases and report on results from whole-genome sequencing and association analyses.
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Affiliation(s)
- Mark Pinese
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Children's Cancer Institute, University of New South Wales, Sydney, NSW, Australia.,School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Paul Lacaze
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Emma M Rath
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Andrew Stone
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Children's Cancer Institute, University of New South Wales, Sydney, NSW, Australia.,School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Marie-Jo Brion
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Adam Ameur
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia.,Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sini Nagpal
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Clare Puttick
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Shane Husson
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Dmitry Degrave
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | | | - Vivian F S Kahl
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Aaron L Statham
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Robyn L Woods
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - John J McNeil
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Moeen Riaz
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Margo Barr
- Centre for Primary Health Care and Equity, University of New South Wales, Sydney, NSW, Australia
| | - Mark R Nelson
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia.,Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Christopher M Reid
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia.,School of Public Health, Curtin University, Perth, WA, Australia
| | - Anne M Murray
- Berman Center for Outcomes and Clinical Research, Hennepin Healthcare Research Institute, Hennepin Healthcare, Minneapolis, MN, USA.,Division of Geriatrics, Department of Medicine, Hennepin County Medical Center and University of Minnesota, Minneapolis, MN, USA
| | - Raj C Shah
- Department of Family Medicine and Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Rory Wolfe
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Joshua R Atkins
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Chantel Fitzsimmons
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Heath M Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Melissa J Green
- School of Psychiatry, University of New South Wales, Sydney, NSW, Australia.,Neuroscience Research Australia, Sydney, NSW, Australia
| | - Vaughan J Carr
- School of Psychiatry, University of New South Wales, Sydney, NSW, Australia.,Neuroscience Research Australia, Sydney, NSW, Australia.,Department of Psychiatry, School of Clinical Sciences, Monash University, Melbourne, VIC, Australia
| | - Mark J Cowley
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Children's Cancer Institute, University of New South Wales, Sydney, NSW, Australia.,School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Hilda A Pickett
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Joseph E Powell
- UNSW Cellular Genomics Futures Institute, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.,Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Warren Kaplan
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Greg Gibson
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ulf Gyllensten
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW, Australia
| | | | - Marcel E Dinger
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - David M Thomas
- Garvan Institute of Medical Research, Sydney, NSW, Australia. .,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
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100
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Bell SC, Mall MA, Gutierrez H, Macek M, Madge S, Davies JC, Burgel PR, Tullis E, Castaños C, Castellani C, Byrnes CA, Cathcart F, Chotirmall SH, Cosgriff R, Eichler I, Fajac I, Goss CH, Drevinek P, Farrell PM, Gravelle AM, Havermans T, Mayer-Hamblett N, Kashirskaya N, Kerem E, Mathew JL, McKone EF, Naehrlich L, Nasr SZ, Oates GR, O'Neill C, Pypops U, Raraigh KS, Rowe SM, Southern KW, Sivam S, Stephenson AL, Zampoli M, Ratjen F. The future of cystic fibrosis care: a global perspective. THE LANCET. RESPIRATORY MEDICINE 2020; 8:65-124. [PMID: 31570318 PMCID: PMC8862661 DOI: 10.1016/s2213-2600(19)30337-6] [Citation(s) in RCA: 553] [Impact Index Per Article: 138.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/19/2019] [Accepted: 08/14/2019] [Indexed: 02/06/2023]
Abstract
The past six decades have seen remarkable improvements in health outcomes for people with cystic fibrosis, which was once a fatal disease of infants and young children. However, although life expectancy for people with cystic fibrosis has increased substantially, the disease continues to limit survival and quality of life, and results in a large burden of care for people with cystic fibrosis and their families. Furthermore, epidemiological studies in the past two decades have shown that cystic fibrosis occurs and is more frequent than was previously thought in populations of non-European descent, and the disease is now recognised in many regions of the world. The Lancet Respiratory Medicine Commission on the future of cystic fibrosis care was established at a time of great change in the clinical care of people with the disease, with a growing population of adult patients, widespread genetic testing supporting the diagnosis of cystic fibrosis, and the development of therapies targeting defects in the cystic fibrosis transmembrane conductance regulator (CFTR), which are likely to affect the natural trajectory of the disease. The aim of the Commission was to bring to the attention of patients, health-care professionals, researchers, funders, service providers, and policy makers the various challenges associated with the changing landscape of cystic fibrosis care and the opportunities available for progress, providing a blueprint for the future of cystic fibrosis care. The discovery of the CFTR gene in the late 1980s triggered a surge of basic research that enhanced understanding of the pathophysiology and the genotype-phenotype relationships of this clinically variable disease. Until recently, available treatments could only control symptoms and restrict the complications of cystic fibrosis, but advances in CFTR modulator therapies to address the basic defect of cystic fibrosis have been remarkable and the field is evolving rapidly. However, CFTR modulators approved for use to date are highly expensive, which has prompted questions about the affordability of new treatments and served to emphasise the considerable gap in health outcomes for patients with cystic fibrosis between high-income countries, and low-income and middle-income countries (LMICs). Advances in clinical care have been multifaceted and include earlier diagnosis through the implementation of newborn screening programmes, formalised airway clearance therapy, and reduced malnutrition through the use of effective pancreatic enzyme replacement and a high-energy, high-protein diet. Centre-based care has become the norm in high-income countries, allowing patients to benefit from the skills of expert members of multidisciplinary teams. Pharmacological interventions to address respiratory manifestations now include drugs that target airway mucus and airway surface liquid hydration, and antimicrobial therapies such as antibiotic eradication treatment in early-stage infections and protocols for maintenance therapy of chronic infections. Despite the recent breakthrough with CFTR modulators for cystic fibrosis, the development of novel mucolytic, anti-inflammatory, and anti-infective therapies is likely to remain important, especially for patients with more advanced stages of lung disease. As the median age of patients with cystic fibrosis increases, with a rapid increase in the population of adults living with the disease, complications of cystic fibrosis are becoming increasingly common. Steps need to be taken to ensure that enough highly qualified professionals are present in cystic fibrosis centres to meet the needs of ageing patients, and new technologies need to be adopted to support communication between patients and health-care providers. In considering the future of cystic fibrosis care, the Commission focused on five key areas, which are discussed in this report: the changing epidemiology of cystic fibrosis (section 1); future challenges of clinical care and its delivery (section 2); the building of cystic fibrosis care globally (section 3); novel therapeutics (section 4); and patient engagement (section 5). In panel 1, we summarise key messages of the Commission. The challenges faced by all stakeholders in building and developing cystic fibrosis care globally are substantial, but many opportunities exist for improved care and health outcomes for patients in countries with established cystic fibrosis care programmes, and in LMICs where integrated multidisciplinary care is not available and resources are lacking at present. A concerted effort is needed to ensure that all patients with cystic fibrosis have access to high-quality health care in the future.
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Affiliation(s)
- Scott C Bell
- Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia; QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
| | - Marcus A Mall
- Charité - Universitätsmedizin Berlin, Berlin Institute of Health, Berlin, Germany; German Center for Lung Research, Berlin, Germany
| | | | - Milan Macek
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czech Republic
| | - Susan Madge
- Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Jane C Davies
- Royal Brompton and Harefield NHS Foundation Trust, London, UK; National Heart and Lung Institute, Imperial College, London, UK
| | - Pierre-Régis Burgel
- Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Paris Descartes, Institut Cochin, Paris, France
| | - Elizabeth Tullis
- St Michael's Hospital, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - Claudio Castaños
- Hospital de Pediatria "Juan P Garrahan", Buenos Aires, Argentina
| | - Carlo Castellani
- Cystic Fibrosis Centre, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Catherine A Byrnes
- Starship Children's Hospital, Auckland, New Zealand; University of Auckland, Auckland, New Zealand
| | - Fiona Cathcart
- Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | | | - Isabelle Fajac
- Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Paris Descartes, Institut Cochin, Paris, France
| | | | - Pavel Drevinek
- Department of Medical Microbiology, Second Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czech Republic
| | | | - Anna M Gravelle
- Cystic Fibrosis Clinic, British Columbia Children's Hospital, Vancouver, BC, Canada
| | - Trudy Havermans
- Cystic Fibrosis Centre, University Hospital Leuven, Leuven, Belgium
| | - Nicole Mayer-Hamblett
- University of Washington, Seattle, WA, USA; Seattle Children's Research Institute, Seattle, WA, USA
| | | | | | - Joseph L Mathew
- Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Edward F McKone
- School of Medicine, St Vincent's University Hospital, Dublin, Ireland; University College Dublin School of Medicine, Dublin, Ireland
| | - Lutz Naehrlich
- Universities of Giessen and Marburg Lung Center, German Center of Lung Research, Justus-Liebig-University Giessen, Giessen, Germany
| | - Samya Z Nasr
- CS Mott Children's Hospital, Ann Arbor, MI, USA; University of Michigan, Ann Arbor, MI, USA
| | | | | | | | | | - Steven M Rowe
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kevin W Southern
- Alder Hey Children's Hospital, Liverpool, UK; University of Liverpool, Liverpool, UK
| | - Sheila Sivam
- Royal Prince Alfred Hospital, Sydney, NSW, Australia; Woolcock Institute of Medical Research, Sydney, NSW, Australia
| | - Anne L Stephenson
- St Michael's Hospital, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - Marco Zampoli
- Division of Paediatric Pulmonology and MRC Unit for Child and Adolescent Health, University of Cape Town, Cape Town, South Africa; Red Cross War Memorial Children's Hospital, Cape Town, South Africa
| | - Felix Ratjen
- University of Toronto, Toronto, ON, Canada; Division of Respiratory Medicine, Department of Paediatrics, Translational Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
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