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Farhat NY, Alexander D, McKee K, Iben J, Rodriguez-Gil JL, Wassif CA, Cawley NX, Balch WE, Porter FD. Sterol O-Acyltransferase 1 ( SOAT1): A Genetic Modifier of Niemann-Pick Disease, Type C1. Int J Mol Sci 2024; 25:4217. [PMID: 38673803 DOI: 10.3390/ijms25084217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/02/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
Niemann-Pick disease type C1 (NPC1) is a lysosomal disorder due to impaired intracellular cholesterol transport out of the endolysosomal compartment.. Marked heterogeneity has been observed in individuals with the same NPC1 genotype, thus suggesting a significant effect of modifier genes. Prior work demonstrated that decreased SOAT1 activity decreased disease severity in an NPC1 mouse model. Thus, we hypothesized that a polymorphism associated with decreased SOAT1 expression might influence the NPC1 phenotype. Phenotyping and genomic sequencing of 117 individuals with NPC1 was performed as part of a Natural History trial. Phenotyping included determination of disease severity and disease burden. Significant clinical heterogeneity is present in individuals homozygous for the NPC1I1061T variant and in siblings. Analysis of the SOAT1 polymorphism, rs1044925 (A>C), showed a significant association of the C-allele with earlier age of neurological onset. The C-allele may be associated with a higher Annualized Severity Index Score as well as increased frequency of liver disease and seizures. A polymorphism associated with decreased expression of SOAT1 appears to be a genetic modifier of the NPC1 phenotype. This finding is consistent with prior data showing decreased phenotypic severity in Npc1-/-:Soat1-/- mice and supports efforts to investigate the potential of SOAT1 inhibitors as a potential therapy for NPC1.
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Affiliation(s)
- Nicole Y Farhat
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Derek Alexander
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kyli McKee
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - James Iben
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jorge L Rodriguez-Gil
- Division of Medical Genetics, Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University, Palo Alto, CA 94304, USA
| | - Christopher A Wassif
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Niamh X Cawley
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Forbes D Porter
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Ginete C, Delgadinho M, Santos B, Miranda A, Silva C, Guerreiro P, Chimusa ER, Brito M. Genetic Modifiers of Sickle Cell Anemia Phenotype in a Cohort of Angolan Children. Genes (Basel) 2024; 15:469. [PMID: 38674403 DOI: 10.3390/genes15040469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
The aim of this study was to identify genetic markers in the HBB Cluster; HBS1L-MYB intergenic region; and BCL11A, KLF1, FOX3, and ZBTB7A genes associated with the heterogeneous phenotypes of Sickle Cell Anemia (SCA) using next-generation sequencing, as well as to assess their influence and prevalence in an Angolan population. Hematological, biochemical, and clinical data were considered to determine patients' severity phenotypes. Samples from 192 patients were sequenced, and 5,019,378 variants of high quality were registered. A catalog of candidate modifier genes that clustered in pathophysiological pathways important for SCA was generated, and candidate genes associated with increasing vaso-occlusive crises (VOC) and with lower fetal hemoglobin (HbF) were identified. These data support the polygenic view of the genetic architecture of SCA phenotypic variability. Two single nucleotide polymorphisms in the intronic region of 2q16.1, harboring the BCL11A gene, are genome-wide and significantly associated with decreasing HbF. A set of variants was identified to nominally be associated with increasing VOC and are potential genetic modifiers harboring phenotypic variation among patients. To the best of our knowledge, this is the first investigation of clinical variation in SCA in Angola using a well-customized and targeted sequencing approach.
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Affiliation(s)
- Catarina Ginete
- H&TRC-Health & Technology Research Center, ESTeSL-Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, 1990-096 Lisbon, Portugal
| | - Mariana Delgadinho
- H&TRC-Health & Technology Research Center, ESTeSL-Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, 1990-096 Lisbon, Portugal
| | - Brígida Santos
- Centro de Investigação em Saúde de Angola (CISA), Bengo 9999, Angola
- Hospital Pediátrico David Bernardino (HPDB), Luanda 3067, Angola
| | - Armandina Miranda
- Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
| | - Carina Silva
- H&TRC-Health & Technology Research Center, ESTeSL-Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, 1990-096 Lisbon, Portugal
- Centro de Estatística e Aplicações, Universidade de Lisboa, 1649-013 Lisbon, Portugal
| | - Paulo Guerreiro
- H&TRC-Health & Technology Research Center, ESTeSL-Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, 1990-096 Lisbon, Portugal
| | - Emile R Chimusa
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Miguel Brito
- H&TRC-Health & Technology Research Center, ESTeSL-Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, 1990-096 Lisbon, Portugal
- Centro de Investigação em Saúde de Angola (CISA), Bengo 9999, Angola
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Monson E, Cideciyan AV, Roman AJ, Sumaroka A, Swider M, Wu V, Viarbitskaya I, Jacobson SG, Fliesler SJ, Pittler SJ. Inherited Retinal Degeneration Caused by Dehydrodolichyl Diphosphate Synthase Mutation-Effect of an ALG6 Modifier Variant. Int J Mol Sci 2024; 25:1004. [PMID: 38256083 PMCID: PMC10816542 DOI: 10.3390/ijms25021004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Modern advances in disease genetics have uncovered numerous modifier genes that play a role in the severity of disease expression. One such class of genetic conditions is known as inherited retinal degenerations (IRDs), a collection of retinal degenerative disorders caused by mutations in over 300 genes. A single missense mutation (K42E) in the gene encoding the enzyme dehydrodolichyl diphosphate synthase (DHDDS), which is required for protein N-glycosylation in all cells and tissues, causes DHDDS-IRD (retinitis pigmentosa type 59 (RP59; OMIM #613861)). Apart from a retinal phenotype, however, DHDDS-IRD is surprisingly non-syndromic (i.e., without any systemic manifestations). To explore disease pathology, we selected five glycosylation-related genes for analysis that are suggested to have disease modifier variants. These genes encode glycosyltransferases (ALG6, ALG8), an ER resident protein (DDOST), a high-mannose oligosaccharyl transferase (MPDU1), and a protein N-glycosylation regulatory protein (TNKS). DNA samples from 11 confirmed DHDDS (K42E)-IRD patients were sequenced at the site of each candidate genetic modifier. Quantitative measures of retinal structure and function were performed across five decades of life by evaluating foveal photoreceptor thickness, visual acuity, foveal sensitivity, macular and extramacular rod sensitivity, and kinetic visual field extent. The ALG6 variant, (F304S), was correlated with greater macular cone disease severity and less peripheral rod disease severity. Thus, modifier gene polymorphisms may account for a significant portion of phenotypic variation observed in human genetic disease. However, the consequences of the polymorphisms may be counterintuitively complex in terms of rod and cone populations affected in different regions of the retina.
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Affiliation(s)
- Elisha Monson
- Department of Optometry and Vision Science, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Artur V. Cideciyan
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Alejandro J. Roman
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Alexander Sumaroka
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Malgorzata Swider
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Vivian Wu
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Iryna Viarbitskaya
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Samuel G. Jacobson
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Steven J. Fliesler
- Departments of Ophthalmology and Biochemistry, and Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York—University at Buffalo, Buffalo, NY 14203, USA;
- Research Service, VA Western NY Healthcare System, Buffalo, NY 14215, USA
| | - Steven J. Pittler
- Department of Optometry and Vision Science, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
- Vision Science Research Center, School of Optometry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Leggatt GP, Seaby EG, Veighey K, Gast C, Gilbert RD, Ennis S. A Role for Genetic Modifiers in Tubulointerstitial Kidney Diseases. Genes (Basel) 2023; 14:1582. [PMID: 37628633 PMCID: PMC10454709 DOI: 10.3390/genes14081582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
With the increased availability of genomic sequencing technologies, the molecular bases for kidney diseases such as nephronophthisis and mitochondrially inherited and autosomal-dominant tubulointerstitial kidney diseases (ADTKD) has become increasingly apparent. These tubulointerstitial kidney diseases (TKD) are monogenic diseases of the tubulointerstitium and result in interstitial fibrosis and tubular atrophy (IF/TA). However, monogenic inheritance alone does not adequately explain the highly variable onset of kidney failure and extra-renal manifestations. Phenotypes vary considerably between individuals harbouring the same pathogenic variant in the same putative monogenic gene, even within families sharing common environmental factors. While the extreme end of the disease spectrum may have dramatic syndromic manifestations typically diagnosed in childhood, many patients present a more subtle phenotype with little to differentiate them from many other common forms of non-proteinuric chronic kidney disease (CKD). This review summarises the expanding repertoire of genes underpinning TKD and their known phenotypic manifestations. Furthermore, we collate the growing evidence for a role of modifier genes and discuss the extent to which these data bridge the historical gap between apparently rare monogenic TKD and polygenic non-proteinuric CKD (excluding polycystic kidney disease).
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Affiliation(s)
- Gary P. Leggatt
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Wessex Kidney Centre, Queen Alexandra Hospital, Portsmouth Hospitals NHS Trust, Portsmouth PO6 3LY, UK
- Renal Department, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Eleanor G. Seaby
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
| | - Kristin Veighey
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Renal Department, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Christine Gast
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Wessex Kidney Centre, Queen Alexandra Hospital, Portsmouth Hospitals NHS Trust, Portsmouth PO6 3LY, UK
| | - Rodney D. Gilbert
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Department of Paediatric Nephrology, Southampton Children’s Hospital, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Sarah Ennis
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
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Ding Y, Wang M, Bu H, Li J, Lin X, Xu X. Application of an F0-based genetic assay in adult zebrafish to identify modifier genes of an inherited cardiomyopathy. Dis Model Mech 2023; 16:dmm049427. [PMID: 35481478 PMCID: PMC9239171 DOI: 10.1242/dmm.049427] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/19/2022] [Indexed: 01/08/2023] Open
Abstract
Modifier genes contribute significantly to our understanding of pathophysiology in human diseases; however, effective approaches to identify modifier genes are still lacking. Here, we aim to develop a rapid F0-based genetic assay in adult zebrafish using the bag3 gene knockout (bag3e2/e2) cardiomyopathy model as a paradigm. First, by utilizing a classic genetic breeding approach, we identified dnajb6b as a deleterious modifier gene for bag3 cardiomyopathy. Next, we established an F0-based genetic assay in adult zebrafish through injection of predicted microhomology-mediated end joining (MMEJ)-inducing single guide RNA/Cas9 protein complex. We showed that effective gene knockdown is maintained in F0 adult fish, enabling recapitulation of both salutary modifying effects of the mtor haploinsufficiency and deleterious modifying effects of the dnajb6b gene on bag3 cardiomyopathy. We finally deployed the F0-based genetic assay to screen differentially expressed genes in the bag3 cardiomyopathy model. As a result, myh9b was identified as a novel modifier gene for bag3 cardiomyopathy. Together, these data prove the feasibility of an F0 adult zebrafish-based genetic assay that can be effectively used to discover modifier genes for inherited cardiomyopathy.
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Affiliation(s)
- Yonghe Ding
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Mingmin Wang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Haisong Bu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiothoracic Surgery, Xiangfan Hospital, Central South University, Changsha 410008, China
| | - Jiarong Li
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Surgery, The Second Xiangfan Hospital of Central South University, Changsha 410011, China
| | - Xueying Lin
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaolei Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
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Tang J, Li N, Li G, Wang J, Yu T, Yao R. Assessment of Rare Genetic Variants to Identify Candidate Modifier Genes Underlying Neurological Manifestations in Neurofibromatosis 1 Patients. Genes (Basel) 2022; 13:genes13122218. [PMID: 36553485 PMCID: PMC9778305 DOI: 10.3390/genes13122218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/30/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Neurological phenotypes such as intellectual disability occur in almost half of patients with neurofibromatosis 1 (NF1). Current genotype-phenotype studies have failed to reveal the mechanism underlying this clinical variability. Despite the presence of pathogenic variants of NF1, modifier genes likely determine the occurrence and severity of neurological phenotypes. Exome sequencing data were used to identify genetic variants in 13 NF1 patients and 457 healthy controls, and this information was used to identify candidate modifier genes underlying neurological phenotypes based on an optimal sequence kernel association test. Thirty-six genes were identified as significant modifying factors in patients with neurological phenotypes and all are highly expressed in the nervous system. A review of the literature confirmed that 19 genes including CUL7, DPH1, and BCO1 are clearly associated with the alteration of neurological functioning and development. Our study revealed the enrichment of rare variants of 19 genes closely related to neurological development and functioning in NF1 patients with neurological phenotypes, indicating possible modifier genes and variants affecting neurodevelopment. Further studies on rare genetic variants of candidate modifier genes may help explain the clinical heterogeneity of NF1.
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Mésinèle J, Ruffin M, Guillot L, Corvol H. Modifier Factors of Cystic Fibrosis Phenotypes: A Focus on Modifier Genes. Int J Mol Sci 2022; 23:ijms232214205. [PMID: 36430680 PMCID: PMC9698440 DOI: 10.3390/ijms232214205] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
Although cystic fibrosis (CF) is recognized as a monogenic disease, due to variants within the CFTR (Cystic Fibrosis Transmembrane Regulator) gene, an extreme clinical heterogeneity is described among people with CF (pwCF). Apart from the exocrine pancreatic status, most studies agree that there is little association between CFTR variants and disease phenotypes. Environmental factors have been shown to contribute to this heterogeneity, accounting for almost 50% of the variability of the lung function of pwCF. Nevertheless, pwCF with similar CFTR variants and sharing the same environment (such as in siblings) may have highly variable clinical manifestations not explained by CFTR variants, and only partly explained by environmental factors. It is recognized that genetic variants located outside the CFTR locus, named "modifier genes", influence the clinical expression of the disease. This short review discusses the latest studies that have described modifier factors associated with the various CF phenotypes as well as the response to the recent CFTR modulator therapies.
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Affiliation(s)
- Julie Mésinèle
- Sorbonne Université, Inserm U938, Centre de Recherche Saint-Antoine (CRSA), 75012 Paris, France
- Inovarion, 75005 Paris, France
| | - Manon Ruffin
- Sorbonne Université, Inserm U938, Centre de Recherche Saint-Antoine (CRSA), 75012 Paris, France
| | - Loïc Guillot
- Sorbonne Université, Inserm U938, Centre de Recherche Saint-Antoine (CRSA), 75012 Paris, France
- Correspondence: (L.G.); (H.C.)
| | - Harriet Corvol
- Sorbonne Université, Inserm U938, Centre de Recherche Saint-Antoine (CRSA), 75012 Paris, France
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Trousseau, Service de Pneumologie Pédiatrique, 75012 Paris, France
- Correspondence: (L.G.); (H.C.)
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Cheng HC, Chi SC, Liang CY, Yu JY, Wang AG. Candidate Modifier Genes for the Penetrance of Leber's Hereditary Optic Neuropathy. Int J Mol Sci 2022; 23:ijms231911891. [PMID: 36233195 PMCID: PMC9569928 DOI: 10.3390/ijms231911891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
Leber’s hereditary optic neuropathy (LHON) is a maternally transmitted disease caused by mitochondria DNA (mtDNA) mutation. It is characterized by acute and subacute visual loss predominantly affecting young men. The mtDNA mutation is transmitted to all maternal lineages. However, only approximately 50% of men and 10% of women harboring a pathogenic mtDNA mutation develop optic neuropathy, reflecting both the incomplete penetrance and its unexplained male prevalence, where over 80% of patients are male. Nuclear modifier genes have been presumed to affect the penetrance of LHON. With conventional genetic methods, prior studies have failed to solve the underlying pathogenesis. Whole exome sequencing (WES) is a new molecular technique for sequencing the protein-coding region of all genes in a whole genome. We performed WES from five families with 17 members. These samples were divided into the proband group (probands with acute onset of LHON, n = 7) and control group (carriers including mother and relative carriers with mtDNSA 11778 mutation, without clinical manifestation of LHON, n = 10). Through whole exome analysis, we found that many mitochondria related (MT-related) nuclear genes have high percentage of variants in either the proband group or control group. The MT genes with a difference over 0.3 of mutation percentage between the proband and control groups include AK4, NSUN4, RDH13, COQ3, and FAHD1. In addition, the pathway analysis revealed that these genes were associated with cofactor metabolism pathways. Family-based analysis showed that several candidate MT genes including METAP1D (c.41G > T), ACACB (c.1029del), ME3 (c.972G > C), NIPSNAP3B (c.280G > C, c.476C > G), and NSUN4 (c.4A > G) were involved in the penetrance of LHON. A GWAS (genome wide association study) was performed, which found that ADGRG5 (Chr16:575620A:G), POLE4 (Chr2:7495872T:G), ERMAP (Chr1:4283044A:G), PIGR (Chr1:2069357C:T;2069358G:A), CDC42BPB (Chr14:102949A:G), PROK1 (Chr1:1104562A:G), BCAN (Chr 1:1566582C:T), and NES (Chr1:1566698A:G,1566705T:C, 1566707T:C) may be involved. The incomplete penetrance and male prevalence are still the major unexplained issues in LHON. Through whole exome analysis, we found several MT genes with a high percentage of variants were involved in a family-based analysis. Pathway analysis suggested a difference in the mutation burden of MT genes underlining the biosynthesis and metabolism pathways. In addition, the GWAS analysis also revealed several candidate nuclear modifier genes. The new technology of WES contributes to provide a highly efficient candidate gene screening function in molecular genetics.
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Affiliation(s)
- Hui-Chen Cheng
- Program in Molecular Medicine, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Department of Ophthalmology, Taipei Veterans General Hospital, 201 Sec. 2, Shih-Pai Rd., Taipei 11217, Taiwan
- Department of Ophthalmology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Department of Life Sciences and Institute of Genome Sciences, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Sheng-Chu Chi
- Department of Ophthalmology, Taipei Veterans General Hospital, 201 Sec. 2, Shih-Pai Rd., Taipei 11217, Taiwan
| | - Chiao-Ying Liang
- Department of Ophthalmology, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Jenn-Yah Yu
- Department of Life Sciences and Institute of Genome Sciences, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - An-Guor Wang
- Department of Ophthalmology, Taipei Veterans General Hospital, 201 Sec. 2, Shih-Pai Rd., Taipei 11217, Taiwan
- Department of Ophthalmology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Correspondence: ; Tel.: +886-2-2875-7325; Fax: +886-2-2876-1351
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Kosac A, Pesovic J, Radenkovic L, Brkusanin M, Radovanovic N, Djurisic M, Radivojevic D, Mladenovic J, Ostojic S, Kovacevic G, Kravljanac R, Savic Pavicevic D, Milic Rasic V. LTBP4, SPP1, and CD40 Variants: Genetic Modifiers of Duchenne Muscular Dystrophy Analyzed in Serbian Patients. Genes (Basel) 2022; 13:genes13081385. [PMID: 36011296 PMCID: PMC9407083 DOI: 10.3390/genes13081385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 02/01/2023] Open
Abstract
Background: Clinical course variability in Duchenne muscular dystrophy (DMD) is partially explained by the mutation location in the DMD gene and variants in modifier genes. We assessed the effect of the SPP1, CD40, and LTBP4 genes and DMD mutation location on loss of ambulation (LoA). Methods: SNPs in SPP1-rs28357094, LTBP4-rs2303729, rs1131620, rs1051303, rs10880, and CD40-rs1883832 were genotyped, and their effect was assessed by survival and hierarchical cluster analysis. Results: Patients on glucocorticoid corticosteroid (GC) therapy experienced LoA one year later (p = 0.04). The modifying effect of SPP1 and CD40 variants, as well as LTBP4 haplotypes, was not observed using a log-rank test and multivariant Cox regression analysis. Cluster analysis revealed two subgroups with statistical trends in differences in age at LoA. Almost all patients in the cluster with later LoA had the protective IAAM LTBP4 haplotype and statistically significantly fewer CD40 genotypes with harmful T allele and “distal” DMD mutations. Conclusions: The modifying effect of SPP1, CD40, and LTBP4 was not replicated in Serbian patients, although our cohort was comparable in terms of its DMD mutation type distribution, SNP allele frequencies, and GC-positive effect with other European cohorts. Cluster analysis may be able to identify patient subgroups carrying a combination of the genetic variants that modify LoA.
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Affiliation(s)
- Ana Kosac
- Department of Neurology, Clinic of Neurology and Psychiatry for Children and Youth, 11000 Belgrade, Serbia
- Correspondence: ; Tel.: +381-11-2658-355
| | - Jovan Pesovic
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia
| | - Lana Radenkovic
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia
| | - Milos Brkusanin
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia
| | - Nemanja Radovanovic
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia
| | - Marina Djurisic
- Laboratory of Medical Genetics, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11000 Belgrade, Serbia
| | - Danijela Radivojevic
- Laboratory of Medical Genetics, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11000 Belgrade, Serbia
| | - Jelena Mladenovic
- Department of Neurology, Clinic of Neurology and Psychiatry for Children and Youth, 11000 Belgrade, Serbia
| | - Slavica Ostojic
- Department of Neurology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11000 Belgrade, Serbia
| | - Gordana Kovacevic
- Department of Neurology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11000 Belgrade, Serbia
| | - Ruzica Kravljanac
- Department of Neurology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11000 Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Dusanka Savic Pavicevic
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia
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Zhou D, Jia S, Yi L, Wu Z, Song Y, Zhang B, Li Y, Yang X, Xu A, Li X, Zhang W, Duan W, Li Z, Qi S, Chen Z, Ouyang Q, Jia J, Huang J, Ou X, You H. OUP accepted manuscript. Metallomics 2022; 14:6561631. [PMID: 35357466 PMCID: PMC9154322 DOI: 10.1093/mtomcs/mfac024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/29/2022] [Indexed: 11/29/2022]
Abstract
The mutations in modifier genes may contribute to some inherited diseases including Wilson disease (WD). This study was designed to identify potential modifier genes that contribute to WD. A total of 10 WD patients with single or no heterozygous ATP7B mutations were recruited for whole-exome sequencing (WES). Five hundred and thirteen candidate genes, of which the genetic variants present in at least two patients, were identified. In order to clarify which proteins might be involved in copper transfer or metabolism processes, the isobaric tags for relative and absolute quantitation (iTRAQ) was performed to identify the differentially expressed proteins between normal and CuSO4-treated cell lines. Thirteen genes/proteins were identified by both WES and iTRAQ, indicating that disease-causing variants of these genes may actually contribute to the aberrant copper ion accumulation. Additionally, the c.86C > T (p.S29L) mutation in the SLC31A2 gene (coding CTR2) has a relative higher frequency in our cohort of WD patients (6/191) than reported (0.0024 in gnomAD database) in our healthy donors (0/109), and CTR2S29L leads to increased intracellular Cu concentration and Cu-induced apoptosis in cultured cell lines. In conclusion, the WES and iTRAQ approaches successfully identified several disease-causing variants in potential modifier genes that may be involved in the WD phenotype.
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Affiliation(s)
| | | | | | | | - Yi Song
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China
- National Clinical Research Center for Digestive Diseases, On behalf of China Registry of Genetic/Metabolic Liver Diseases (CR-GMLD) Group, Beijing, China
| | - Bei Zhang
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China
- National Clinical Research Center for Digestive Diseases, On behalf of China Registry of Genetic/Metabolic Liver Diseases (CR-GMLD) Group, Beijing, China
| | - Yanmeng Li
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China
- National Clinical Research Center for Digestive Diseases, On behalf of China Registry of Genetic/Metabolic Liver Diseases (CR-GMLD) Group, Beijing, China
| | - Xiaoxi Yang
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China
- National Clinical Research Center for Digestive Diseases, On behalf of China Registry of Genetic/Metabolic Liver Diseases (CR-GMLD) Group, Beijing, China
| | - Anjian Xu
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China
- National Clinical Research Center for Digestive Diseases, On behalf of China Registry of Genetic/Metabolic Liver Diseases (CR-GMLD) Group, Beijing, China
| | - Xiaojin Li
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China
- National Clinical Research Center for Digestive Diseases, On behalf of China Registry of Genetic/Metabolic Liver Diseases (CR-GMLD) Group, Beijing, China
| | - Wei Zhang
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Beijing, China
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China
- National Clinical Research Center for Digestive Diseases, On behalf of China Registry of Genetic/Metabolic Liver Diseases (CR-GMLD) Group, Beijing, China
| | - Weijia Duan
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Beijing, China
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China
- National Clinical Research Center for Digestive Diseases, On behalf of China Registry of Genetic/Metabolic Liver Diseases (CR-GMLD) Group, Beijing, China
| | - Zhenkun Li
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China
- National Clinical Research Center for Digestive Diseases, On behalf of China Registry of Genetic/Metabolic Liver Diseases (CR-GMLD) Group, Beijing, China
| | - Saiping Qi
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China
- National Clinical Research Center for Digestive Diseases, On behalf of China Registry of Genetic/Metabolic Liver Diseases (CR-GMLD) Group, Beijing, China
| | - Zhibin Chen
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China
- National Clinical Research Center for Digestive Diseases, On behalf of China Registry of Genetic/Metabolic Liver Diseases (CR-GMLD) Group, Beijing, China
| | - Qin Ouyang
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China
- National Clinical Research Center for Digestive Diseases, On behalf of China Registry of Genetic/Metabolic Liver Diseases (CR-GMLD) Group, Beijing, China
| | | | | | | | - Hong You
- Correspondence: E-mail: (Hong You)
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Han J, Ritchey B, Opoku E, Smith JD. Fine Mapping of the Mouse Ath28 Locus Yields Three Atherosclerosis Modifying Sub-Regions. Genes (Basel) 2021; 13:70. [PMID: 35052410 PMCID: PMC8774523 DOI: 10.3390/genes13010070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/22/2021] [Accepted: 12/24/2021] [Indexed: 11/17/2022] Open
Abstract
A mouse strain intercross between Apoe-/- AKR/J and DBA/2J mice identified three replicated atherosclerosis quantitative trait loci (QTLs). Our objective was to fine map mouse atherosclerosis modifier genes within a genomic region known to affect lesion development in apoE-deficient (Apoe-/-) mice. We dissected the Ath28 QTL on the distal end of chromosome 2 by breeding a panel of congenic strains and measuring aortic root lesion area in 16-week-old male and female mice fed regular laboratory diets. The parental congenic strain contained ~9.65 Mb of AKR/J DNA from chromosome 2 on the DBA/2J genetic background, which had lesions 55% and 47% smaller than female and male DBA/2J mice, respectively (p < 0.001). Seven additional congenic lines identified three separate regions associated with the lesion area, named Ath28.1, Ath28.2, and Ath28.3, where the AKR/J alleles were atherosclerosis-protective for two regions and atherosclerosis-promoting for the other region. These results were replicated in both sexes, and in combined analysis after adjusting for sex. The congenic lines did not greatly impact total and HDL cholesterol levels or body weight. Bioinformatic analyses identified all coding and non-coding genes in the Ath28.1 sub-region, as well as strain sequence differences that may be impactful. Even within a <10 Mb region of the mouse genome, evidence supports the presence of at least three atherosclerosis modifier genes that differ between the AKR/J and DBA/2J mouse strains, supporting the polygenic nature of atherosclerosis susceptibility.
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Affiliation(s)
| | | | | | - Jonathan D. Smith
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH 44195, USA; (J.H.); (B.R.); (E.O.)
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12
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Makhdoom EUH, Waseem SS, Iqbal M, Abdullah U, Hussain G, Asif M, Budde B, Höhne W, Tinschert S, Saadi SM, Yousaf H, Ali Z, Fatima A, Kaygusuz E, Khan A, Jameel M, Khan S, Tariq M, Anjum I, Altmüller J, Thiele H, Höning S, Baig SM, Nürnberg P, Hussain MS. Modifier Genes in Microcephaly: A Report on WDR62, CEP63, RAD50 and PCNT Variants Exacerbating Disease Caused by Biallelic Mutations of ASPM and CENPJ. Genes (Basel) 2021; 12:731. [PMID: 34068194 PMCID: PMC8153008 DOI: 10.3390/genes12050731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 11/09/2022] Open
Abstract
Congenital microcephaly is the clinical presentation of significantly reduced head circumference at birth. It manifests as both non-syndromic-microcephaly primary hereditary (MCPH)-and syndromic forms and shows considerable inter- and intrafamilial variability. It has been hypothesized that additional genetic variants may be responsible for this variability, but data are sparse. We have conducted deep phenotyping and genotyping of five Pakistani multiplex families with either MCPH (n = 3) or Seckel syndrome (n = 2). In addition to homozygous causal variants in ASPM or CENPJ, we discovered additional heterozygous modifier variants in WDR62, CEP63, RAD50 and PCNT-genes already known to be associated with neurological disorders. MCPH patients carrying an additional heterozygous modifier variant showed more severe phenotypic features. Likewise, the phenotype of Seckel syndrome caused by a novel CENPJ variant was aggravated to microcephalic osteodysplastic primordial dwarfism type II (MOPDII) in conjunction with an additional PCNT variant. We show that the CENPJ missense variant impairs splicing and decreases protein expression. We also observed centrosome amplification errors in patient cells, which were twofold higher in MOPDII as compared to Seckel cells. Taken together, these observations advocate for consideration of additional variants in related genes for their role in modifying the expressivity of the phenotype and need to be considered in genetic counseling and risk assessment.
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Affiliation(s)
- Ehtisham Ul Haq Makhdoom
- Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (E.U.H.M.); (S.S.W.); (M.I.); (M.A.); (B.B.); (W.H.); (J.A.); (H.T.); (P.N.)
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, PIEAS, Faisalabad 38000, Pakistan; (S.M.S.); (H.Y.); (A.K.); (M.J.); (S.K.); (M.T.); (S.M.B.)
- Neurochemicalbiology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, Faisalabad 38000, Pakistan;
| | - Syeda Seema Waseem
- Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (E.U.H.M.); (S.S.W.); (M.I.); (M.A.); (B.B.); (W.H.); (J.A.); (H.T.); (P.N.)
- Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany;
| | - Maria Iqbal
- Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (E.U.H.M.); (S.S.W.); (M.I.); (M.A.); (B.B.); (W.H.); (J.A.); (H.T.); (P.N.)
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, PIEAS, Faisalabad 38000, Pakistan; (S.M.S.); (H.Y.); (A.K.); (M.J.); (S.K.); (M.T.); (S.M.B.)
- Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany;
| | - Uzma Abdullah
- University Institute of Biochemistry and Biotechnology (UIBB), PMAS-Arid Agriculture University, Rawalpindi 46000, Pakistan;
| | - Ghulam Hussain
- Neurochemicalbiology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, Faisalabad 38000, Pakistan;
| | - Maria Asif
- Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (E.U.H.M.); (S.S.W.); (M.I.); (M.A.); (B.B.); (W.H.); (J.A.); (H.T.); (P.N.)
- Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany;
| | - Birgit Budde
- Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (E.U.H.M.); (S.S.W.); (M.I.); (M.A.); (B.B.); (W.H.); (J.A.); (H.T.); (P.N.)
| | - Wolfgang Höhne
- Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (E.U.H.M.); (S.S.W.); (M.I.); (M.A.); (B.B.); (W.H.); (J.A.); (H.T.); (P.N.)
| | - Sigrid Tinschert
- Zentrum Medizinische Genetik, Medizinische Universität, 6020 Innsbruck, Austria;
| | - Saadia Maryam Saadi
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, PIEAS, Faisalabad 38000, Pakistan; (S.M.S.); (H.Y.); (A.K.); (M.J.); (S.K.); (M.T.); (S.M.B.)
| | - Hammad Yousaf
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, PIEAS, Faisalabad 38000, Pakistan; (S.M.S.); (H.Y.); (A.K.); (M.J.); (S.K.); (M.T.); (S.M.B.)
| | - Zafar Ali
- Centre for Biotechnology and Microbiology, University of Swat, Swat 19130, Pakistan;
| | - Ambrin Fatima
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74000, Pakistan;
| | - Emrah Kaygusuz
- Bilecik Şeyh Edebali University, Molecular Biology and Genetics, Gülümbe Campus, Bilecik 11230, Turkey;
| | - Ayaz Khan
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, PIEAS, Faisalabad 38000, Pakistan; (S.M.S.); (H.Y.); (A.K.); (M.J.); (S.K.); (M.T.); (S.M.B.)
| | - Muhammad Jameel
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, PIEAS, Faisalabad 38000, Pakistan; (S.M.S.); (H.Y.); (A.K.); (M.J.); (S.K.); (M.T.); (S.M.B.)
| | - Sheraz Khan
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, PIEAS, Faisalabad 38000, Pakistan; (S.M.S.); (H.Y.); (A.K.); (M.J.); (S.K.); (M.T.); (S.M.B.)
| | - Muhammad Tariq
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, PIEAS, Faisalabad 38000, Pakistan; (S.M.S.); (H.Y.); (A.K.); (M.J.); (S.K.); (M.T.); (S.M.B.)
| | - Iram Anjum
- Department of Biotechnology, Kinnaird College for Women, Lahore 54000, Pakistan;
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (E.U.H.M.); (S.S.W.); (M.I.); (M.A.); (B.B.); (W.H.); (J.A.); (H.T.); (P.N.)
| | - Holger Thiele
- Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (E.U.H.M.); (S.S.W.); (M.I.); (M.A.); (B.B.); (W.H.); (J.A.); (H.T.); (P.N.)
| | - Stefan Höning
- Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany;
| | - Shahid Mahmood Baig
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, PIEAS, Faisalabad 38000, Pakistan; (S.M.S.); (H.Y.); (A.K.); (M.J.); (S.K.); (M.T.); (S.M.B.)
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74000, Pakistan;
- Pakistan Science Foundation (PSF), 1- Constitution Avenue, G-5/2, Islamabad 44000, Pakistan
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (E.U.H.M.); (S.S.W.); (M.I.); (M.A.); (B.B.); (W.H.); (J.A.); (H.T.); (P.N.)
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
| | - Muhammad Sajid Hussain
- Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (E.U.H.M.); (S.S.W.); (M.I.); (M.A.); (B.B.); (W.H.); (J.A.); (H.T.); (P.N.)
- Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany;
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
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Xu F, Chen Y, Tillman KA, Cui Y, Williams RW, Bhattacharya SK, Lu L, Sun Y. Characterizing modifier genes of cardiac fibrosis phenotype in hypertrophic cardiomyopathy. Int J Cardiol 2021; 330:135-141. [PMID: 33529666 PMCID: PMC8105878 DOI: 10.1016/j.ijcard.2021.01.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/18/2021] [Accepted: 01/24/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND Clinical phenotypes of hypertrophic cardiomyopathy (HCM) vary greatly even among patients with the same gene mutations. This variability is largely regulated by unidentified modifier loci. The purpose of the study is to identify modifier genes for cardiac fibrosis-a major phenotype of HCM-using the BXD family, a murine cohort. METHODS The relative severity of cardiac fibrosis was estimated by quantitation of cardiac collagen volume fraction (CCVF) across 66 members of the BXD family. Quantitative trait locus (QTL) mapping for cardiac fibrosis was done using GeneNetwork. Candidate modifier loci and genes associated with fibrosis were prioritized based on an explicit scoring system. Networks of correlation between fibrosis and cardiac transcriptomes were evaluated to generate causal models of disease susceptibility. RESULTS CCVF levels varied greatly within this family. Interval mapping identified a significant CCVF-related QTL on chromosome (Chr) 2 in males, and a significant QTL on Chr 4 Mb in females. The scoring system highlighted two strong candidate genes in the Chr 2 locus-Nek6 and Nr6a1. Both genes are highly expressed in the heart. Cardiac Nek6 mRNA levels are significantly correlated with CCVF. Nipsnap3b and Fktn are lead candidate genes for the Chr 4 locus, and both are also highly expressed in heart. Cardiac Nipsnap3b gene expression correlates well with CCVF. CONCLUSION Our study demonstrated that candidate modifier genes of cardiac fibrosis phenotype in HCM are different in males and females. Nek6 and Nr6a1 are strong candidates in males, while Nipsnap3b and Fktn are top candidates in females.
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Affiliation(s)
- Fuyi Xu
- Division of Cardiovascular Diseases, Department of Medicine, Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Yuanjian Chen
- Division of Cardiovascular Diseases, Department of Medicine, Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Kaitlin A Tillman
- Division of Cardiovascular Diseases, Department of Medicine, Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Yan Cui
- Division of Cardiovascular Diseases, Department of Medicine, Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Robert W Williams
- Division of Cardiovascular Diseases, Department of Medicine, Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Syamal K Bhattacharya
- Division of Cardiovascular Diseases, Department of Medicine, Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Lu Lu
- Division of Cardiovascular Diseases, Department of Medicine, Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States of America.
| | - Yao Sun
- Division of Cardiovascular Diseases, Department of Medicine, Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States of America.
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14
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Sepahzad A, Morris-Rosendahl DJ, Davies JC. Cystic Fibrosis Lung Disease Modifiers and Their Relevance in the New Era of Precision Medicine. Genes (Basel) 2021; 12:genes12040562. [PMID: 33924524 PMCID: PMC8069009 DOI: 10.3390/genes12040562] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/08/2021] [Accepted: 04/08/2021] [Indexed: 02/06/2023] Open
Abstract
Our understanding of cystic fibrosis (CF) has grown exponentially since the discovery of the cystic fibrosis transmembrane conductance regulator (CFTR) gene in 1989. With evolving genetic and genomic tools, we have come to better understand the role of CFTR genotypes in the pathophysiology of the disease. This, in turn, has paved the way for the development of modulator therapies targeted at mutations in the CFTR, which are arguably one of the greatest advances in the treatment of CF. These modulator therapies, however, do not target all the mutations in CFTR that are seen in patients with CF and, furthermore, a variation in response is seen in patients with the same genotype who are taking modulator therapies. There is growing evidence to support the role of non-CFTR modifiers, both genetic and environmental, in determining the variation seen in CF morbidity and mortality and also in the response to existing therapies. This review focusses on key findings from studies using candidate gene and genome-wide approaches to identify CF modifier genes of lung disease in cystic fibrosis and considers the interaction between modifiers and the response to modulator therapies. As the use of modulator therapies expands and we gain data around outcomes, it will be of great interest to investigate this interaction further. Going forward, it will also be crucial to better understand the relative influence of genomic versus environmental factors. With this understanding, we can truly begin to deliver personalised care by better profiling the likely disease phenotype for each patient and their response to treatment.
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Affiliation(s)
- Afsoon Sepahzad
- Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield Hospitals, London SW3 6NP, UK;
| | | | - Jane C. Davies
- Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield Hospitals, London SW3 6NP, UK;
- National Heart & Lung Institute, Imperial College London, Emmanuel Kay Building, 1b Manresa Rd, London SW3 6LR, UK
- Correspondence:
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Mao M, Popli T, Jeanne M, Hoff K, Sen S, Gould DB. Identification of fibronectin 1 as a candidate genetic modifier in a Col4a1 mutant mouse model of Gould syndrome. Dis Model Mech 2021; 14:dmm048231. [PMID: 34424299 PMCID: PMC8106953 DOI: 10.1242/dmm.048231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/02/2021] [Indexed: 12/12/2022] Open
Abstract
Collagen type IV alpha 1 and alpha 2 (COL4A1 and COL4A2) are major components of almost all basement membranes. COL4A1 and COL4A2 mutations cause a multisystem disorder that can affect any organ but typically involves the cerebral vasculature, eyes, kidneys and skeletal muscles. In recent years, patient advocacy and family support groups have united under the name of Gould syndrome. The manifestations of Gould syndrome are highly variable, and animal studies suggest that allelic heterogeneity and genetic context contribute to the clinical variability. We previously characterized a mouse model of Gould syndrome caused by a Col4a1 mutation in which the severities of ocular anterior segment dysgenesis (ASD), myopathy and intracerebral hemorrhage (ICH) were dependent on genetic background. Here, we performed a genetic modifier screen to provide insight into the mechanisms contributing to Gould syndrome pathogenesis and identified a single locus [modifier of Gould syndrome 1 (MoGS1)] on Chromosome 1 that suppressed ASD. A separate screen showed that the same locus ameliorated myopathy. Interestingly, MoGS1 had no effect on ICH, suggesting that this phenotype could be mechanistically distinct. We refined the MoGS1 locus to a 4.3 Mb interval containing 18 protein-coding genes, including Fn1, which encodes the extracellular matrix component fibronectin 1. Molecular analysis showed that the MoGS1 locus increased Fn1 expression, raising the possibility that suppression is achieved through a compensatory extracellular mechanism. Furthermore, we found evidence of increased integrin-linked kinase levels and focal adhesion kinase phosphorylation in Col4a1 mutant mice that is partially restored by the MoGS1 locus, implicating the involvement of integrin signaling. Taken together, our results suggest that tissue-specific mechanistic heterogeneity contributes to the variable expressivity of Gould syndrome and that perturbations in integrin signaling may play a role in ocular and muscular manifestations.
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Affiliation(s)
- Mao Mao
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Tanav Popli
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Marion Jeanne
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Kendall Hoff
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Saunak Sen
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Preventive Medicine, University of Tennessee Health Science Center, 66 North Pauline St, Memphis, TN 38163, USA
| | - Douglas B. Gould
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
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16
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Bazrafshan S, Kushlaf H, Kakroo M, Quinlan J, Becker RC, Sadayappan S. Genetic Modifiers of Hereditary Neuromuscular Disorders and Cardiomyopathy. Cells 2021; 10:cells10020349. [PMID: 33567613 PMCID: PMC7915259 DOI: 10.3390/cells10020349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/26/2021] [Accepted: 02/03/2021] [Indexed: 12/18/2022] Open
Abstract
Novel genetic variants exist in patients with hereditary neuromuscular disorders (NMD), including muscular dystrophy. These patients also develop cardiac manifestations. However, the association between these gene variants and cardiac abnormalities is understudied. To determine genetic modifiers and features of cardiac disease in NMD patients, we have reviewed electronic medical records of 651 patients referred to the Muscular Dystrophy Association Care Center at the University of Cincinnati and characterized the clinical phenotype of 14 patients correlating with their next-generation sequencing data. The data were retrieved from the electronic medical records of the 14 patients included in the current study and comprised neurologic and cardiac phenotype and genetic reports which included comparative genomic hybridization array and NGS. Novel associations were uncovered in the following eight patients diagnosed with Limb-girdle Muscular Dystrophy, Bethlem Myopathy, Necrotizing Myopathy, Charcot-Marie-Tooth Disease, Peripheral Polyneuropathy, and Valosin-containing Protein-related Myopathy. Mutations in COL6A1, COL6A3, SGCA, SYNE1, FKTN, PLEKHG5, ANO5, and SMCHD1 genes were the most common, and the associated cardiac features included bundle branch blocks, ventricular chamber dilation, septal thickening, and increased outflow track gradients. Our observations suggest that features of cardiac disease and modifying gene mutations in patients with NMD require further investigation to better characterize genotype–phenotype relationships.
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Affiliation(s)
- Sholeh Bazrafshan
- Heart, Lung and Vascular Institute, Division of Cardiovascular Health and Disease, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (S.B.); (M.K.); (R.C.B.)
| | - Hani Kushlaf
- Department of Neurology and Rehabilitation Medicine, Neuromuscular Center, University of Cincinnati Gardner Neuroscience Institute, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (H.K.); (J.Q.)
| | - Mashhood Kakroo
- Heart, Lung and Vascular Institute, Division of Cardiovascular Health and Disease, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (S.B.); (M.K.); (R.C.B.)
| | - John Quinlan
- Department of Neurology and Rehabilitation Medicine, Neuromuscular Center, University of Cincinnati Gardner Neuroscience Institute, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (H.K.); (J.Q.)
| | - Richard C. Becker
- Heart, Lung and Vascular Institute, Division of Cardiovascular Health and Disease, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (S.B.); (M.K.); (R.C.B.)
| | - Sakthivel Sadayappan
- Heart, Lung and Vascular Institute, Division of Cardiovascular Health and Disease, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (S.B.); (M.K.); (R.C.B.)
- Correspondence: ; Tel.: +1-513-558-7498
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Li W, Hua R, Wang M, Zhang D, Zhu J, Zhang S, Yang Y, Cheng J, Zhou H, Zhang J, He J. H19 gene polymorphisms and Wilms tumor risk in Chinese children: a four-center case-control study. Mol Genet Genomic Med 2021; 9:e1584. [PMID: 33403826 PMCID: PMC8077085 DOI: 10.1002/mgg3.1584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/05/2020] [Accepted: 12/15/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Wilms tumor is the most common pediatric renal cancer. However, genetic bases behind Wilms tumor remain largely unknown. H19 is a critical maternally imprinted gene. Previous studies indicated that single nucleotide polymorphisms (SNPs) in the H19 can modify the risk of several human malignancies. Epigenetic errors at the H19 locus lead to biallelic silencing in Wilms tumors. Genetic variations in the H19 may be related to Wilms tumor susceptibility. METHODS We conducted a four-center study to investigate whether H19 SNP was a predisposing factor to Wilms tumor. Three polymorphisms in the H19 (rs2839698 G > A, rs3024270 C > G, rs217727 G > A) were genotyped in 355 cases and 1070 cancer-free controls, using Taqman method. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to evaluate the strength of the associations. RESULTS We found that all of these three polymorphisms were significantly associated with Wilms tumor risk alterations. The rs2839698 G > A polymorphism (AG vs. GG: adjusted OR = 0.74, 95% CI = 0.57-0.96, p = 0.024; AA vs. GG: adjusted OR = 1.52, 95% CI = 1.05-2.22, p = 0.027), the rs3024270 C > G polymorphism (CG vs. CC: adjusted OR = 0.61, 95% CI = 0.46-0.81, p = 0.0007; and the rs217727 polymorphism (AG vs. GG: adjusted OR = 0.76, 95% CI = 0.58-0.99, p = 0.035). The Carriers of 1, 2, and 1-2 risk genotypes were inclined to develop Wilms tumor compared with those without risk genotype (adjusted OR = 1.36, 95% CI = 1.02-1.80, p = 0.037; adjusted OR = 1.84, 95% CI = 1.27-2.67, p = 0.001; adjusted OR = 1.50, 95% CI = 1.17-1.92, p = 0.002, respectively). The stratified analysis further revealed that rs2839698 AA, rs217727 AA, and 1-2 risk genotypes could strongly increase Wilms tumor risk among children above 18 months of age, males, and with clinical stage I+II disease. CONCLUSION Our findings indicate that genetic variations in the H19 may confer Wilms tumor risk.
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Affiliation(s)
- Wenya Li
- Department of Pediatric SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Rui‐Xi Hua
- Department of OncologyThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
- Department of Pediatric SurgeryGuangzhou Institute of PediatricsGuangdong Provincial Key Laboratory of Research in Structural Birth Defect DiseaseGuangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
| | - Mi Wang
- Department of Pediatric SurgeryGuangzhou Institute of PediatricsGuangdong Provincial Key Laboratory of Research in Structural Birth Defect DiseaseGuangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
| | - Da Zhang
- Department of Pediatric SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Jinhong Zhu
- Department of Pediatric SurgeryGuangzhou Institute of PediatricsGuangdong Provincial Key Laboratory of Research in Structural Birth Defect DiseaseGuangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
- Department of Clinical LaboratoryBiobankHarbin Medical University Cancer HospitalHarbinChina
| | - Songyang Zhang
- Department of Pediatric SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Yang Yang
- Department of Pediatric SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Jiwen Cheng
- Department of Pediatric Surgerythe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Haixia Zhou
- Department of HematologyThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Jiao Zhang
- Department of Pediatric SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Jing He
- Department of Pediatric SurgeryGuangzhou Institute of PediatricsGuangdong Provincial Key Laboratory of Research in Structural Birth Defect DiseaseGuangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
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Crawford H, Scerif G, Wilde L, Beggs A, Stockton J, Sandhu P, Shelley L, Oliver C, McCleery J. Genetic modifiers in rare disorders: the case of fragile X syndrome. Eur J Hum Genet 2021; 29:173-183. [PMID: 32862204 PMCID: PMC7852869 DOI: 10.1038/s41431-020-00711-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/29/2020] [Accepted: 08/04/2020] [Indexed: 12/11/2022] Open
Abstract
Methods employed in genome-wide association studies are not feasible ways to explore genotype-phenotype associations in rare disorders due to limited statistical power. An alternative approach is to examine relationships among specific single nucleotide polymorphisms (SNPs), selected a priori, and behavioural characteristics. Here, we adopt this strategy to examine relationships between three SNPs (5-HTTLPR, MAOA, COMT) and specific clinically-relevant behaviours that are phenotypic of fragile X syndrome (FXS) but vary in severity and frequency across individuals. Sixty-four males with FXS participated in the current study. Data from standardised informant measures of challenging behaviour (defined as physical aggression, property destruction, stereotyped behaviour, and self-injury), autism symptomatology, attention-deficit-hyperactivity-disorder characteristics, repetitive behaviour and mood/interest and pleasure were compared between each SNP genotype. No association was observed between behavioural characteristics and either 5-HTTLPR (serotonin) or MAOA (monoamine oxidase) genotypes. However, compared to the COMT (dopamine) AG and GG genotypes, the AA genotype was associated with greater interest and pleasure in the environment, and with reduced risk for property destruction, stereotyped behaviour and compulsive behaviour. The results suggest that common genetic variation in the COMT genotype affecting dopamine levels in the brain may contribute to the variability of challenging and repetitive behaviours and interest and pleasure in this population. This study identifies a role for additional genetic risk in understanding the neural and genetic mechanisms contributing to phenotypic variability in neurodevelopmental disorders, and highlights the merit of investigating SNPs that are selected a priori on a theoretical basis in rare populations.
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Affiliation(s)
- Hayley Crawford
- Faculty of Health and Life Sciences, Coventry University, Coventry, UK.
- Warwick Medical School, University of Warwick, Warwick, UK.
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK.
| | - Gaia Scerif
- Attention, Brain and Cognitive Development Group, Department of Experimental Psychology, University of Oxford, Oxford, UK
| | - Lucy Wilde
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
- The Open University, Milton Keynes, UK
| | - Andrew Beggs
- Surgical Research Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Joanne Stockton
- Surgical Research Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Pria Sandhu
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
| | - Lauren Shelley
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
| | - Chris Oliver
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
| | - Joseph McCleery
- Department of Psychology, Saint Joseph's University, Philadelphia, PA, USA
- Center for Autism Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
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19
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Sawyer JK, Kabiri Z, Montague RA, Allen SR, Stewart R, Paramore SV, Cohen E, Zaribafzadeh H, Counter CM, Fox DT. Exploiting codon usage identifies intensity-specific modifiers of Ras/MAPK signaling in vivo. PLoS Genet 2020; 16:e1009228. [PMID: 33296356 PMCID: PMC7752094 DOI: 10.1371/journal.pgen.1009228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/21/2020] [Accepted: 10/27/2020] [Indexed: 01/05/2023] Open
Abstract
Signal transduction pathways are intricately fine-tuned to accomplish diverse biological processes. An example is the conserved Ras/mitogen-activated-protein-kinase (MAPK) pathway, which exhibits context-dependent signaling output dynamics and regulation. Here, by altering codon usage as a novel platform to control signaling output, we screened the Drosophila genome for modifiers specific to either weak or strong Ras-driven eye phenotypes. Our screen enriched for regions of the genome not previously connected with Ras phenotypic modification. We mapped the underlying gene from one modifier to the ribosomal gene RpS21. In multiple contexts, we show that RpS21 preferentially influences weak Ras/MAPK signaling outputs. These data show that codon usage manipulation can identify new, output-specific signaling regulators, and identify RpS21 as an in vivo Ras/MAPK phenotypic regulator. Cellular communication is critical in controlling the growth of organs and must be carefully regulated to prevent disease. The Ras signaling pathway is frequently used for cellular communication of tissue growth regulation but can operate at different signaling strengths. Here, we used a novel strategy to identify genes that specifically tune weak or strong Ras signaling states. We find that the gene RpS21 preferentially tunes weak Ras signaling states.
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Affiliation(s)
- Jessica K. Sawyer
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Zahra Kabiri
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Ruth A. Montague
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Scott R. Allen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Rebeccah Stewart
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Sarah V. Paramore
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Erez Cohen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Hamed Zaribafzadeh
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Christopher M. Counter
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- * E-mail: (CMC); (DTF)
| | - Donald T. Fox
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- * E-mail: (CMC); (DTF)
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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Patel V, Asatryan B, Siripanthong B, Munroe PB, Tiku-Owens A, Lopes LR, Khanji MY, Protonotarios A, Santangeli P, Muser D, Marchlinski FE, Brady PA, Chahal CAA. State of the Art Review on Genetics and Precision Medicine in Arrhythmogenic Cardiomyopathy. Int J Mol Sci 2020; 21:ijms21186615. [PMID: 32927679 PMCID: PMC7554944 DOI: 10.3390/ijms21186615] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022] Open
Abstract
Arrhythmogenic cardiomyopathy (ACM) is an inherited cardiomyopathy characterised by ventricular arrhythmia and an increased risk of sudden cardiac death (SCD). Numerous genetic determinants and phenotypic manifestations have been discovered in ACM, posing a significant clinical challenge. Further to this, wider evaluation of family members has revealed incomplete penetrance and variable expressivity in ACM, suggesting a complex genotype-phenotype relationship. This review details the genetic basis of ACM with specific genotype-phenotype associations, providing the reader with a nuanced perspective of this condition; whilst also proposing a future roadmap to delivering precision medicine-based management in ACM.
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Affiliation(s)
- Viraj Patel
- Department of Cardiology, Royal Papworth Hospital, Cambridge CB2 0AY, UK;
| | - Babken Asatryan
- Department of Cardiology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland;
| | | | - Patricia B. Munroe
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK;
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Anjali Tiku-Owens
- Division of Cardiovascular Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA; (A.T.-O.); (P.S.); (D.M.); (F.E.M.)
| | - Luis R. Lopes
- Department of Cardiology, St Bartholomew’s Hospital, London EC1A 7BE, UK; (L.R.L.); (M.Y.K.); (A.P.)
- Centre for Heart Muscle Disease, UCL Institute of Cardiovascular Science, London WC1E 6BT, UK
| | - Mohammed Y. Khanji
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
- Department of Cardiology, St Bartholomew’s Hospital, London EC1A 7BE, UK; (L.R.L.); (M.Y.K.); (A.P.)
| | - Alexandros Protonotarios
- Department of Cardiology, St Bartholomew’s Hospital, London EC1A 7BE, UK; (L.R.L.); (M.Y.K.); (A.P.)
- Centre for Heart Muscle Disease, UCL Institute of Cardiovascular Science, London WC1E 6BT, UK
| | - Pasquale Santangeli
- Division of Cardiovascular Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA; (A.T.-O.); (P.S.); (D.M.); (F.E.M.)
| | - Daniele Muser
- Division of Cardiovascular Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA; (A.T.-O.); (P.S.); (D.M.); (F.E.M.)
| | - Francis E. Marchlinski
- Division of Cardiovascular Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA; (A.T.-O.); (P.S.); (D.M.); (F.E.M.)
| | - Peter A. Brady
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Division of Cardiology, Department of Medicine, Advocate Illinois Masonic Medical Center, Chicago, IL 60657, USA
| | - C. Anwar A. Chahal
- Department of Cardiology, Royal Papworth Hospital, Cambridge CB2 0AY, UK;
- Division of Cardiovascular Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA; (A.T.-O.); (P.S.); (D.M.); (F.E.M.)
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Correspondence: ; Tel.: +1-267-252-3461
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22
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Fuller ZL, Koury SA, Leonard CJ, Young RE, Ikegami K, Westlake J, Richards S, Schaeffer SW, Phadnis N. Extensive Recombination Suppression and Epistatic Selection Causes Chromosome-Wide Differentiation of a Selfish Sex Chromosome in Drosophila pseudoobscura. Genetics 2020; 216:205-226. [PMID: 32732371 PMCID: PMC7463281 DOI: 10.1534/genetics.120.303460] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/27/2020] [Indexed: 11/18/2022] Open
Abstract
Sex-Ratio (SR) chromosomes are selfish X-chromosomes that distort Mendelian segregation and are commonly associated with inversions. These chromosomal rearrangements suppress recombination with Standard (ST) X-chromosomes and are hypothesized to maintain multiple alleles important for distortion in a single large haplotype. Here, we conduct a multifaceted study of the multiply inverted Drosophila pseudoobscura SR chromosome to understand the evolutionary history, genetic architecture, and present-day dynamics that shape this enigmatic selfish chromosome. The D. pseudoobscura SR chromosome has three nonoverlapping inversions of the right arm of the metacentric X-chromosome: basal, medial, and terminal. We find that 23 of 29 Mb of the D. pseudoobscuraX-chromosome right arm is highly differentiated between the Standard and SR arrangements, including a 6.6 Mb collinear region between the medial and terminal inversions. Although crossing-over is heavily suppressed on this chromosome arm, we discover it is not completely eliminated, with measured rates indicating recombination suppression alone cannot explain patterns of differentiation or the near-perfect association of the three SR chromosome inversions in nature. We then demonstrate the ancient basal and medial inversions of the SR chromosome contain genes sufficient to cause weak distortion. In contrast, the younger terminal inversion cannot distort by itself, but contains at least one modifier gene necessary for full manifestation of strong sex chromosome distortion. By parameterizing population genetic models for chromosome-wide linkage disequilibrium with our experimental results, we infer that strong selection acts to maintain the near-perfect association of SR chromosome inversions in present-day populations. Based on comparative genomic analyses, direct recombination experiments, segregation distortion assays, and population genetic modeling, we conclude the combined action of suppressed recombination and strong, ongoing, epistatic selection shape the D. pseudoobscura SR arrangement into a highly differentiated chromosome.
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Affiliation(s)
- Zachary L Fuller
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Spencer A Koury
- School of Biological Sciences, University of Utah, Salt Lake City, Utah 84112
| | | | - Randee E Young
- School of Biological Sciences, University of Utah, Salt Lake City, Utah 84112
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Kobe Ikegami
- School of Biological Sciences, University of Utah, Salt Lake City, Utah 84112
| | - Jonathan Westlake
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030
| | - Stephen W Schaeffer
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Nitin Phadnis
- School of Biological Sciences, University of Utah, Salt Lake City, Utah 84112
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Gerdes Gyuricza I, Barbosa de Souza R, Farinha-Arcieri LE, Ribeiro Fernandes G, Veiga Pereira L. Is HSPG2 a modifier gene for Marfan syndrome? Eur J Hum Genet 2020; 28:1292-1296. [PMID: 32514132 PMCID: PMC7608216 DOI: 10.1038/s41431-020-0666-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/17/2020] [Accepted: 05/12/2020] [Indexed: 11/26/2022] Open
Abstract
Marfan syndrome (MFS) is a connective tissue disease caused by variants in the FBN1 gene. Nevertheless, other genes influence the manifestations of the disease, characterized by high clinical variability even within families. We mapped modifier loci for cardiovascular and skeletal manifestations in the mg∆loxPneo mouse model for MFS and the synthenic loci in the human genome. Corroborating our findings, one of those loci was identified also as a modifier locus in MFS patients. Here, we investigate the HSPG2 gene, located in this region, as a candidate modifier gene for MFS. We show a correlation between Fbn1 and Hspg2 expression in spinal column and aorta in non-isogenic mg∆loxPneo mice. Moreover, we show that mice with severe phenotypes present lower expression of Hspg2 than those mildly affected. Thus, we propose that HSPG2 is a strong candidate modifier gene for MFS and its role in modulating disease severity should be investigated in patients.
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Affiliation(s)
- Isabela Gerdes Gyuricza
- National Laboratory for Embryonic Stem Cells (LaNCE), Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Rodrigo Barbosa de Souza
- National Laboratory for Embryonic Stem Cells (LaNCE), Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Luis Ernesto Farinha-Arcieri
- National Laboratory for Embryonic Stem Cells (LaNCE), Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Gustavo Ribeiro Fernandes
- National Laboratory for Embryonic Stem Cells (LaNCE), Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Lygia Veiga Pereira
- National Laboratory for Embryonic Stem Cells (LaNCE), Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, 05508-900, Brazil.
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Coco-Martin RM, Sanchez-Tocino HT, Desco C, Usategui-Martín R, Tellería JJ. PRPH2-Related Retinal Diseases: Broadening the Clinical Spectrum and Describing a New Mutation. Genes (Basel) 2020; 11:genes11070773. [PMID: 32660024 PMCID: PMC7397286 DOI: 10.3390/genes11070773] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/30/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
Over 175 pathogenic mutations in the Peripherin-2 (PRPH2) gene are linked to various retinal diseases. We report the phenotype and genotype of eight families (24 patients) with retinal diseases associated with seven distinct PRPH2 gene mutations. We identified a new mutation, c.824_828+3delinsCATTTGGGCTCCTCATTTGG, in a patient with adult-onset vitelliform macular dystrophy (AVMD). One family with the p.Arg46Ter mutation presented with the already described AVMD phenotype, but another family presented with the same mutation and two heterozygous pathogenic mutations (p.Leu2027Phe and p.Gly1977Ser) in the ATP Binding Cassette Subfamily A Member 4 (ABCA4) gene that cause extensive chorioretinal atrophy (ECA), which could be a blended phenotype. The p.Lys154del PRPH2 gene mutation associated with the p.Arg2030Glu mutation in the ABCA4 gene was found in a patient with multifocal pattern dystrophy simulating fundus flavimaculatus (PDsFF), for whom we considered ABCA4 as a possible modifying gene. The mutation p.Gly167Ser was already known to cause pattern dystrophy, but we also found ECA, PDsFF, and autosomal-dominant retinitis pigmentosa (ADRP) as possible phenotypes. Finally, we identified the mutation p.Arg195Leu in a large family with common ancestry, which previously was described to cause central areolar choroidal dystrophy (CACD), but we also found ADRP and observed that it caused ECA more frequently than CACD in this family.
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Affiliation(s)
- Rosa M. Coco-Martin
- Instituto Universitario de Oftalmobiologia Aplicada, Universidad de Valladolid, 47011 Valladolid, Spain; (R.U.-M.); (J.J.T.)
- Red Temática de Investigación Cooperativa en Salud de Oftalmologia (Oftared), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-983-423-559 (ext. 4738)
| | | | - Carmen Desco
- Fisabio Oftalmologia Medica, 46035 Valencia, Spain;
| | - Ricardo Usategui-Martín
- Instituto Universitario de Oftalmobiologia Aplicada, Universidad de Valladolid, 47011 Valladolid, Spain; (R.U.-M.); (J.J.T.)
| | - Juan J. Tellería
- Instituto Universitario de Oftalmobiologia Aplicada, Universidad de Valladolid, 47011 Valladolid, Spain; (R.U.-M.); (J.J.T.)
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25
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Milind N, Preuss C, Haber A, Ananda G, Mukherjee S, John C, Shapley S, Logsdon BA, Crane PK, Carter GW. Transcriptomic stratification of late-onset Alzheimer's cases reveals novel genetic modifiers of disease pathology. PLoS Genet 2020; 16:e1008775. [PMID: 32492070 PMCID: PMC7295244 DOI: 10.1371/journal.pgen.1008775] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 06/15/2020] [Accepted: 04/09/2020] [Indexed: 11/18/2022] Open
Abstract
Late-Onset Alzheimer's disease (LOAD) is a common, complex genetic disorder well-known for its heterogeneous pathology. The genetic heterogeneity underlying common, complex diseases poses a major challenge for targeted therapies and the identification of novel disease-associated variants. Case-control approaches are often limited to examining a specific outcome in a group of heterogenous patients with different clinical characteristics. Here, we developed a novel approach to define relevant transcriptomic endophenotypes and stratify decedents based on molecular profiles in three independent human LOAD cohorts. By integrating post-mortem brain gene co-expression data from 2114 human samples with LOAD, we developed a novel quantitative, composite phenotype that can better account for the heterogeneity in genetic architecture underlying the disease. We used iterative weighted gene co-expression network analysis (WGCNA) to reduce data dimensionality and to isolate gene sets that are highly co-expressed within disease subtypes and represent specific molecular pathways. We then performed single variant association testing using whole genome-sequencing data for the novel composite phenotype in order to identify genetic loci that contribute to disease heterogeneity. Distinct LOAD subtypes were identified for all three study cohorts (two in ROSMAP, three in Mayo Clinic, and two in Mount Sinai Brain Bank). Single variant association analysis identified a genome-wide significant variant in TMEM106B (p-value < 5×10-8, rs1990620G) in the ROSMAP cohort that confers protection from the inflammatory LOAD subtype. Taken together, our novel approach can be used to stratify LOAD into distinct molecular subtypes based on affected disease pathways.
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Affiliation(s)
- Nikhil Milind
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- Program in Genetics, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Christoph Preuss
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Annat Haber
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | | | - Shubhabrata Mukherjee
- Department of Medicine, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Cai John
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Sarah Shapley
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- Program in Neuroscience, Department of Biology and Geology, Baldwin Wallace University, Berea, Ohio, United States of America
| | | | - Paul K. Crane
- Department of Medicine, School of Medicine, University of Washington, Seattle, Washington, United States of America
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26
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Aksit MA, Pace RG, Vecchio-Pagán B, Ling H, Rommens JM, Boelle PY, Guillot L, Raraigh KS, Pugh E, Zhang P, Strug LJ, Drumm ML, Knowles MR, Cutting GR, Corvol H, Blackman SM. Genetic Modifiers of Cystic Fibrosis-Related Diabetes Have Extensive Overlap With Type 2 Diabetes and Related Traits. J Clin Endocrinol Metab 2020; 105:5599821. [PMID: 31697830 PMCID: PMC7236628 DOI: 10.1210/clinem/dgz102] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/02/2019] [Indexed: 02/08/2023]
Abstract
CONTEXT Individuals with cystic fibrosis (CF) develop a distinct form of diabetes characterized by β-cell dysfunction and islet amyloid accumulation similar to type 2 diabetes (T2D), but generally have normal insulin sensitivity. CF-related diabetes (CFRD) risk is determined by both CFTR, the gene responsible for CF, and other genetic variants. OBJECTIVE To identify genetic modifiers of CFRD and determine the genetic overlap with other types of diabetes. DESIGN AND PATIENTS A genome-wide association study was conducted for CFRD onset on 5740 individuals with CF. Weighted polygenic risk scores (PRSs) for type 1 diabetes (T1D), T2D, and diabetes endophenotypes were tested for association with CFRD. RESULTS Genome-wide significance was obtained for variants at a novel locus (PTMA) and 2 known CFRD genetic modifiers (TCF7L2 and SLC26A9). PTMA and SLC26A9 variants were CF-specific; TCF7L2 variants also associated with T2D. CFRD was strongly associated with PRSs for T2D, insulin secretion, postchallenge glucose concentration, and fasting plasma glucose, and less strongly with T1D PRSs. CFRD was inconsistently associated with PRSs for insulin sensitivity and was not associated with a PRS for islet autoimmunity. A CFRD PRS comprising variants selected from these PRSs (with a false discovery rate < 0.1) and the genome-wide significant variants was associated with CFRD in a replication population. CONCLUSIONS CFRD and T2D have more etiologic and mechanistic overlap than previously known, aligning along pathways involving β-cell function rather than insulin sensitivity. Two CFRD risk loci are unrelated to T2D and may affect multiple aspects of CF. An 18-variant PRS stratifies risk of CFRD in an independent population.
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Affiliation(s)
- Melis A Aksit
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rhonda G Pace
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - Hua Ling
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Johanna M Rommens
- The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
| | - Pierre-Yves Boelle
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, iPLESP, AP-HP, Hôpital Saint-Antoine, Paris, France
| | - Loic Guillot
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Karen S Raraigh
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Peng Zhang
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Lisa J Strug
- The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
| | | | - Michael R Knowles
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Garry R Cutting
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Harriet Corvol
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Scott M Blackman
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Division of Pediatric Endocrinology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Correspondence and Reprint Requests: Scott M. Blackman, McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205. E-mail:
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27
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Pineau F, Caimmi D, Magalhães M, Fremy E, Mohamed A, Mely L, Leroy S, Murris M, Claustres M, Chiron R, De Sario A. Blood co-expression modules identify potential modifier genes of diabetes and lung function in cystic fibrosis. PLoS One 2020; 15:e0231285. [PMID: 32302349 PMCID: PMC7164665 DOI: 10.1371/journal.pone.0231285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/19/2020] [Indexed: 01/11/2023] Open
Abstract
Cystic fibrosis (CF) is a rare genetic disease that affects the respiratory and digestive systems. Lung disease is variable among CF patients and associated with the development of comorbidities and chronic infections. The rate of lung function deterioration depends not only on the type of mutations in CFTR, the disease-causing gene, but also on modifier genes. In the present study, we aimed to identify genes and pathways that (i) contribute to the pathogenesis of cystic fibrosis and (ii) modulate the associated comorbidities. We profiled blood samples in CF patients and healthy controls and analyzed RNA-seq data with Weighted Gene Correlation Network Analysis (WGCNA). Interestingly, lung function, body mass index, the presence of diabetes, and chronic P. aeruginosa infections correlated with four modules of co-expressed genes. Detailed inspection of networks and hub genes pointed to cell adhesion, leukocyte trafficking and production of reactive oxygen species as central mechanisms in lung function decline and cystic fibrosis-related diabetes. Of note, we showed that blood is an informative surrogate tissue to study the contribution of inflammation to lung disease and diabetes in CF patients. Finally, we provided evidence that WGCNA is useful to analyze–omic datasets in rare genetic diseases as patient cohorts are inevitably small.
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Affiliation(s)
- Fanny Pineau
- EA7402, Laboratoire de Génétique de Maladies Rares (LGMR), University of Montpellier, Montpellier, France
| | - Davide Caimmi
- CRCM, Arnaud de Villeneuve Hospital, Montpellier, France
| | - Milena Magalhães
- EA7402, Laboratoire de Génétique de Maladies Rares (LGMR), University of Montpellier, Montpellier, France
| | - Enora Fremy
- EA7402, Laboratoire de Génétique de Maladies Rares (LGMR), University of Montpellier, Montpellier, France
| | - Abdillah Mohamed
- EA7402, Laboratoire de Génétique de Maladies Rares (LGMR), University of Montpellier, Montpellier, France
| | | | | | | | - Mireille Claustres
- EA7402, Laboratoire de Génétique de Maladies Rares (LGMR), University of Montpellier, Montpellier, France
- CHU Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
| | - Raphael Chiron
- CRCM, Arnaud de Villeneuve Hospital, Montpellier, France
| | - Albertina De Sario
- EA7402, Laboratoire de Génétique de Maladies Rares (LGMR), University of Montpellier, Montpellier, France
- * E-mail:
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28
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Saferali A, Tang AC, Strug LJ, Quon BS, Zlosnik J, Sandford AJ, Turvey SE. Immunomodulatory function of the cystic fibrosis modifier gene BPIFA1. PLoS One 2020; 15:e0227067. [PMID: 31931521 PMCID: PMC6957340 DOI: 10.1371/journal.pone.0227067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 12/10/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Cystic fibrosis (CF) is characterized by a progressive decline in lung function due to airway obstruction, infection, and inflammation. CF patients are particularly susceptible to respiratory infection by a variety of pathogens, and the inflammatory response in CF is dysregulated and prolonged. BPI fold containing family A, member 1 (BPIFA1) and BPIFB1 are proteins expressed in the upper airways that may have innate immune activity. We previously identified polymorphisms in the BPIFA1/BPIFB1 region associated with CF lung disease severity. METHODS We evaluated whether the BPIFA1/BPIFB1 associations with lung disease severity replicated in individuals with CF participating in the International CF Gene Modifier Consortium (n = 6,365). Furthermore, we investigated mechanisms by which the BPIFA1 and BPIFB1 proteins may modify lung disease in CF. RESULTS The association of the G allele of rs1078761 with reduced lung function was replicated in an independent cohort of CF patients (p = 0.001, n = 2,921) and in a meta-analysis of the full consortium (p = 2.39x10-5, n = 6,365). Furthermore, we found that rs1078761G which is associated with reduced lung function was also associated with reduced BPIFA1, but not BPIFB1, protein levels in saliva from CF patients. Functional assays indicated that BPIFA1 and BPIFB1 do not have an anti-bacterial role against P. aeruginosa but may have an immunomodulatory function in CF airway epithelial cells. Gene expression profiling using RNAseq identified Rho GTPase signaling pathways to be altered in CF airway epithelial cells in response to treatment with recombinant BPIFA1 and BPIFB1 proteins. CONCLUSIONS BPIFA1 and BPIFB1 have immunomodulatory activity and genetic variation associated with low levels of these proteins may increase CF lung disease severity.
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Affiliation(s)
- Aabida Saferali
- Centre for Heart Lung Innovation, University of British Columbia and St Paul’s Hospital, Vancouver, British Columbia, Canada
- Department of Pediatrics, University of British Columbia and BC Children’s Hospital, Vancouver, British Columbia, Canada
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Anthony C. Tang
- Department of Pediatrics, University of British Columbia and BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Lisa J. Strug
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Bradley S. Quon
- Centre for Heart Lung Innovation, University of British Columbia and St Paul’s Hospital, Vancouver, British Columbia, Canada
| | - James Zlosnik
- Department of Pediatrics, University of British Columbia and BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Andrew J. Sandford
- Centre for Heart Lung Innovation, University of British Columbia and St Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Stuart E. Turvey
- Department of Pediatrics, University of British Columbia and BC Children’s Hospital, Vancouver, British Columbia, Canada
- * E-mail:
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29
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Abstract
Familial cerebral cavernous malformation type 1 (CCM1) is an autosomal dominant disease caused by mutations in the Krev Interaction Trapped 1 (KRIT1/CCM1) gene, and characterized by brain lesions that can cause hemorrhagic strokes, seizures, and neurological deficits. Carriers of the same genetic mutation can present with variable symptoms and severity of disease, suggesting the influence of modifier factors. Genetic modifiers of CCM1 disease severity have been recently identified and included common genetic variants in inflammatory, immune response, and oxidative stress genes and pathways. Here, we describe the genotyping of CCM1 patients with the same gene mutation (Q455X) using a high-throughput genotyping array optimized for individuals of Hispanic/Latino ancestry. We then review the quality control steps following the genome-wide genotyping. Genome-wide genotyping of larger cohorts of CCM1 patients might reveal additional genetic variants contributing to the disease severity of CCM1.
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Affiliation(s)
- Hélène Choquet
- Division of Research, Kaiser Permanente Northern California (KPNC), Oakland, CA, USA.
| | - Helen Kim
- Department of Anesthesia and Perioperative Care, School of Medicine, University of California San Francisco (UCSF), San Francisco, CA, USA
- Institute for Human Genetics, UCSF, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, USA
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30
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To TL, Cuadros AM, Shah H, Hung WHW, Li Y, Kim SH, Rubin DHF, Boe RH, Rath S, Eaton JK, Piccioni F, Goodale A, Kalani Z, Doench JG, Root DE, Schreiber SL, Vafai SB, Mootha VK. A Compendium of Genetic Modifiers of Mitochondrial Dysfunction Reveals Intra-organelle Buffering. Cell 2019; 179:1222-1238.e17. [PMID: 31730859 PMCID: PMC7053407 DOI: 10.1016/j.cell.2019.10.032] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 09/12/2019] [Accepted: 10/23/2019] [Indexed: 12/18/2022]
Abstract
Mitochondrial dysfunction is associated with a spectrum of human conditions, ranging from rare, inborn errors of metabolism to the aging process. To identify pathways that modify mitochondrial dysfunction, we performed genome-wide CRISPR screens in the presence of small-molecule mitochondrial inhibitors. We report a compendium of chemical-genetic interactions involving 191 distinct genetic modifiers, including 38 that are synthetic sick/lethal and 63 that are suppressors. Genes involved in glycolysis (PFKP), pentose phosphate pathway (G6PD), and defense against lipid peroxidation (GPX4) scored high as synthetic sick/lethal. A surprisingly large fraction of suppressors are pathway intrinsic and encode mitochondrial proteins. A striking example of such "intra-organelle" buffering is the alleviation of a chemical defect in complex V by simultaneous inhibition of complex I, which benefits cells by rebalancing redox cofactors, increasing reductive carboxylation, and promoting glycolysis. Perhaps paradoxically, certain forms of mitochondrial dysfunction may best be buffered with "second site" inhibitors to the organelle.
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Affiliation(s)
- Tsz-Leung To
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Hardik Shah
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Wendy H W Hung
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Yang Li
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sharon H Kim
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Daniel H F Rubin
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ryan H Boe
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Sneha Rath
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - John K Eaton
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Amy Goodale
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Zohra Kalani
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - John G Doench
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Stuart L Schreiber
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Scott B Vafai
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Vamsi K Mootha
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.
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31
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Lustyk D, Kinský S, Ullrich KK, Yancoskie M, Kašíková L, Gergelits V, Sedlacek R, Chan YF, Odenthal-Hesse L, Forejt J, Jansa P. Genomic Structure of Hstx2 Modifier of Prdm9-Dependent Hybrid Male Sterility in Mice. Genetics 2019; 213:1047-1063. [PMID: 31562180 PMCID: PMC6827376 DOI: 10.1534/genetics.119.302554] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 09/23/2019] [Indexed: 02/06/2023] Open
Abstract
F1 hybrids between mouse inbred strains PWD and C57BL/6 represent the most thoroughly genetically defined model of hybrid sterility in vertebrates. Hybrid male sterility can be fully reconstituted from three components of this model, the Prdm9 gene, intersubspecific homeology of Mus musculus musculus and Mus musculus domesticus autosomes, and the X-linked Hstx2 locus. Hstx2 modulates the extent of Prdm9-dependent meiotic arrest and harbors two additional factors responsible for intersubspecific introgression-induced oligospermia (Hstx1) and meiotic recombination rate (Meir1). To facilitate positional cloning and to overcome the recombination suppression within the 4.3 Mb encompassing the Hstx2 locus, we designed Hstx2-CRISPR and SPO11/Cas9 transgenes aimed to induce DNA double-strand breaks specifically within the Hstx2 locus. The resulting recombinant reduced the Hstx2 locus to 2.70 Mb (chromosome X: 66.51-69.21 Mb). The newly defined Hstx2 locus still operates as the major X-linked factor of the F1 hybrid sterility, and controls meiotic chromosome synapsis and meiotic recombination rate. Despite extensive further crosses, the 2.70 Mb Hstx2 interval behaved as a recombination cold spot with reduced PRDM9-mediated H3K4me3 hotspots and absence of DMC1-defined DNA double-strand-break hotspots. To search for structural anomalies as a possible cause of recombination suppression, we used optical mapping and observed high incidence of subspecies-specific structural variants along the X chromosome, with a striking copy number polymorphism of the microRNA Mir465 cluster. This observation together with the absence of a strong sterility phenotype in Fmr1 neighbor (Fmr1nb) null mutants support the role of microRNA as a likely candidate for Hstx2.
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Affiliation(s)
- Diana Lustyk
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
- Faculty of Science, Charles University, Prague CZ-12000, Czech Republic
| | - Slavomír Kinský
- The Czech Centre for Phenogenomics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Kristian Karsten Ullrich
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
| | - Michelle Yancoskie
- Molecular Basis and Evolution of Complex Traits Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen 72076, Germany
| | - Lenka Kašíková
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Vaclav Gergelits
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Radislav Sedlacek
- The Czech Centre for Phenogenomics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Yingguang Frank Chan
- Molecular Basis and Evolution of Complex Traits Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen 72076, Germany
| | - Linda Odenthal-Hesse
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
| | - Jiri Forejt
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Petr Jansa
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
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Swahn H, Sabith Ebron J, Lamar K, Yin S, Kerschner JL, NandyMazumdar M, Coppola C, Mendenhall EM, Leir S, Harris A. Coordinate regulation of ELF5 and EHF at the chr11p13 CF modifier region. J Cell Mol Med 2019; 23:7726-7740. [PMID: 31557407 PMCID: PMC6815777 DOI: 10.1111/jcmm.14646] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/02/2019] [Accepted: 08/10/2019] [Indexed: 12/21/2022] Open
Abstract
E74-like factor 5 (ELF5) and ETS-homologous factor (EHF) are epithelial selective ETS family transcription factors (TFs) encoded by genes at chr11p13, a region associated with cystic fibrosis (CF) lung disease severity. EHF controls many key processes in lung epithelial function so its regulatory mechanisms are important. Using CRISPR/Cas9 technology, we removed three key cis-regulatory elements (CREs) from the chr11p13 region and also activated multiple open chromatin sites with CRISPRa in airway epithelial cells. Deletion of the CREs caused subtle changes in chromatin architecture and site-specific increases in EHF and ELF5. CRISPRa had most effect on ELF5 transcription. ELF5 levels are low in airway cells but higher in LNCaP (prostate) and T47D (breast) cancer cells. ATAC-seq in these lines revealed novel peaks of open chromatin at the 5' end of chr11p13 associated with an expressed ELF5 gene. Furthermore, 4C-seq assays identified direct interactions between the active ELF5 promoter and sites within the EHF locus, suggesting coordinate regulation between these TFs. ChIP-seq for ELF5 in T47D cells revealed ELF5 occupancy within EHF introns 1 and 6, and siRNA-mediated depletion of ELF5 enhanced EHF expression. These results define a new role for ELF5 in lung epithelial biology.
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Affiliation(s)
- Hannah Swahn
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Jey Sabith Ebron
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Kay‐Marie Lamar
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Shiyi Yin
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Jenny L. Kerschner
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Monali NandyMazumdar
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Candice Coppola
- Department of Biological SciencesUniversity of Alabama in HuntsvilleHuntsvilleALUSA
| | - Eric M. Mendenhall
- Department of Biological SciencesUniversity of Alabama in HuntsvilleHuntsvilleALUSA
| | - Shih‐Hsing Leir
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Ann Harris
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
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Schlaak RA, Frei A, Schottstaedt AM, Tsaih SW, Fish BL, Harmann L, Liu Q, Gasperetti T, Medhora M, North PE, Strande JL, Sun Y, Rui H, Flister MJ, Bergom C. Mapping genetic modifiers of radiation-induced cardiotoxicity to rat chromosome 3. Am J Physiol Heart Circ Physiol 2019; 316:H1267-H1280. [PMID: 30848680 PMCID: PMC6620678 DOI: 10.1152/ajpheart.00482.2018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 02/08/2023]
Abstract
Radiation therapy is used in ~50% of cancer patients to reduce the risk of recurrence and in some cases improve survival. Despite these benefits, doses can be limited by toxicity in multiple organs, including the heart. The underlying causes and biomarkers of radiation-induced cardiotoxicity are currently unknown, prompting the need for experimental models with inherent differences in sensitivity and resistance to the development of radiation-induced cardiotoxicity. We have identified the parental SS (Dahl salt-sensitive/Mcwi) rat strain to be a highly-sensitized model of radiation-induced cardiotoxicity. In comparison, substitution of rat chromosome 3 from the resistant BN (Brown Norway) rat strain onto the SS background (SS-3BN consomic) significantly attenuated radiation-induced cardiotoxicity. SS-3BN rats had less radiation-induced cardiotoxicity than SS rats, as measured by survival, pleural and pericardial effusions, echocardiogram parameters, and histological damage. Mast cells, previously shown to have predominantly protective roles in radiation-induced cardiotoxicity, were increased in the more resistant SS-3BN hearts postradiation. RNA sequencing from SS and SS-3BN hearts at 1 wk postradiation revealed 5,098 differentially expressed candidate genes across the transcriptome and 350 differentially expressed genes on rat chromosome 3, which coincided with enrichment of multiple pathways, including mitochondrial dysfunction, sirtuin signaling, and ubiquitination. Upstream regulators of enriched pathways included the oxidative stress modulating transcription factor, Nrf2, which is located on rat chromosome 3. Nrf2 target genes were also differentially expressed in the SS vs. SS-3BN consomic hearts postradiation. Collectively, these data confirm the existence of heritable modifiers in radiation-induced cardiotoxicity and provide multiple biomarkers, pathways, and candidate genes for future analyses. NEW & NOTEWORTHY This novel study reveals that heritable genetic factors have the potential to modify normal tissue sensitivity to radiation. Gene variant(s) on rat chromosome 3 can contribute to enhanced cardiotoxicity displayed in the SS rats vs. the BN and SS-3BN consomic rats. Identifying genes that lead to understanding the mechanisms of radiation-induced cardiotoxicity represents a novel method to personalize radiation treatment, as well as predict the development of radiation-induced cardiotoxicity.
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Affiliation(s)
- Rachel A Schlaak
- Department of Pharmacology and Toxicology, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Anne Frei
- Department of Radiation Oncology, Medical College of Wisconsin , Milwaukee, Wisconsin
| | | | - Shirng-Wern Tsaih
- Department of Physiology, Medical College of Wisconsin , Milwaukee, Wisconsin
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Brian L Fish
- Department of Radiation Oncology, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Leanne Harmann
- Department of Medicine, Division of Cardiovascular Medicine, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Qian Liu
- Interdisciplinary Program in Biomedical Sciences, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Tracy Gasperetti
- Department of Radiation Oncology, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Meetha Medhora
- Department of Radiation Oncology, Medical College of Wisconsin , Milwaukee, Wisconsin
- Cardiovascular Center, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Paula E North
- Department of Pathology, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Jennifer L Strande
- Department of Medicine, Division of Cardiovascular Medicine, Medical College of Wisconsin , Milwaukee, Wisconsin
- Cardiovascular Center, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Yunguang Sun
- Department of Pathology, Medical College of Wisconsin , Milwaukee, Wisconsin
- Cancer Center, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Hallgeir Rui
- Department of Pathology, Medical College of Wisconsin , Milwaukee, Wisconsin
- Cancer Center, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Michael J Flister
- Department of Medicine, Case Western Reserve University , Cleveland, Ohio
- Department of Physiology, Medical College of Wisconsin , Milwaukee, Wisconsin
- Cardiovascular Center, Medical College of Wisconsin , Milwaukee, Wisconsin
- Cancer Center, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Carmen Bergom
- Department of Radiation Oncology, Medical College of Wisconsin , Milwaukee, Wisconsin
- Cardiovascular Center, Medical College of Wisconsin , Milwaukee, Wisconsin
- Cancer Center, Medical College of Wisconsin , Milwaukee, Wisconsin
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ElAlfy MS, Ebeid FSE, Kamal TM, Eissa DS, Ismail EAR, Mohamed SH. Angiotensinogen M235T Gene Polymorphism is a Genetic Determinant of Cerebrovascular and Cardiopulmonary Morbidity in Adolescents with Sickle Cell Disease. J Stroke Cerebrovasc Dis 2019; 28:441-449. [PMID: 30409744 DOI: 10.1016/j.jstrokecerebrovasdis.2018.10.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/09/2018] [Accepted: 10/13/2018] [Indexed: 01/19/2023] Open
Affiliation(s)
- Mohsen Saleh ElAlfy
- Pediatrics Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
| | | | - Tarek Mostafa Kamal
- Medical Genetics Pediatric Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
| | - Deena Samir Eissa
- Clinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
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Kanwal S, Perveen S. Association of SNP in JPH1 gene with severity of disease in Charcot Marie Tooth 2K patients. J PAK MED ASSOC 2019; 69:241-243. [PMID: 30804591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phenotype varies among the various types of Charcot Marie Tooth Neuropathies(CMT), However the problem arises in cases of same gene but gives a huge variety of phenotype in terms of early and late onset and severity of the disease. To check the impact of rs139723190 SNP on severity of the CMT 2k patients; being a genetic modifier of GDAP1. In the current study CMT 2k patients with early and late onset were analyzed for association of rs139723190 SNP in JPH1 gene responsible for CMT type severe and mild phenotypes. Single nucleotide polymorphisms (SNPs) lead to genetic differences in CMT patients on the basis of severity of the disease. The results of the present study suggest that variants of JPH1 may contribute to the genetic susceptibility as it plays a vital role as genetic modifier in CMT 2K. Candidates risk variants should be further evaluated in studies with a larger sample size.
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Abstract
The Hippo Pathway comprises a vast network of components that integrate diverse signals including mechanical cues and cell surface or cell-surface-associated molecules to define cellular outputs of growth, proliferation, cell fate, and cell survival on both the cellular and tissue level. Because of the importance of the regulators, core components, and targets of this pathway in human health and disease, individual components were often identified by efforts in mammalian models or for a role in a specific process such as stress response or cell death. However, multiple components were originally discovered in the Drosophila system, and the breakthrough of conceiving that these components worked together in a signaling pathway came from a series of Drosophila genetic screens and fundamental genetic and phenotypic characterization efforts. In this chapter, we will review the original discoveries leading to the conceptual framework of these components as a tumor suppressor network. We will review chronologically the early efforts that established our initial understanding of the core machinery that then launched the growing and vibrant field to be discussed throughout later chapters of this book.
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Affiliation(s)
- Rewatee Gokhale
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Cathie M Pfleger
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Graduate School of Biomedical Sciences, The Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Meroni M, Longo M, Rametta R, Dongiovanni P. Genetic and Epigenetic Modifiers of Alcoholic Liver Disease. Int J Mol Sci 2018; 19:ijms19123857. [PMID: 30513996 PMCID: PMC6320903 DOI: 10.3390/ijms19123857] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 10/31/2018] [Accepted: 11/28/2018] [Indexed: 12/12/2022] Open
Abstract
Alcoholic liver disease (ALD), a disorder caused by excessive alcohol consumption is a global health issue. More than two billion people consume alcohol in the world and about 75 million are classified as having alcohol disorders. ALD embraces a wide spectrum of hepatic lesions including steatosis, alcoholic steatohepatitis (ASH), fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). ALD is a complex disease where environmental, genetic, and epigenetic factors contribute to its pathogenesis and progression. The severity of alcohol-induced liver disease depends on the amount, method of usage and duration of alcohol consumption as well as on age, gender, presence of obesity, and genetic susceptibility. Genome-wide association studies and candidate gene studies have identified genetic modifiers of ALD that can be exploited as non-invasive biomarkers, but which do not completely explain the phenotypic variability. Indeed, ALD development and progression is also modulated by epigenetic factors. The premise of this review is to discuss the role of genetic variants and epigenetic modifications, with particular attention being paid to microRNAs, as pathogenic markers, risk predictors, and therapeutic targets in ALD.
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Affiliation(s)
- Marica Meroni
- General Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Pad. Granelli, via F Sforza 35, 20122 Milan, Italy.
| | - Miriam Longo
- General Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Pad. Granelli, via F Sforza 35, 20122 Milan, Italy.
| | - Raffaela Rametta
- General Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Pad. Granelli, via F Sforza 35, 20122 Milan, Italy.
| | - Paola Dongiovanni
- General Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Pad. Granelli, via F Sforza 35, 20122 Milan, Italy.
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Andreou S, Panayiotou E, Michailidou K, Pirpa P, Hadjisavvas A, El Salloukh A, Barnes D, Antoniou A, Agathangelou P, Papastavrou K, Christodoulou K, Tanteles GA, Kyriakides T. Epidemiology of ATTRV30M neuropathy in Cyprus and the modifier effect of complement C1q on the age of disease onset. Amyloid 2018; 25:220-226. [PMID: 30572722 DOI: 10.1080/13506129.2018.1534731] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/17/2018] [Accepted: 10/08/2018] [Indexed: 01/08/2023]
Abstract
BACKGROUND ATTRV30M amyloidosis is a lethal autosomal dominant sensorimotor and autonomic neuropathy caused by amyloid deposition composed of aggregated misfolded TTR monomers with the V30M mutation. The age of onset in patients with ATTRV30M varies in different foci and the mechanism behind it is still unknown. METHODS The tertiary neurology center following all ATTRV30M patients in Cyprus was used to collect demographic data to estimate; prevalence, incidence, penetrance, anticipation, time from disease onset to diagnosis and transplantation. Ocular, cardiac and leptomeningeal involvement in transplanted patients was explored. Correlation of C1q tagging SNPs with age of disease onset was carried out. RESULTS Prevalence and incidence for ATTRV30M neuropathy in Cyprus are 5.4/100,000 and 0.3/100,000 respectively. Mean age of onset is 40.6 years and anticipation is 8.3 years. Penetrance reaches 51% and 75% by the ages of 50 and 80 years respectively. In liver transplanted patients rates of ocular, cardiac and leptomeningeal involvement were estimated to be 60%, 20% and 16%, respectively. C1q polymorphisms correlated with age of disease onset. CONCLUSIONS ATTRV30M neuropathy has a rising prevalence in Cyprus due to improved survival of patients. Late onset complications are becoming a major problem. Complement C1q appears to be a modifier in this disease.
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Affiliation(s)
- Savanna Andreou
- a Department of Neuropathology/Neurology Clinic A , The Cyprus Institute of Neurology & Genetics , Nicosia , Cyprus
| | - Elena Panayiotou
- a Department of Neuropathology/Neurology Clinic A , The Cyprus Institute of Neurology & Genetics , Nicosia , Cyprus
| | - Kyriaki Michailidou
- b Department of Electron Microscopy/Molecular Pathology , The Cyprus Institute of Neurology & Genetics , Nicosia , Cyprus
| | - Panayiota Pirpa
- b Department of Electron Microscopy/Molecular Pathology , The Cyprus Institute of Neurology & Genetics , Nicosia , Cyprus
| | - Andreas Hadjisavvas
- b Department of Electron Microscopy/Molecular Pathology , The Cyprus Institute of Neurology & Genetics , Nicosia , Cyprus
| | | | - Daniel Barnes
- d Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology , University of Cambridge , Cambridge , UK
| | - Antonis Antoniou
- d Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology , University of Cambridge , Cambridge , UK
| | - Petros Agathangelou
- a Department of Neuropathology/Neurology Clinic A , The Cyprus Institute of Neurology & Genetics , Nicosia , Cyprus
| | | | - Kyproula Christodoulou
- f Neurogenetics Department , The Cyprus Institute of Neurology & Genetics , Nicosia , Cyprus
| | - George A Tanteles
- g Clinical Genetics Clinic , The Cyprus Institute of Neurology & Genetics , Nicosia , Cyprus
| | - Theodoros Kyriakides
- a Department of Neuropathology/Neurology Clinic A , The Cyprus Institute of Neurology & Genetics , Nicosia , Cyprus
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Abstract
Genetic conditions, even those associated with identical gene mutations, can present with variable clinical manifestations. One widely accepted explanation for this phenomenon is the existence of genetic factors capable of modifying the consequences of disease-causing mutations (modifier genes). Here, we address the concepts and principles by which genetic factors may be involved in modifying risk for cardiac arrhythmia, then discuss the current knowledge and interpretation of their contribution to clinical heterogeneity. We illustrate these concepts in the context of two important clinical conditions associated with risk for sudden cardiac death including a monogenic disorder (congenital long QT syndrome) in which the impact of modifier genes has been established, and a complex trait (life-threatening arrhythmias in acute myocardial infarction) for which the search for genetic modifiers of arrhythmic risk is more challenging. Advances in understanding the contribution of modifier genes to a higher or lower propensity towards sudden death should improve patient-specific risk stratification and be a major step towards precision medicine.
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Affiliation(s)
- Peter J Schwartz
- Istituto Auxologico Italiano, IRCCS, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Via Pier Lombardo, 22, Milan, Italy
- Corresponding author. Tel: +39 02 55000408, Fax: +39 02 55000411, ;
| | - Lia Crotti
- Istituto Auxologico Italiano, IRCCS, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Via Pier Lombardo, 22, Milan, Italy
- Department of Medicine and Surgery, University of Milano-Bicocca, Via Cadore, 48, Monza, Italy
- Istituto Auxologico Italiano, IRCCS, Department of Cardiovascular, Neural and Metabolic Sciences, San Luca Hospital, Piazzale Brescia 20, Milan, Italy
| | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Searle 8-510, East Superior Street, Chicago, IL, USA
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Philp AR, Riquelme TT, Millar-Büchner P, González R, Sepúlveda FV, Cid LP, Flores CA. Kcnn4 is a modifier gene of intestinal cystic fibrosis preventing lethality in the Cftr-F508del mouse. Sci Rep 2018; 8:9320. [PMID: 29915289 PMCID: PMC6006244 DOI: 10.1038/s41598-018-27465-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 06/04/2018] [Indexed: 02/07/2023] Open
Abstract
Nearly 70% of cystic fibrosis (CF) patients bear the phenylalanine-508 deletion but disease severity differs greatly, and is not explained by the existence of different mutations in compound heterozygous. Studies demonstrated that genes other than CFTR relate to intestinal disease in humans and CF-mouse. Kcnn4, the gene encoding the calcium-activated potassium channel KCa3.1, important for intestinal secretion, is present in a locus linked with occurrence of intestinal CF-disease in mice and humans. We reasoned that it might be a CF-modifier gene and bred a CF-mouse with Kcnn4 silencing, finding that lethality was almost abolished. Silencing of Kcnn4 did not improve intestinal secretory functions, but rather corrected increased circulating TNF-α level and reduced intestinal mast cell increase. Given the importance of mast cells in intestinal disease additional double mutant CF-animals were tested, one lacking mast cells (C-kitW-sh/W-sh) and Stat6-/- to block IgE production. While mast cell depletion had no effect, silencing Stat6 significantly reduced lethality. Our results show that Kcnn4 is an intestinal CF modifier gene partially acting through a STAT6-dependent mechanism.
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Affiliation(s)
- Amber R Philp
- Centro de Estudios Científicos (CECs), Arturo Prat 514, Valdivia, Chile
- Universidad Austral de Chile, Valdivia, Chile
| | - Texia T Riquelme
- Centro de Estudios Científicos (CECs), Arturo Prat 514, Valdivia, Chile
| | - Pamela Millar-Büchner
- Centro de Estudios Científicos (CECs), Arturo Prat 514, Valdivia, Chile
- Department of Translational Pulmonology, Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany
| | - Rodrigo González
- Centro de Estudios Científicos (CECs), Arturo Prat 514, Valdivia, Chile
| | | | - L Pablo Cid
- Centro de Estudios Científicos (CECs), Arturo Prat 514, Valdivia, Chile
| | - Carlos A Flores
- Centro de Estudios Científicos (CECs), Arturo Prat 514, Valdivia, Chile.
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Arakawa T, Uchiyama D, Ohgami T, Ohgami R, Murata T, Honma Y, Hamada H, Kuroda Y, Taguchi K, Kitazaki K, Kubo T. A fertility-restoring genotype of beet (Beta vulgaris L.) is composed of a weak restorer-of-fertility gene and a modifier gene tightly linked to the Rf1 locus. PLoS One 2018; 13:e0198409. [PMID: 29856854 PMCID: PMC5983528 DOI: 10.1371/journal.pone.0198409] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 05/19/2018] [Indexed: 11/23/2022] Open
Abstract
Cytoplasmic male sterility (CMS) is a plant trait that involves interactions between nuclear- and mitochondrial genomes. In CMS, the nuclear restorer-of-fertility gene (Rf), a suppressor of male-sterility inducing mitochondria, is one of the best known genetic factors. Other unidentified genetic factors may exist but have not been well characterized. In sugar beet (Beta vulgaris L.), CMS is used for hybrid seed production, but few male-sterility inducing nuclear genotypes exist. Such genotypes could be introduced from a closely related plant such as leaf beet, but first the fertility restoring genotype of the related plant must be characterized. Here, we report the discovery of a Japanese leaf beet accession ‘Fukkoku-ouba’ that has both male-sterility inducing and fertility restoring genotypes. We crossed the leaf beet accession with a sugar beet CMS line, developed succeeding generations, and examined the segregation of two DNA markers that are linked to two sugar beet Rfs, Rf1 and Rf2. Only the Rf2 marker co-segregated with fertility restoration in every generation, implying that the Rf1 locus in leaf beet is occupied by a non-restoring allele. Fertility restoration was incomplete without a genetic factor closely linked to Rf1, leading to the assumption that the Rf1 locus encodes a modifier that cannot restore fertility by itself but perhaps strengthens another Rf. We sequenced the apparently non-restoring ‘Fukkoku-ouba’ rf1 gene-coding region and found that it closely resembles a restoring allele. The protein product demonstrated its potential to suppress CMS in transgenic suspension cells. In contrast, ‘Fukkoku-ouba’ rf1 transcript abundance was highly reduced compared to that of the restoring Rf1. Consistently, changes in protein complexes containing CMS-associated mitochondrial protein in anthers were very minor. Accordingly, we concluded that ‘Fukkoku-ouba’ rf1 is a hypomorph that acts as a non-restoring allele but has the potential to support another Rf, i.e. it is a modifier candidate.
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Affiliation(s)
- Takumi Arakawa
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Daisuke Uchiyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Takashi Ohgami
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Ryo Ohgami
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Tomoki Murata
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yujiro Honma
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hiroyuki Hamada
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yosuke Kuroda
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Memuro, Japan
| | - Kazunori Taguchi
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Memuro, Japan
| | | | - Tomohiko Kubo
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
- * E-mail:
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Abstract
Thalassemia is a disorder of hemoglobin characterized by reduced or absent production of one of the globin chains in human red blood cells with relative excess of the other. Impaired synthesis of β-globin results in β-thalassemia, whereas defective synthesis of α-globin leads to α-thalassemia. Despite being a monogenic disorder, thalassemia exhibits remarkable clinical heterogeneity that is directly related to the intracellular imbalance between α- and β-like globin chains. Novel insights into the genetic modifiers have contributed to the understanding of the correlation between genotype and phenotype and are being explored as therapeutic pathways to cure this life-limiting disease.
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Affiliation(s)
- Sachith Mettananda
- Molecular Hematology Unit, Medical Research Council (MRC), Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK; Department of Paediatrics, Faculty of Medicine, University of Kelaniya, Thalagolla Road, Ragama 11010, Sri Lanka
| | - Douglas R Higgs
- Molecular Hematology Unit, Medical Research Council (MRC), Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK; National Institute for Health Research, Oxford Biomedical Research Centre, Blood Theme, Oxford University Hospitals, Headington, Oxford OX3 9DU, UK.
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Phelps IG, Dempsey JC, Grout ME, Isabella CR, Tully HM, Doherty D, Bachmann-Gagescu R. Interpreting the clinical significance of combined variants in multiple recessive disease genes: systematic investigation of Joubert syndrome yields little support for oligogenicity. Genet Med 2018; 20:223-233. [PMID: 28771248 PMCID: PMC5797514 DOI: 10.1038/gim.2017.94] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/19/2017] [Indexed: 01/11/2023] Open
Abstract
PurposeNext-generation sequencing (NGS) often identifies multiple rare predicted-deleterious variants (RDVs) in different genes associated with a recessive disorder in a given patient. Such variants have been proposed to contribute to digenicity/oligogenicity or "triallelism" or to act as genetic modifiers.MethodsUsing the recessive ciliopathy Joubert syndrome (JBTS) as a model, we investigated these possibilities systematically, relying on NGS of known JBTS genes in a large JBTS and two control cohorts.Results65% of affected individuals had a recessive genetic cause, while 4.9% were candidates for di-/oligogenicity, harboring heterozygous RDVs in two or more genes, compared with 4.2-8% in controls (P = 0.66-0.21). Based on Exome Aggregation Consortium (ExAC) allele frequencies, the probability of cumulating RDVs in any two JBTS genes is 9.3%. We found no support for triallelism, as no unaffected siblings carried the same biallelic RDVs as their affected relative. Sixty percent of individuals sharing identical causal RDVs displayed phenotypic discordance. Although 38% of affected individuals harbored RDVs in addition to the causal mutations, their presence did not correlate with phenotypic severity.ConclusionOur data offer little support for triallelism or digenicity/oligogenicity as clinically relevant inheritance modes in JBTS. While phenotypic discordance supports the existence of genetic modifiers, identifying clinically relevant modifiers remains challenging.
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Affiliation(s)
- Ian G. Phelps
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | - Megan E. Grout
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | - Hannah M. Tully
- Department of Neurology, University of Washington, Seattle, Washington
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington
| | - Ruxandra Bachmann-Gagescu
- Institute of Medical Genetics, University of Zurich, Switzerland
- Institute of Molecular Life Sciences, University of Zurich, Switzerland
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Lai LW, Erickson RP, Bernas M, Witte MH. From childhood onset lymphedema to fatal fetal hydrops: Possible modifying genes for a FOXC2 mutation. Lymphology 2018; 51:85-88. [PMID: 30253460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We performed whole exome sequencing in a family with FOXC2 mutation where the phenotype in one generation was strikingly more severe. Although there were 3 mutations shared by 2 fatal fetal hydrops cases and not the mildly affected mother, none of them were likely to be the cause of the marked phenotypic change.
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Affiliation(s)
- L W Lai
- Department of Chemistry and Biochemistry, University of Arizona College of Medicine, Tucson, USA
| | - R P Erickson
- Department of Pediatrics, University of Arizona College of Medicine, Tucson, USA
| | - M Bernas
- Department of Surgery, University of Arizona College of Medicine, Tucson, USA
- Department of Medical Education, TCU and UNTHSC School of Medicine, Fort Worth, USA
| | - M H Witte
- Department of Surgery, University of Arizona College of Medicine, Tucson, USA
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Fernandez-Jimenez N, Sklias A, Ecsedi S, Cahais V, Degli-Esposti D, Jay A, Ancey PB, Woo HD, Hernandez-Vargas H, Herceg Z. Lowly methylated region analysis identifies EBF1 as a potential epigenetic modifier in breast cancer. Epigenetics 2017; 12:964-972. [PMID: 29099283 PMCID: PMC5788421 DOI: 10.1080/15592294.2017.1373919] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/21/2017] [Accepted: 08/28/2017] [Indexed: 01/03/2023] Open
Abstract
Breast cancer (BC) encompasses heterogeneous pathologies with different subtypes exhibiting distinct molecular changes, including those related to DNA methylation. However, the role of these changes in mediating BC heterogeneity is poorly understood. Lowly methylated regions (LMRs), non-CpG island loci that usually contain transcription factor (TF) binding sites, have been suggested to act as regulatory elements that define cellular identity. In this study, we aimed to identify the key subtype-specific TFs that may lead to LMR generation and shape the BC methylome and transcription program. We initially used whole-genome bisulfite sequencing (WGBS) data available at The Cancer Genome Atlas (TCGA) portal to identify subtype-specific LMRs. Differentially methylated regions (DMRs) within the BC PAM50 subtype-specific LMRs were selected by comparing tumors and normal tissues in a larger TCGA cohort assessed by HumanMethylation450 BeadChip (450K) arrays and TF enrichment analyses were performed. To assess the impact of LMRs on gene expression, TCGA RNA sequencing data were downloaded and Pearson correlations between methylation levels of loci presenting subtype-specific TF motifs and expression of the nearest genes were calculated. WGBS methylome data revealed a large number of LMRs for each of the BC subtypes. Analysis of these LMRs in the 450K datasets available for a larger sample set identified 7,765, 5,657, and 19 differentially methylated positions (DMPs) between normal adjacent tissues and tumor tissues from basal, luminal, and HER2-enriched subtypes, respectively. Unsupervised clustering showed that the discriminatory power of the top DMPs was remarkably strong for basal BC. Interestingly, in this particular subtype, we found 4,409 differentially hypomethylated positions grouped into 1,185 DMRs with a strong enrichment for the early B-cell factor 1 (EBF1) motifs. The methylation levels of the DMRs containing EBF1 motifs showed a strong negative correlation with the expression of 719 nearby genes, including BTS2 and CD74, two oncogenes known to be specific for basal BC subtype and for poor outcome. This study identifies LMRs specific to the three main BC subtypes and reveals EBF1 as a potentially important regulator of BC subtype-specific methylation and gene expression program.
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Affiliation(s)
- Nora Fernandez-Jimenez
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
| | - Athena Sklias
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
| | - Szilvia Ecsedi
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
| | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
| | - Davide Degli-Esposti
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
| | - Antonin Jay
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
| | - Pierre Benoit Ancey
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
| | - Hae Dong Woo
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
| | - Hector Hernandez-Vargas
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
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46
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Quattrocelli M, Capote J, Ohiri JC, Warner JL, Vo AH, Earley JU, Hadhazy M, Demonbreun AR, Spencer MJ, McNally EM. Genetic modifiers of muscular dystrophy act on sarcolemmal resealing and recovery from injury. PLoS Genet 2017; 13:e1007070. [PMID: 29065150 PMCID: PMC5669489 DOI: 10.1371/journal.pgen.1007070] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 11/03/2017] [Accepted: 10/11/2017] [Indexed: 12/17/2022] Open
Abstract
Genetic disruption of the dystrophin complex produces muscular dystrophy characterized by a fragile muscle plasma membrane leading to excessive muscle degeneration. Two genetic modifiers of Duchenne Muscular Dystrophy implicate the transforming growth factor β (TGFβ) pathway, osteopontin encoded by the SPP1 gene and latent TGFβ binding protein 4 (LTBP4). We now evaluated the functional effect of these modifiers in the context of muscle injury and repair to elucidate their mechanisms of action. We found that excess osteopontin exacerbated sarcolemmal injury, and correspondingly, that loss of osteopontin reduced injury extent both in isolated myofibers and in muscle in vivo. We found that ablation of osteopontin was associated with reduced expression of TGFβ and TGFβ-associated pathways. We identified that increased TGFβ resulted in reduced expression of Anxa1 and Anxa6, genes encoding key components of the muscle sarcolemma resealing process. Genetic manipulation of Ltbp4 in dystrophic muscle also directly modulated sarcolemmal resealing, and Ltbp4 alleles acted in concert with Anxa6, a distinct modifier of muscular dystrophy. These data provide a model in which a feed forward loop of TGFβ and osteopontin directly impacts the capacity of muscle to recover from injury, and identifies an intersection of genetic modifiers on muscular dystrophy. Genetic modifiers for muscular dystrophy have been identified through transcriptomic and genomic profiling in humans and mouse models. Two modifiers, Ltbp4 and Spp1, encode extracellular proteins while a third modifier, Anxa6, specifies a membrane-associated protein. Using a model of muscle injury, we assessed the interaction of these modifiers, identifying a feed forward loop between Ltbp4 and Spp1 that promotes TGFβ signaling. This feed forward loop is expected to contribute to the progressive nature of muscular dystrophy. We also evaluated the interaction between Anxa6 and Ltbp4, identifying an additive effect of these two genetic modifiers.
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MESH Headings
- Animals
- Annexin A1/genetics
- Annexin A1/metabolism
- Annexin A6/genetics
- Annexin A6/metabolism
- Female
- Gene Expression Regulation
- Genes, Modifier
- Latent TGF-beta Binding Proteins/physiology
- Male
- Mice
- Mice, Inbred DBA
- Mice, Knockout
- Muscle, Skeletal/injuries
- Muscle, Skeletal/physiology
- Muscular Dystrophy, Animal/genetics
- Muscular Dystrophy, Animal/metabolism
- Muscular Dystrophy, Animal/pathology
- Osteopontin/genetics
- Osteopontin/metabolism
- Receptors, Transforming Growth Factor beta/genetics
- Receptors, Transforming Growth Factor beta/metabolism
- Recovery of Function
- Sarcolemma/physiology
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Affiliation(s)
- Mattia Quattrocelli
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Joanna Capote
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Joyce C. Ohiri
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - James L. Warner
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Andy H. Vo
- Committee on Development, Regeneration, and Stem Cell Biology, The University of Chicago, Chicago, Illinois, United States of America
| | - Judy U. Earley
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Michele Hadhazy
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Alexis R. Demonbreun
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Melissa J. Spencer
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Elizabeth M. McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- * E-mail:
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47
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Abstract
This commentary will focus on how we can use our knowledge about the complexity of human disease and its pathogenesis to identify novel approaches to therapy. We know that even for single gene Mendelian disorders, patients with identical mutations often have different presentations and outcomes. This lack of genotype-phenotype correlation led us and others to examine the roles of modifier genes in the context of biological networks. These investigations have utilized vertebrate and invertebrate model organisms. Since one of the goals of research on modifier genes and networks is to identify novel therapeutic targets, the challenges to patient access and compliance because of the high costs of medications for rare genetic diseases must be recognized. A recent article explored protective modifiers, including plastin 3 (PLS3) and coronin 1C (CORO1C), in spinal muscular atrophy (SMA). SMA is an autosomal recessive deficit of survival motor neuron protein (SMN) caused by mutations in SMN1. However, the severity of SMA is determined primarily by the number of SMN2 copies, and this results in significant phenotypic variability. PLS3 was upregulated in siblings who were asymptomatic compared with those who had SMA2 or SMA3, but identical homozygous SMN1 deletions and equal numbers of SMN2 copies. CORO1C was identified by interrogation of the PLS3 interactome. Overexpression of these proteins rescued endocytosis in SMA models. In addition, antisense RNA for upregulation of SMN2 protein expression is being developed as another way of modifying the SMA phenotype. These investigations suggest the practical application of protective modifiers to rescue SMA phenotypes. Other examples of the potential therapeutic value of novel protective modifiers will be discussed, including in Duchenne muscular dystrophy and glycerol kinase deficiency. This work shows that while we live in an exciting era of genomic sequencing, a functional understanding of biology, the impact of its disruption, and possibilities for its repair have never been more important as we search for new therapies.
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Affiliation(s)
- Edward R B McCabe
- March of Dimes Foundation, United States; Department of Pediatrics, David Geffen School of Medicine at UCLA, United States.
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48
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Howell MD, Ottesen EW, Singh NN, Anderson RL, Seo J, Sivanesan S, Whitley EM, Singh RN. TIA1 is a gender-specific disease modifier of a mild mouse model of spinal muscular atrophy. Sci Rep 2017; 7:7183. [PMID: 28775379 PMCID: PMC5543135 DOI: 10.1038/s41598-017-07468-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 06/26/2017] [Indexed: 02/08/2023] Open
Abstract
Spinal muscular atrophy (SMA) is caused by deletions or mutations of Survival Motor Neuron 1 (SMN1) gene. The nearly identical SMN2 cannot compensate for SMN1 loss due to exon 7 skipping. The allele C (C +/+) mouse recapitulates a mild SMA-like phenotype and offers an ideal system to monitor the role of disease-modifying factors over a long time. T-cell-restricted intracellular antigen 1 (TIA1) regulates SMN exon 7 splicing. TIA1 is reported to be downregulated in obese patients, although it is not known if the effect is gender-specific. We show that female Tia1-knockout (Tia1 -/-) mice gain significant body weight (BW) during early postnatal development. We next examined the effect of Tia1 deletion in novel C +/+/Tia1 -/- mice. Underscoring the opposing effects of Tia1 deletion and low SMN level on BW gain, both C +/+ and C +/+/Tia1 -/- females showed similar BW gain trajectory at all time points during our study. We observed early tail necrosis in C +/+/Tia1 -/- females but not in males. We show enhanced impairment of male reproductive organ development and exacerbation of the C +/+/Tia1 -/- testis transcriptome. Our findings implicate a protein factor as a gender-specific modifier of a mild mouse model of SMA.
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Affiliation(s)
- Matthew D Howell
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, 50011, USA
| | - Eric W Ottesen
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, 50011, USA
| | - Natalia N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, 50011, USA
| | - Rachel L Anderson
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, 50011, USA
| | - Joonbae Seo
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, 50011, USA
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | | | - Elizabeth M Whitley
- Department of Veterinary Pathology, Iowa State University, Ames, IA, 50011-1250, USA
- Pathogenesis, LLC, Gainesville, Florida, 32614, USA
| | - Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, 50011, USA.
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49
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Deveson IW, Holleley CE, Blackburn J, Marshall Graves JA, Mattick JS, Waters PD, Georges A. Differential intron retention in Jumonji chromatin modifier genes is implicated in reptile temperature-dependent sex determination. Sci Adv 2017; 3:e1700731. [PMID: 28630932 PMCID: PMC5470834 DOI: 10.1126/sciadv.1700731] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
In many vertebrates, sex of offspring is determined by external environmental cues rather than by sex chromosomes. In reptiles, for instance, temperature-dependent sex determination (TSD) is common. Despite decades of work, the mechanism by which temperature is converted into a sex-determining signal remains mysterious. This is partly because it is difficult to distinguish the primary molecular events of TSD from the confounding downstream signatures of sexual differentiation. We use the Australian central bearded dragon, in which chromosomal sex determination is overridden at high temperatures to produce sex-reversed female offspring, as a unique model to identify TSD-specific features of the transcriptome. We show that an intron is retained in mature transcripts from each of two Jumonji family genes, JARID2 and JMJD3, in female dragons that have been sex-reversed by temperature but not in normal chromosomal females or males. JARID2 is a component of the master chromatin modifier Polycomb Repressive Complex 2, and the mammalian sex-determining factor SRY is directly regulated by an independent but closely related Jumonji family member. We propose that the perturbation of JARID2/JMJD3 function by intron retention alters the epigenetic landscape to override chromosomal sex-determining cues, triggering sex reversal at extreme temperatures. Sex reversal may then facilitate a transition from genetic sex determination to TSD, with JARID2/JMJD3 intron retention preserved as the decisive regulatory signal. Significantly, we also observe sex-associated differential retention of the equivalent introns in JARID2/JMJD3 transcripts expressed in embryonic gonads from TSD alligators and turtles, indicative of a reptile-wide mechanism controlling TSD.
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Affiliation(s)
- Ira W. Deveson
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales (UNSW), Sydney, New South Wales, Australia
| | - Clare E. Holleley
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - James Blackburn
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St. Vincent’s Clinical School, UNSW, Sydney, New South Wales, Australia
| | - Jennifer A. Marshall Graves
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
- School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - John S. Mattick
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales (UNSW), Sydney, New South Wales, Australia
- St. Vincent’s Clinical School, UNSW, Sydney, New South Wales, Australia
- Neuroscience Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Paul D. Waters
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales (UNSW), Sydney, New South Wales, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
- Corresponding author.
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50
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Muranen TA, Greco D, Blomqvist C, Aittomäki K, Khan S, Hogervorst F, Verhoef S, Pharoah PD, Dunning AM, Shah M, Luben R, Bojesen SE, Nordestgaard BG, Schoemaker M, Swerdlow A, García-Closas M, Figueroa J, Dörk T, Bogdanova NV, Hall P, Li J, Khusnutdinova E, Bermisheva M, Kristensen V, Borresen-Dale AL, Peto J, dos Santos Silva I, Couch FJ, Olson JE, Hillemans P, Park-Simon TW, Brauch H, Hamann U, Burwinkel B, Marme F, Meindl A, Schmutzler RK, Cox A, Cross SS, Sawyer EJ, Tomlinson I, Lambrechts D, Moisse M, Lindblom A, Margolin S, Hollestelle A, Martens JW, Fasching PA, Beckmann MW, Andrulis IL, Knight JA, Anton-Culver H, Ziogas A, Giles GG, Milne RL, Brenner H, Arndt V, Mannermaa A, Kosma VM, Chang-Claude J, Rudolph A, Devilee P, Seynaeve C, Hopper JL, Southey MC, John EM, Whittemore AS, Bolla MK, Wang Q, Michailidou K, Dennis J, Easton DF, Schmidt MK, Nevanlinna H. Genetic modifiers of CHEK2*1100delC-associated breast cancer risk. Genet Med 2017; 19:599-603. [PMID: 27711073 PMCID: PMC5382131 DOI: 10.1038/gim.2016.147] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 07/27/2016] [Indexed: 01/06/2023] Open
Abstract
PURPOSE CHEK2*1100delC is a founder variant in European populations that confers a two- to threefold increased risk of breast cancer (BC). Epidemiologic and family studies have suggested that the risk associated with CHEK2*1100delC is modified by other genetic factors in a multiplicative fashion. We have investigated this empirically using data from the Breast Cancer Association Consortium (BCAC). METHODS Using genotype data from 39,139 (624 1100delC carriers) BC patients and 40,063 (224) healthy controls from 32 BCAC studies, we analyzed the combined risk effects of CHEK2*1100delC and 77 common variants in terms of a polygenic risk score (PRS) and pairwise interaction. RESULTS The PRS conferred odds ratios (OR) of 1.59 (95% CI: 1.21-2.09) per standard deviation for BC for CHEK2*1100delC carriers and 1.58 (1.55-1.62) for noncarriers. No evidence of deviation from the multiplicative model was found. The OR for the highest quintile of the PRS was 2.03 (0.86-4.78) for CHEK2*1100delC carriers, placing them in the high risk category according to UK NICE guidelines. The OR for the lowest quintile was 0.52 (0.16-1.74), indicating a lifetime risk close to the population average. CONCLUSION Our results confirm the multiplicative nature of risk effects conferred by CHEK2*1100delC and the common susceptibility variants. Furthermore, the PRS could identify carriers at a high lifetime risk for clinical actions.Genet Med advance online publication 06 October 2016.
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Affiliation(s)
- Taru A. Muranen
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Dario Greco
- Unit of Systems Toxicology, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Sofia Khan
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Frans Hogervorst
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Senno Verhoef
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Paul D.P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Robert Luben
- Clinical Gerontology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Stig E. Bojesen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Børge G. Nordestgaard
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Minouk Schoemaker
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Montserrat García-Closas
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | | | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jingmei Li
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Elza Khusnutdinova
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
- Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia
| | - Marina Bermisheva
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
- Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Radiumhospitalet, Oslo University Hospital, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Biology, Oslo University Hospital, University of Oslo, Oslo, Norway
- K.G. Jebsen Center for Breast Cancer Research, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anne-Lise Borresen-Dale
- Department of Genetics, Institute for Cancer Research, Radiumhospitalet, Oslo University Hospital, University of Oslo, Oslo, Norway
- K.G. Jebsen Center for Breast Cancer Research, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - NBCS Investigators
- Department of Genetics, Institute for Cancer Research, Radiumhospitalet, Oslo University Hospital, University of Oslo, Oslo, Norway
- Department of Oncology, Radiumhospitalet, Oslo University Hospital, University of Oslo, Oslo, Norway
- Department of Radiology, Radiumhospitalet, Oslo University Hospital, University of Oslo, Oslo, Norway
- National Resource Centre for Long-term Studies after Cancer, Cancer Clinic, Radiumhospitalet, Oslo University Hospital, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Biology, Oslo University Hospital, University of Oslo, Oslo, Norway
- K.G. Jebsen Center for Breast Cancer Research, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Breast and Endocrine Surgery, Institute for Clinical Medicine, Ullevaal University Hospital, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, Akershus University Hospital, University of Oslo, Oslo, Norway
- Department of Oncology, Ullevaal University Hospital, University of Oslo, Oslo, Norway
- Department of Pathology, Akershus University Hospital, Lørenskog, Norway
- Department of Surgery, Akershus University Hospital, Lørenskog, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
- Section of Oncology, Institute of Medicine, University of Bergen, Bergen, Norway
- Norwegian Centre for Integrated Care and Telemedicine, University Hospital of North Norway, Tromsø, Norway
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Isabel dos Santos Silva
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Janet E. Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Peter Hillemans
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | | | - Hiltrud Brauch
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Burwinkel
- Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Frederik Marme
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
| | - Rita K. Schmutzler
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Center for Hereditary Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), University Hospital of Cologne, Cologne, Germany
| | - Angela Cox
- Sheffield Cancer Research, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Simon S. Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Elinor J. Sawyer
- Research Oncology, Guy’s Hospital, King's College London, London, UK
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
- Vesalius Research Center, VIB, Leuven, Belgium
| | - Matthieu Moisse
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Sara Margolin
- Department of Oncology - Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Antoinette Hollestelle
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John W.M. Martens
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Peter A. Fasching
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Matthias W. Beckmann
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Irene L. Andrulis
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
| | - Julia A. Knight
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
| | | | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, CA, USA
| | - Argyrios Ziogas
- Department of Epidemiology, University of California Irvine, Irvine, CA, USA
| | - Graham G. Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global health, The University of Melbourne, Melbourne, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
| | - Roger L. Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global health, The University of Melbourne, Melbourne, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
| | - Hermann Brenner
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Arto Mannermaa
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Cancer Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Veli-Matti Kosma
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Cancer Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Caroline Seynaeve
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global health, The University of Melbourne, Melbourne, Australia
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Esther M. John
- Department of Epidemiology, Cancer Prevention Institute of California, Fremont, CA, USA
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Alice S. Whittemore
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Marjanka K. Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
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