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Kooblall KG, Stevenson M, Heilig R, Stewart M, Wright B, Lockstone H, Buck D, Fischer R, Wells S, Lines KE, Teboul L, Hennekam RC, Thakker RV. Identification of cellular retinoic acid binding protein 2 (CRABP2) as downstream target of nuclear factor I/X (NFIX): implications for skeletal dysplasia syndromes. JBMR Plus 2024; 8:ziae060. [PMID: 38827116 PMCID: PMC11144382 DOI: 10.1093/jbmrpl/ziae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/04/2024] [Indexed: 06/04/2024] Open
Abstract
Nuclear factor I/X (NFIX) mutations are associated with 2 skeletal dysplasias, Marshall-Smith (MSS) and Malan (MAL) syndromes. NFIX encodes a transcription factor that regulates expression of genes, including Bobby sox (BBX) and glial fibrillary acidic protein (GFAP) in neural progenitor cells and astrocytes, respectively. To elucidate the role of NFIX mutations in MSS, we studied their effects in fibroblast cell lines obtained from 5 MSS unrelated patients and 3 unaffected individuals. The 5 MSS NFIX frameshift mutations in exons 6-8 comprised 3 deletions (c.819-732_1079-948del, c.819-471_1079-687del, c.819-592_1079-808del), an insertion (c.1037_1038insT), and a duplication (c.1090dupG). Quantitative reverse transcription polymerase chain reaction (qRT-PCR) and western blot analyses using MSS and unrelated control fibroblasts and in vitro expression studies in monkey kidney fibroblast (COS-7) cells showed that frameshift mutations in NFIX exons 6-8 generated mutant transcripts that were not cleared by nonsense-mediated-decay mechanisms and encoded truncated NFIX proteins. Moreover, BBX or GFAP expression was unaffected in the majority of MSS fibroblasts. To identify novel NFIX downstream target genes, RNA sequencing and proteomics analyses were performed on mouse embryonic fibroblast (MEF) cells derived from control Nfix+/+, Nfix+/Del2, Nfix+/Del24, NfixDel24/Del24, Nfix+/Del140, and NfixDel140/Del140 mice, compared with NfixDel2/Del2 mice which had developmental, skeletal, and neural abnormalities. This identified 191 transcripts and 815 proteins misregulated in NfixDel2/Del2 MEFs with ≥2-fold-change (P <0 .05). Validation studies using qRT-PCR and western blot analyses confirmed that 2 genes, cellular retinoic acid binding protein 2 (Crabp2) and vascular cell adhesion molecule 1 (Vcam1), were misregulated at the RNA and protein levels in NfixDel2/Del2 MEFs, and that CRABP2 and VCAM1 expressions were altered in 60%-100% of MSS fibroblast cells. Furthermore, in vitro luciferase reporter assays confirmed that NFIX directly regulates CRABP2 promoter activity. Thus, these altered genes and pathways may represent possible targets for drugs as potential treatments and therapies for MSS.
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Affiliation(s)
- Kreepa G Kooblall
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LJ, United Kingdom
| | - Mark Stevenson
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LJ, United Kingdom
| | - Raphael Heilig
- Target Discovery Unit, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Michelle Stewart
- MRC Harwell, Mary Lyon Centre, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom
| | - Benjamin Wright
- Oxford Genomics Centre, The Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Helen Lockstone
- Oxford Genomics Centre, The Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - David Buck
- Oxford Genomics Centre, The Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Roman Fischer
- Target Discovery Unit, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Sara Wells
- MRC Harwell, Mary Lyon Centre, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom
| | - Kate E Lines
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LJ, United Kingdom
| | - Lydia Teboul
- MRC Harwell, Mary Lyon Centre, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom
| | - Raoul C Hennekam
- Department of Pediatrics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Rajesh V Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LJ, United Kingdom
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Wei X, Ma Y, Xie B, Gui C, Shi M, Wei X, Huang Y, Fan X, Wei Q, Huang Q, Deng L, Zhang C, Deng X, Gui B, Chen Y. Complex genotype-phenotype correlation of MYH11: new insights from monozygotic twins with highly variable expressivity and outcomes. BMC Med Genomics 2024; 17:135. [PMID: 38773466 PMCID: PMC11110423 DOI: 10.1186/s12920-024-01908-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 05/13/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Thoracic aortic aneurysm/dissection (TAAD) and patent ductus arteriosus (PDA) are serious autosomal-dominant diseases affecting the cardiovascular system. They are mainly caused by variants in the MYH11 gene, which encodes the heavy chain of myosin 11. The aim of this study was to evaluate the genotype-phenotype correlation of MYH11 from a distinctive perspective based on a pair of monozygotic twins. METHODS The detailed phenotypic characteristics of the monozygotic twins from the early fetal stage to the infancy stage were traced and compared with each other and with those of previously documented cases. Whole-exome and Sanger sequencing techniques were used to identify and validate the candidate variants, facilitating the analysis of the genotype-phenotype correlation of MYH11. RESULTS The monozygotic twins were premature and presented with PDA, pulmonary hypoplasia, and pulmonary hypertension. The proband developed heart and brain abnormalities during the fetal stage and died at 18 days after birth, whereas his sibling was discharged after being cured and developed normally post follow-up. A novel variant c.766 A > G p. (Ile256Val) in MYH11 (NM_002474.2) was identified in the monozygotic twins and classified as a likely pathogenic variant according to the American College of Medical Genetics/Association for Molecular Pathology guidelines. Reviewing the reported cases (n = 102) showed that the penetrance of MYH11 was 82.35%, and the most common feature was TAAD (41.18%), followed by PDA (22.55%), compound TAAD and PDA (9.80%), and other vascular abnormalities (8.82%). The constituent ratios of null variants among the cases with TAAD (8.60%), PDA (43.8%), or compound TAAD and PDA (28.6%) were significantly different (P = 0.01). Further pairwise comparison of the ratios among these groups showed that there were significant differences between the TAAD and PDA groups (P = 0.006). CONCLUSION This study expands the mutational spectrum of MYH11 and provides new insights into the genotype-phenotype correlation of MYH11 based on the monozygotic twins with variable clinical features and outcomes, indicating that cryptic modifiers and complex mechanisms beside the genetic variants may be involved in the condition.
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Affiliation(s)
- Xiaojiao Wei
- The Second School of Medicine, Guangxi Medical University, Nanning, China
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yunting Ma
- The Second School of Medicine, Guangxi Medical University, Nanning, China
| | - Bobo Xie
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chunrong Gui
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Meizhen Shi
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xianda Wei
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yan Huang
- Department of Obstetrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xin Fan
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qiaozhen Wei
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qingmei Huang
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Li Deng
- Department of Obstetrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chi Zhang
- Department of Ultrasonic, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiaoli Deng
- Department of Ultrasonic, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Baoheng Gui
- The Second School of Medicine, Guangxi Medical University, Nanning, China.
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China.
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China.
| | - Yujun Chen
- The Second School of Medicine, Guangxi Medical University, Nanning, China.
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China.
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China.
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Sewerin S, Aurnhammer C, Skubic C, Blagotinšek Cokan K, Jeruc J, Rozman D, Pfister F, Dittrich K, Mayer B, Schönauer R, Petzold F, Halbritter J. Mechanisms of pathogenicity and the quest for genetic modifiers of kidney disease in branchiootorenal syndrome. Clin Kidney J 2024; 17:sfad260. [PMID: 38213489 PMCID: PMC10783239 DOI: 10.1093/ckj/sfad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Indexed: 01/13/2024] Open
Abstract
Backgound Branchiootorenal (BOR) syndrome is an autosomal dominant disorder caused by pathogenic EYA1 variants and clinically characterized by auricular malformations with hearing loss, branchial arch anomalies, and congenital anomalies of the kidney and urinary tract. BOR phenotypes are highly variable and heterogenous. While random monoallelic expression is assumed to explain this phenotypic heterogeneity, the potential role of modifier genes has not yet been explored. Methods Through thorough phenotyping and exome sequencing, we studied one family with disease presentation in at least four generations in both clinical and genetic terms. Functional investigation of the single associated EYA1 variant c.1698+1G>A included splice site analysis and assessment of EYA1 distribution in patient-derived fibroblasts. The candidate modifier gene CYP51A1 was evaluated by histopathological analysis of murine Cyp51+/- and Cyp51-/- kidneys. As the gene encodes the enzyme lanosterol 14α-demethylase, we assessed sterol intermediates in patient blood samples as well. Results The EYA1 variant c.1698+1G>A resulted in functional deletion of the EYA domain by exon skipping. The EYA domain mediates protein-protein interactions between EYA1 and co-regulators of transcription. EYA1 abundance was reduced in the nuclear compartment of patient-derived fibroblasts, suggesting impaired nuclear translocation of these protein complexes. Within the affected family, renal phenotypes spanned from normal kidney function in adulthood to chronic kidney failure in infancy. By analyzing exome sequencing data for variants that potentially play roles as genetic modifiers, we identified a canonical splice site alteration in CYP51A1 as the strongest candidate variant. Conclusion In this study, we demonstrate pathogenicity of EYA1 c.1698+1G>A, propose a mechanism for dysfunction of mutant EYA1, and conjecture CYP51A1 as a potential genetic modifier of renal involvement in BOR syndrome.
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Affiliation(s)
- Sebastian Sewerin
- Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
- Current affiliation: Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Cene Skubic
- Institute of Biochemistry, Centre for Functional Genomics and Bio-Chips, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Kaja Blagotinšek Cokan
- Institute of Biochemistry, Centre for Functional Genomics and Bio-Chips, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jera Jeruc
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Damjana Rozman
- Institute of Biochemistry, Centre for Functional Genomics and Bio-Chips, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Frederick Pfister
- Institute of Pathology, University of Erlangen Medical Center, Erlangen, Germany
- Current affiliation: Humanpathologie Dr. med. Manfred Weiß MVZ GmbH, Erlangen-Tennenlohe, Germany
| | - Katalin Dittrich
- Division of Pediatric Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Brigitte Mayer
- Division of Pediatric Nephrology, University of Dresden Medical Center, Dresden, Germany
| | - Ria Schönauer
- Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
- Current affiliation: Department of Nephrology and Medical Intensive Care, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Friederike Petzold
- Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Jan Halbritter
- Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
- Current affiliation: Department of Nephrology and Medical Intensive Care, Charité Universitätsmedizin Berlin, Berlin, Germany
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Similuk M, Kuijpers T. Nature and nurture: understanding phenotypic variation in inborn errors of immunity. Front Cell Infect Microbiol 2023; 13:1183142. [PMID: 37780853 PMCID: PMC10538643 DOI: 10.3389/fcimb.2023.1183142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/17/2023] [Indexed: 10/03/2023] Open
Abstract
The overall disease burden of pediatric infection is high, with widely varying clinical outcomes including death. Among the most vulnerable children, those with inborn errors of immunity, reduced penetrance and variable expressivity are common but poorly understood. There are several genetic mechanisms that influence phenotypic variation in inborn errors of immunity, as well as a body of knowledge on environmental influences and specific pathogen triggers. Critically, recent advances are illuminating novel nuances for fundamental concepts on disease penetrance, as well as raising new areas of inquiry. The last few decades have seen the identification of almost 500 causes of inborn errors of immunity, as well as major advancements in our ability to characterize somatic events, the microbiome, and genotypes across large populations. The progress has not been linear, and yet, these developments have accumulated into an enhanced ability to diagnose and treat inborn errors of immunity, in some cases with precision therapy. Nonetheless, many questions remain regarding the genetic and environmental contributions to phenotypic variation both within and among families. The purpose of this review is to provide an updated summary of key concepts in genetic and environmental contributions to phenotypic variation within inborn errors of immunity, conceptualized as including dynamic, reciprocal interplay among factors unfolding across the key dimension of time. The associated findings, potential gaps, and implications for research are discussed in turn for each major influencing factor. The substantial challenge ahead will be to organize and integrate information in such a way that accommodates the heterogeneity within inborn errors of immunity to arrive at a more comprehensive and accurate understanding of how the immune system operates in health and disease. And, crucially, to translate this understanding into improved patient care for the millions at risk for serious infection and other immune-related morbidity.
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Affiliation(s)
- Morgan Similuk
- Centralized Sequencing Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Taco Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children’s Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
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5
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Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, Yuan B, Boone PM, Groopman EE, Délot EC, Jain D, Sanchis-Juan A, Starita LM, Talkowski M, Montgomery SB, Bamshad MJ, Chong JX, Wheeler MT, Berger SI, O'Donnell-Luria A, Sedlazeck FJ, Miller DE. Beyond the exome: What's next in diagnostic testing for Mendelian conditions. Am J Hum Genet 2023; 110:1229-1248. [PMID: 37541186 PMCID: PMC10432150 DOI: 10.1016/j.ajhg.2023.06.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 08/06/2023] Open
Abstract
Despite advances in clinical genetic testing, including the introduction of exome sequencing (ES), more than 50% of individuals with a suspected Mendelian condition lack a precise molecular diagnosis. Clinical evaluation is increasingly undertaken by specialists outside of clinical genetics, often occurring in a tiered fashion and typically ending after ES. The current diagnostic rate reflects multiple factors, including technical limitations, incomplete understanding of variant pathogenicity, missing genotype-phenotype associations, complex gene-environment interactions, and reporting differences between clinical labs. Maintaining a clear understanding of the rapidly evolving landscape of diagnostic tests beyond ES, and their limitations, presents a challenge for non-genetics professionals. Newer tests, such as short-read genome or RNA sequencing, can be challenging to order, and emerging technologies, such as optical genome mapping and long-read DNA sequencing, are not available clinically. Furthermore, there is no clear guidance on the next best steps after inconclusive evaluation. Here, we review why a clinical genetic evaluation may be negative, discuss questions to be asked in this setting, and provide a framework for further investigation, including the advantages and disadvantages of new approaches that are nascent in the clinical sphere. We present a guide for the next best steps after inconclusive molecular testing based upon phenotype and prior evaluation, including when to consider referral to research consortia focused on elucidating the underlying cause of rare unsolved genetic disorders.
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Affiliation(s)
- Monica H Wojcik
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chloe M Reuter
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shruti Marwaha
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Michael H Duyzend
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Hayk Barseghyan
- Center for Genetics Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC 20010, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics and Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Philip M Boone
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Emily E Groopman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Emmanuèle C Délot
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA; Center for Genetics Medicine Research, Children's National Research and Innovation Campus, Washington, DC, USA; Department of Pediatrics, George Washington University, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Deepti Jain
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Michael Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen B Montgomery
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael J Bamshad
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jessica X Chong
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Matthew T Wheeler
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Seth I Berger
- Center for Genetics Medicine Research and Rare Disease Institute, Children's National Hospital, Washington, DC 20010, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Danny E Miller
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA.
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6
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Kooblall KG, Stevenson M, Stewart M, Harris L, Zalucki O, Dewhurst H, Butterfield N, Leng H, Hough TA, Ma D, Siow B, Potter P, Cox RD, Brown SD, Horwood N, Wright B, Lockstone H, Buck D, Vincent TL, Hannan FM, Bassett JD, Williams GR, Lines KE, Piper M, Wells S, Teboul L, Hennekam RC, Thakker RV. A Mouse Model with a Frameshift Mutation in the Nuclear Factor I/X ( NFIX) Gene Has Phenotypic Features of Marshall-Smith Syndrome. JBMR Plus 2023; 7:e10739. [PMID: 37283649 PMCID: PMC10241085 DOI: 10.1002/jbm4.10739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023] Open
Abstract
The nuclear factor I/X (NFIX) gene encodes a ubiquitously expressed transcription factor whose mutations lead to two allelic disorders characterized by developmental, skeletal, and neural abnormalities, namely, Malan syndrome (MAL) and Marshall-Smith syndrome (MSS). NFIX mutations associated with MAL mainly cluster in exon 2 and are cleared by nonsense-mediated decay (NMD) leading to NFIX haploinsufficiency, whereas NFIX mutations associated with MSS are clustered in exons 6-10 and escape NMD and result in the production of dominant-negative mutant NFIX proteins. Thus, different NFIX mutations have distinct consequences on NFIX expression. To elucidate the in vivo effects of MSS-associated NFIX exon 7 mutations, we used CRISPR-Cas9 to generate mouse models with exon 7 deletions that comprised: a frameshift deletion of two nucleotides (Nfix Del2); in-frame deletion of 24 nucleotides (Nfix Del24); and deletion of 140 nucleotides (Nfix Del140). Nfix +/Del2, Nfix +/Del24, Nfix +/Del140, Nfix Del24/Del24, and Nfix Del140/Del140 mice were viable, normal, and fertile, with no skeletal abnormalities, but Nfix Del2/Del2 mice had significantly reduced viability (p < 0.002) and died at 2-3 weeks of age. Nfix Del2 was not cleared by NMD, and NfixDel2/Del2 mice, when compared to Nfix +/+ and Nfix +/Del2 mice, had: growth retardation; short stature with kyphosis; reduced skull length; marked porosity of the vertebrae with decreased vertebral and femoral bone mineral content; and reduced caudal vertebrae height and femur length. Plasma biochemistry analysis revealed Nfix Del2/Del2 mice to have increased total alkaline phosphatase activity but decreased C-terminal telopeptide and procollagen-type-1-N-terminal propeptide concentrations compared to Nfix +/+ and Nfix +/Del2 mice. Nfix Del2/Del2 mice were also found to have enlarged cerebral cortices and ventricular areas but smaller dentate gyrus compared to Nfix +/+ mice. Thus, Nfix Del2/Del2 mice provide a model for studying the in vivo effects of NFIX mutants that escape NMD and result in developmental abnormalities of the skeletal and neural tissues that are associated with MSS. © 2023 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Kreepa G. Kooblall
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
| | - Mark Stevenson
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
| | - Michelle Stewart
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | | | - Oressia Zalucki
- The School of Biomedical Sciences and The Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
| | - Hannah Dewhurst
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Natalie Butterfield
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Houfu Leng
- Centre for OA Pathogenesis Versus Arthritis, The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS)Medical Sciences Division University of OxfordOxfordUK
| | - Tertius A. Hough
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Da Ma
- Department of Internal MedicineWake Forest University School of MedicineWinston‐SalemNCUSA
| | | | - Paul Potter
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Roger D. Cox
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Stephen D.M. Brown
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Nicole Horwood
- Centre for OA Pathogenesis Versus Arthritis, The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS)Medical Sciences Division University of OxfordOxfordUK
| | - Benjamin Wright
- Oxford Genomics Centre, The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Helen Lockstone
- Oxford Genomics Centre, The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - David Buck
- Oxford Genomics Centre, The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Tonia L. Vincent
- Centre for OA Pathogenesis Versus Arthritis, The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS)Medical Sciences Division University of OxfordOxfordUK
| | - Fadil M. Hannan
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
- Nuffield Department of Women's and Reproductive HealthUniversity of OxfordOxfordUK
| | - J.H. Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Graham R. Williams
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Kate E. Lines
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
| | - Michael Piper
- The School of Biomedical Sciences and The Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
| | - Sara Wells
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Lydia Teboul
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Raoul C. Hennekam
- Department of Pediatrics, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Rajesh V. Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
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7
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Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, Yuan B, Boone PM, Groopman EE, Délot EC, Jain D, Sanchis-Juan A, Starita LM, Talkowski M, Montgomery SB, Bamshad MJ, Chong JX, Wheeler MT, Berger SI, O’Donnell-Luria A, Sedlazeck FJ, Miller DE. Beyond the exome: what's next in diagnostic testing for Mendelian conditions. ARXIV 2023:arXiv:2301.07363v1. [PMID: 36713248 PMCID: PMC9882576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Despite advances in clinical genetic testing, including the introduction of exome sequencing (ES), more than 50% of individuals with a suspected Mendelian condition lack a precise molecular diagnosis. Clinical evaluation is increasingly undertaken by specialists outside of clinical genetics, often occurring in a tiered fashion and typically ending after ES. The current diagnostic rate reflects multiple factors, including technical limitations, incomplete understanding of variant pathogenicity, missing genotype-phenotype associations, complex gene-environment interactions, and reporting differences between clinical labs. Maintaining a clear understanding of the rapidly evolving landscape of diagnostic tests beyond ES, and their limitations, presents a challenge for non-genetics professionals. Newer tests, such as short-read genome or RNA sequencing, can be challenging to order and emerging technologies, such as optical genome mapping and long-read DNA or RNA sequencing, are not available clinically. Furthermore, there is no clear guidance on the next best steps after inconclusive evaluation. Here, we review why a clinical genetic evaluation may be negative, discuss questions to be asked in this setting, and provide a framework for further investigation, including the advantages and disadvantages of new approaches that are nascent in the clinical sphere. We present a guide for the next best steps after inconclusive molecular testing based upon phenotype and prior evaluation, including when to consider referral to a consortium such as GREGoR, which is focused on elucidating the underlying cause of rare unsolved genetic disorders.
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Affiliation(s)
- Monica H. Wojcik
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Division of Newborn Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Chloe M. Reuter
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Shruti Marwaha
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030 USA
| | - Michael H. Duyzend
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Hayk Barseghyan
- Center for Genetics Medicine Research, Children’s National Research Institute, Children’s National Hospital, Washington, DC 20010 USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037 USA
| | - Bo Yuan
- Department of Molecular and Human Genetics and Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030 USA
| | - Philip M. Boone
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Emily E. Groopman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Emmanuèle C. Délot
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037 USA
- Center for Genetics Medicine Research, Children’s National Research and Innovation Campus, Washington, DC, USA
- Department of Pediatrics, George Washington University, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037 USA
| | - Deepti Jain
- Department of Biostatistics, School of Public Health, University of Washington, Seattle WA 98195 USA
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | | | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195 USA
| | - Michael Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Stephen B. Montgomery
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305 USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Michael J. Bamshad
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195 USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
| | - Jessica X. Chong
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
| | - Matthew T. Wheeler
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Seth I. Berger
- Center for Genetics Medicine Research and Rare Disease Institute, Children’s National Hospital, Washington, DC 20010 USA
| | - Anne O’Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030 USA
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005 USA
| | - Danny E. Miller
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195 USA
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8
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Hahn LC, Georgiou M, Almushattat H, van Schooneveld MJ, de Carvalho ER, Wesseling NL, Ten Brink JB, Florijn RJ, Lissenberg-Witte BI, Strubbe I, van Cauwenbergh C, de Zaeytijd J, Walraedt S, de Baere E, Mukherjee R, McKibbin M, Meester-Smoor MA, Thiadens AAHJ, Al-Khuzaei S, Akyol E, Lotery AJ, van Genderen MM, Ossewaarde-van Norel J, van den Born LI, Hoyng CB, Klaver CCW, Downes SM, Bergen AA, Leroy BP, Michaelides M, Boon CJF. The Natural History of Leber Congenital Amaurosis and Cone-Rod Dystrophy Associated with Variants in the GUCY2D Gene. Ophthalmol Retina 2022; 6:711-722. [PMID: 35314386 DOI: 10.1016/j.oret.2022.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/20/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To describe the spectrum of Leber congenital amaurosis (LCA) and cone-rod dystrophy (CORD) associated with the GUCY2D gene and to identify potential end points and optimal patient selection for future therapeutic trials. DESIGN International, multicenter, retrospective cohort study. SUBJECTS Eighty-two patients with GUCY2D-associated LCA or CORD from 54 families. METHODS Medical records were reviewed for medical history, best-corrected visual acuity (BCVA), ophthalmoscopy, visual fields, full-field electroretinography, and retinal imaging (fundus photography, spectral-domain OCT [SD-OCT], fundus autofluorescence). MAIN OUTCOMES MEASURES Age of onset, evolution of BCVA, genotype-phenotype correlations, anatomic characteristics on funduscopy, and multimodal imaging. RESULTS Fourteen patients with autosomal recessive LCA and 68 with autosomal dominant CORD were included. The median follow-up times were 5.2 years (interquartile range [IQR] 2.6-8.8 years) for LCA and 7.2 years (IQR 2.2-14.2 years) for CORD. Generally, LCA presented in the first year of life. The BCVA in patients with LCA ranged from no light perception to 1.00 logarithm of the minimum angle of resolution (logMAR) and remained relatively stable during follow-up. Imaging for LCA was limited but showed little to no structural degeneration. In patients with CORD, progressive vision loss started around the second decade of life. The BCVA declined annually by 0.022 logMAR (P < 0.001) with no difference between patients with the c.2513G>A and the c.2512C>T GUCY2D variants (P = 0.798). At the age of 40 years, the probability of being blind or severely visually impaired was 32%. The integrity of the ellipsoid zone (EZ) and that of the external limiting membrane (ELM) on SD-OCT correlated significantly with BCVA (Spearman ρ = 0.744, P = 0.001, and ρ = 0.712, P < 0.001, respectively) in those with CORD. CONCLUSIONS Leber congenital amaurosis associated with GUCY2D caused severe congenital visual impairment with relatively intact macular anatomy on funduscopy and available imaging, suggesting long preservation of photoreceptors. Despite large variability, GUCY2D-associated CORD generally presented during adolescence, with a progressive loss of vision, and culminated in severe visual impairment during mid-to-late adulthood. The integrity of the ELM and EZ may be suitable structural end points for therapeutic studies of GUCY2D-associated CORD.
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Affiliation(s)
- Leo C Hahn
- Department of Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Michalis Georgiou
- Moorfields Eye Hospital National Health Service Foundation Trust, London, United Kingdom
| | - Hind Almushattat
- Department of Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Mary J van Schooneveld
- Department of Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands; Bartiméus Diagnostic Center for Complex Visual Disorders, Zeist, The Netherlands
| | - Emanuel R de Carvalho
- Moorfields Eye Hospital National Health Service Foundation Trust, London, United Kingdom
| | - Nieneke L Wesseling
- Department of Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Jacoline B Ten Brink
- Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Ralph J Florijn
- Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Birgit I Lissenberg-Witte
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ine Strubbe
- Department of Ophthalmology, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Caroline van Cauwenbergh
- Department of Ophthalmology, Ghent University Hospital, Ghent University, Ghent, Belgium; Center for Medical Genetics Ghent, Ghent University Hospital & Ghent University, Ghent, Belgium
| | - Julie de Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Sophie Walraedt
- Department of Ophthalmology, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Elfride de Baere
- Department of Ophthalmology, Ghent University Hospital, Ghent University, Ghent, Belgium; Center for Medical Genetics Ghent, Ghent University Hospital & Ghent University, Ghent, Belgium
| | - Rajarshi Mukherjee
- Department of Ophthalmology, St James's University Hospital, Leeds, United Kingdom
| | - Martin McKibbin
- Department of Ophthalmology, St James's University Hospital, Leeds, United Kingdom
| | | | | | - Saoud Al-Khuzaei
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals National Health Service Foundation Trust, & Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, United Kingdom
| | - Engin Akyol
- Eye Unit, University Hospital Southampton, Southampton, United Kingdom
| | - Andrew J Lotery
- Eye Unit, University Hospital Southampton, Southampton, United Kingdom
| | - Maria M van Genderen
- Bartiméus Diagnostic Center for Complex Visual Disorders, Zeist, The Netherlands; Department of Ophthalmology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Susan M Downes
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals National Health Service Foundation Trust, & Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, United Kingdom
| | - Arthur A Bergen
- Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands; The Netherlands Institute for Neuroscience (NIN-KNAW), Amsterdam, The Netherlands
| | - Bart P Leroy
- Department of Ophthalmology, Ghent University Hospital, Ghent University, Ghent, Belgium; Center for Medical Genetics Ghent, Ghent University Hospital & Ghent University, Ghent, Belgium; Division of Ophthalmology and Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michel Michaelides
- Moorfields Eye Hospital National Health Service Foundation Trust, London, United Kingdom; UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Camiel J F Boon
- Department of Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands; Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands.
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9
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Leparulo A, Bisio M, Redolfi N, Pozzan T, Vassanelli S, Fasolato C. Accelerated Aging Characterizes the Early Stage of Alzheimer's Disease. Cells 2022; 11:238. [PMID: 35053352 PMCID: PMC8774248 DOI: 10.3390/cells11020238] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/12/2021] [Accepted: 01/08/2022] [Indexed: 02/01/2023] Open
Abstract
For Alzheimer's disease (AD), aging is the main risk factor, but whether cognitive impairments due to aging resemble early AD deficits is not yet defined. When working with mouse models of AD, the situation is just as complicated, because only a few studies track the progression of the disease at different ages, and most ignore how the aging process affects control mice. In this work, we addressed this problem by comparing the aging process of PS2APP (AD) and wild-type (WT) mice at the level of spontaneous brain electrical activity under anesthesia. Using local field potential recordings, obtained with a linear probe that traverses the posterior parietal cortex and the entire hippocampus, we analyzed how multiple electrical parameters are modified by aging in AD and WT mice. With this approach, we highlighted AD specific features that appear in young AD mice prior to plaque deposition or that are delayed at 12 and 16 months of age. Furthermore, we identified aging characteristics present in WT mice but also occurring prematurely in young AD mice. In short, we found that reduction in the relative power of slow oscillations (SO) and Low/High power imbalance are linked to an AD phenotype at its onset. The loss of SO connectivity and cortico-hippocampal coupling between SO and higher frequencies as well as the increase in UP-state and burst durations are found in young AD and old WT mice. We show evidence that the aging process is accelerated by the mutant PS2 itself and discuss such changes in relation to amyloidosis and gliosis.
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Affiliation(s)
- Alessandro Leparulo
- Department of Biomedical Sciences, University of Padua, Via U. Bassi 58/B, 35131 Padua, Italy; (A.L.); (M.B.); (N.R.); (T.P.)
| | - Marta Bisio
- Department of Biomedical Sciences, University of Padua, Via U. Bassi 58/B, 35131 Padua, Italy; (A.L.); (M.B.); (N.R.); (T.P.)
| | - Nelly Redolfi
- Department of Biomedical Sciences, University of Padua, Via U. Bassi 58/B, 35131 Padua, Italy; (A.L.); (M.B.); (N.R.); (T.P.)
| | - Tullio Pozzan
- Department of Biomedical Sciences, University of Padua, Via U. Bassi 58/B, 35131 Padua, Italy; (A.L.); (M.B.); (N.R.); (T.P.)
- Neuroscience Institute-Italian National Research Council (CNR), Via U. Bassi 58/B, 35131 Padua, Italy
- Venetian Institute of Molecular Medicine (VIMM), Via G. Orus 2B, 35129 Padua, Italy
| | - Stefano Vassanelli
- Department of Biomedical Sciences, University of Padua, Via U. Bassi 58/B, 35131 Padua, Italy; (A.L.); (M.B.); (N.R.); (T.P.)
- Padua Neuroscience Center (PNC), University of Padua, Via G. Orus 2B, 35129 Padua, Italy
| | - Cristina Fasolato
- Department of Biomedical Sciences, University of Padua, Via U. Bassi 58/B, 35131 Padua, Italy; (A.L.); (M.B.); (N.R.); (T.P.)
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10
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Kingdom R, Wright CF. Incomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts. Front Genet 2022; 13:920390. [PMID: 35983412 PMCID: PMC9380816 DOI: 10.3389/fgene.2022.920390] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 12/20/2022] Open
Abstract
The same genetic variant found in different individuals can cause a range of diverse phenotypes, from no discernible clinical phenotype to severe disease, even among related individuals. Such variants can be said to display incomplete penetrance, a binary phenomenon where the genotype either causes the expected clinical phenotype or it does not, or they can be said to display variable expressivity, in which the same genotype can cause a wide range of clinical symptoms across a spectrum. Both incomplete penetrance and variable expressivity are thought to be caused by a range of factors, including common variants, variants in regulatory regions, epigenetics, environmental factors, and lifestyle. Many thousands of genetic variants have been identified as the cause of monogenic disorders, mostly determined through small clinical studies, and thus, the penetrance and expressivity of these variants may be overestimated when compared to their effect on the general population. With the wealth of population cohort data currently available, the penetrance and expressivity of such genetic variants can be investigated across a much wider contingent, potentially helping to reclassify variants that were previously thought to be completely penetrant. Research into the penetrance and expressivity of such genetic variants is important for clinical classification, both for determining causative mechanisms of disease in the affected population and for providing accurate risk information through genetic counseling. A genotype-based definition of the causes of rare diseases incorporating information from population cohorts and clinical studies is critical for our understanding of incomplete penetrance and variable expressivity. This review examines our current knowledge of the penetrance and expressivity of genetic variants in rare disease and across populations, as well as looking into the potential causes of the variation seen, including genetic modifiers, mosaicism, and polygenic factors, among others. We also considered the challenges that come with investigating penetrance and expressivity.
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Affiliation(s)
- Rebecca Kingdom
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
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11
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Happle R. Can Waardenburg syndrome type 2 be explained by epigenetic mosaicism? Am J Med Genet A 2021; 185:1304-1306. [PMID: 33438357 DOI: 10.1002/ajmg.a.62075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Rudolf Happle
- Department of Dermatology, Medical Center, University of Freiburg, Freiburg, Germany
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12
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A novel SGCE variant is associated with myoclonus-dystonia with phenotypic variability. Neurol Sci 2020; 41:3779-3781. [PMID: 32955639 DOI: 10.1007/s10072-020-04718-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/12/2020] [Indexed: 10/23/2022]
Abstract
Myoclonus-dystonia associated with epsilon-sarcoglycan gene (SGCE) is a rare disorder characterized by myoclonus involving the upper body (neck, trunk, upper limbs) and proximal muscles associated with dystonia in more than half of the patients. When the clinical picture is clearly identified, more than half of the cases are associated with mutations in the SGCE gene. We herein describe a family with myoclonus-dystonia associated with a novel mutation in exon 7 of SGCE, c.904A>T (p.Lys302Ter) [Chr7:(GRCh38):g.94600779 T>A], which was absent in a non-affected member. A video recording of two of the affected members is provided. While the index case presents a severe cervical dystonia even affecting back posture, his sibling shows a much milder phenotype with mild myoclonic jerks. None of them had alcohol responsiveness or psychiatric comorbidity.
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13
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Milone R, Gnazzo M, Stefanutti E, Serafin D, Novelli A. A new missense mutation in DPF2 gene related to Coffin Siris syndrome 7: Description of a mild phenotype expanding DPF2-related clinical spectrum and differential diagnosis among similar syndromes epigenetically determined. Brain Dev 2020; 42:192-198. [PMID: 31706665 DOI: 10.1016/j.braindev.2019.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/15/2019] [Accepted: 10/21/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND Coffin-Siris syndrome (CSS) is a neurodevelopmental disorder characterized by somatic dysmorphic features, developmental and speech delay. It is due to mutations in many different genes, belonging to BAF chromatin-remodelling complex. The last gene involved in this complex, recently individuated and related to CSS, was DPF2, although only nine patients have been reported until now. METHOD Here we report on a boy with a history of developmental delay, especially regarding speech and language, and dysmorphic features resembling a syndromic condition. Array-Comparative Genomic Hybridization (CGH) and a custom Next Generation Sequencing (NGS) panel including developmental delay related genes were executed. RESULTS Array-CGH was negative while NGS panel revealed a novel mutation in DPF2 gene. CONCLUSIONS We add the clinical description of another patient with a novel mutation in DPF2, with a mild phenotype, thus trying to contribute to enlarge CSS phenotypic variability. Moreover, we briefly discuss about cohesinopathies and major differential diagnosis among syndromes with phenotypes overlapping to CSS.
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Affiliation(s)
- Roberta Milone
- U.O. Neuropsichiatria Infantile, AULSS 7 Pedemontana Regione Veneto, Distretto 2 Alto Vicentino, Thiene, VI, Italy.
| | - Maria Gnazzo
- Medical Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Elena Stefanutti
- U.O. Neuropsichiatria Infantile, AULSS 7 Pedemontana Regione Veneto, Distretto 2 Alto Vicentino, Thiene, VI, Italy
| | - Dorella Serafin
- U.O. Neuropsichiatria Infantile, AULSS 7 Pedemontana Regione Veneto, Distretto 2 Alto Vicentino, Thiene, VI, Italy
| | - Antonio Novelli
- Medical Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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14
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Yordanova I, Pavlova Z, Kirov A, Todorov T, Alexiev A, Sarafov S, Mateva L, Chamova T, Gospodinova M, Mitev V, Tournev I, Todorova A. Monoallelic expression of the TTR gene as a contributor to the age at onset and penetrance of TTR-related amyloidosis. Gene 2019; 705:16-21. [PMID: 30981840 DOI: 10.1016/j.gene.2019.04.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 11/18/2022]
Abstract
TTR-related amyloidosis (ATTR) is manifested in two allelic forms: familial amyloid polyneuropathy (TTR-FAP) and cardiomyopathy (TTR-FAC), both caused by mutations in the TTR gene. The most prevalent mutation in Bulgaria is p.Glu89Gln. Markedly different age at onset and disease penetrance is noticed in Bulgarian p.Glu89Gln cases even in a single family or between genetically identical twins. The present study aimed to evaluate the transcription profile of the TTR gene in order to better understand the difference in disease onset and penetrance. Six p.Glu89Gln positive families were selected from our registry, based on intrafamilial differences in disease onset and penetrance. Plasma and urine specimens were collected from 13 patients and subjected to transcription analysis. Both mutant and wild type transcripts were visualized in a mixed transcription profile, which is the traditional model of autosomal gene expression. The results from a relative quantification of the mutant versus wild type transcript showed presence of the mutant transcript between 0.14 and 1.14 times against the wild type. In addition, monoallelic expression signature was also detected. Based on our results we propose a model of natural selection, which includes age-related allele exclusion or suppression: predominant expression of a wild type (at an early age) and mutant (at the process of ageing) alleles. The intrafamilial differences in disease onset and penetrance need to be considered in genetic counselling and in follow-up of mutation carriers.
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Affiliation(s)
- Iglika Yordanova
- Genetic Medico-Diagnostic Laboratory Genica, Sofia, Bulgaria; IMDL Genome Center "Bulgaria", Sofia, Bulgaria
| | - Zornitza Pavlova
- IMDL Genome Center "Bulgaria", Sofia, Bulgaria; Department of Medical Chemistry and Biochemistry, Medical University Sofia, Sofia, Bulgaria
| | | | - Tihomir Todorov
- Genetic Medico-Diagnostic Laboratory Genica, Sofia, Bulgaria; IMDL Genome Center "Bulgaria", Sofia, Bulgaria
| | - Assen Alexiev
- Clinic of Gastroenterology, University Hospital "St. Ivan Rilski", Medical University-Sofia, Bulgaria
| | - Stayko Sarafov
- Clinic of Nervous Diseases, University Hospital "Alexandrovska", Department of Neurology, Medical University Sofia, Sofia, Bulgaria
| | - Lyudmila Mateva
- Clinic of Gastroenterology, University Hospital "St. Ivan Rilski", Medical University-Sofia, Bulgaria
| | - Teodora Chamova
- Clinic of Nervous Diseases, University Hospital "Alexandrovska", Department of Neurology, Medical University Sofia, Sofia, Bulgaria
| | | | - Vanyo Mitev
- Department of Medical Chemistry and Biochemistry, Medical University Sofia, Sofia, Bulgaria
| | - Ivailo Tournev
- Clinic of Nervous Diseases, University Hospital "Alexandrovska", Department of Neurology, Medical University Sofia, Sofia, Bulgaria; Department for Cognitive Science and Psychology, New Bulgarian University, Sofia, Bulgaria
| | - Albena Todorova
- Genetic Medico-Diagnostic Laboratory Genica, Sofia, Bulgaria; IMDL Genome Center "Bulgaria", Sofia, Bulgaria; Department of Medical Chemistry and Biochemistry, Medical University Sofia, Sofia, Bulgaria
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Vinogradova S, Saksena SD, Ward HN, Vigneau S, Gimelbrant AA. MaGIC: a machine learning tool set and web application for monoallelic gene inference from chromatin. BMC Bioinformatics 2019; 20:106. [PMID: 30819107 PMCID: PMC6394031 DOI: 10.1186/s12859-019-2679-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 02/13/2019] [Indexed: 01/13/2023] Open
Abstract
Background A large fraction of human and mouse autosomal genes are subject to random monoallelic expression (MAE), an epigenetic mechanism characterized by allele-specific gene expression that varies between clonal cell lineages. MAE is highly cell-type specific and mapping it in a large number of cell and tissue types can provide insight into its biological function. Its detection, however, remains challenging. Results We previously reported that a sequence-independent chromatin signature identifies, with high sensitivity and specificity, genes subject to MAE in multiple tissue types using readily available ChIP-seq data. Here we present an implementation of this method as a user-friendly, open-source software pipeline for monoallelic gene inference from chromatin (MaGIC). The source code for the MaGIC pipeline and the Shiny app is available at https://github.com/gimelbrantlab/magic. Conclusion The pipeline can be used by researchers to map monoallelic expression in a variety of cell types using existing models and to train new models with additional sets of chromatin marks. Electronic supplementary material The online version of this article (10.1186/s12859-019-2679-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Svetlana Vinogradova
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Sachit D Saksena
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Henry N Ward
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,University of Minnesota-Twin Cities, Bioinformatics and Computational Biology Program, Minneapolis, MN, 55455, USA
| | - Sébastien Vigneau
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Alexander A Gimelbrant
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
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