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Heredia-Torrejón M, Montañez R, González-Meneses A, Carcavilla A, Medina MA, Lechuga-Sancho AM. VUS next in rare diseases? Deciphering genetic determinants of biomolecular condensation. Orphanet J Rare Dis 2024; 19:327. [PMID: 39243101 PMCID: PMC11380411 DOI: 10.1186/s13023-024-03307-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 08/06/2024] [Indexed: 09/09/2024] Open
Abstract
The diagnostic odysseys for rare disease patients are getting shorter as next-generation sequencing becomes more widespread. However, the complex genetic diversity and factors influencing expressivity continue to challenge accurate diagnosis, leaving more than 50% of genetic variants categorized as variants of uncertain significance.Genomic expression intricately hinges on localized interactions among its products. Conventional variant prioritization, biased towards known disease genes and the structure-function paradigm, overlooks the potential impact of variants shaping the composition, location, size, and properties of biomolecular condensates, genuine membraneless organelles swiftly sensing and responding to environmental changes, and modulating expressivity.To address this complexity, we propose to focus on the nexus of genetic variants within biomolecular condensates determinants. Scrutinizing variant effects in these membraneless organelles could refine prioritization, enhance diagnostics, and unveil the molecular underpinnings of rare diseases. Integrating comprehensive genome sequencing, transcriptomics, and computational models can unravel variant pathogenicity and disease mechanisms, enabling precision medicine. This paper presents the rationale driving our proposal and describes a protocol to implement this approach. By fusing state-of-the-art knowledge and methodologies into the clinical practice, we aim to redefine rare diseases diagnosis, leveraging the power of scientific advancement for more informed medical decisions.
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Affiliation(s)
- María Heredia-Torrejón
- Inflammation, Nutrition, Metabolism and Oxidative Stress Research Laboratory, Biomedical Research and Innovation Institute of Cadiz (INiBICA), Cadiz, Spain
- Mother and Child Health and Radiology Department. Area of Clinical Genetics, University of Cadiz. Faculty of Medicine, Cadiz, Spain
| | - Raúl Montañez
- Inflammation, Nutrition, Metabolism and Oxidative Stress Research Laboratory, Biomedical Research and Innovation Institute of Cadiz (INiBICA), Cadiz, Spain.
- Department of Molecular Biology and Biochemistry, University of Malaga, Andalucía Tech, E-29071, Málaga, Spain.
| | - Antonio González-Meneses
- Division of Dysmorphology, Department of Paediatrics, Virgen del Rocio University Hospital, Sevilla, Spain
- Department of Paediatrics, Medical School, University of Sevilla, Sevilla, Spain
| | - Atilano Carcavilla
- Pediatric Endocrinology Department, Hospital Universitario La Paz, 28046, Madrid, Spain
- Multidisciplinary Unit for RASopathies, Hospital Universitario La Paz, 28046, Madrid, Spain
| | - Miguel A Medina
- Department of Molecular Biology and Biochemistry, University of Malaga, Andalucía Tech, E-29071, Málaga, Spain.
- Biomedical Research Institute and nanomedicine platform of Málaga IBIMA-BIONAND, E-29071, Málaga, Spain.
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, E-28029, Madrid, Spain.
| | - Alfonso M Lechuga-Sancho
- Inflammation, Nutrition, Metabolism and Oxidative Stress Research Laboratory, Biomedical Research and Innovation Institute of Cadiz (INiBICA), Cadiz, Spain
- Division of Endocrinology, Department of Paediatrics, Puerta del Mar University Hospital, Cádiz, Spain
- Area of Paediatrics, Department of Child and Mother Health and Radiology, Medical School, University of Cadiz, Cadiz, Spain
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2
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Mackay TFC, Anholt RRH. Pleiotropy, epistasis and the genetic architecture of quantitative traits. Nat Rev Genet 2024; 25:639-657. [PMID: 38565962 PMCID: PMC11330371 DOI: 10.1038/s41576-024-00711-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 04/04/2024]
Abstract
Pleiotropy (whereby one genetic polymorphism affects multiple traits) and epistasis (whereby non-linear interactions between genetic polymorphisms affect the same trait) are fundamental aspects of the genetic architecture of quantitative traits. Recent advances in the ability to characterize the effects of polymorphic variants on molecular and organismal phenotypes in human and model organism populations have revealed the prevalence of pleiotropy and unexpected shared molecular genetic bases among quantitative traits, including diseases. By contrast, epistasis is common between polymorphic loci associated with quantitative traits in model organisms, such that alleles at one locus have different effects in different genetic backgrounds, but is rarely observed for human quantitative traits and common diseases. Here, we review the concepts and recent inferences about pleiotropy and epistasis, and discuss factors that contribute to similarities and differences between the genetic architecture of quantitative traits in model organisms and humans.
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Affiliation(s)
- Trudy F C Mackay
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
| | - Robert R H Anholt
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
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3
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Glenn RA, Do SC, Guruvayurappan K, Corrigan EK, Santini L, Medina-Cano D, Singer S, Cho H, Liu J, Broman K, Czechanski A, Reinholdt L, Koche R, Furuta Y, Kunz M, Vierbuchen T. A PLURIPOTENT STEM CELL PLATFORM FOR IN VITRO SYSTEMS GENETICS STUDIES OF MOUSE DEVELOPMENT. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597758. [PMID: 38895226 PMCID: PMC11185710 DOI: 10.1101/2024.06.06.597758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The directed differentiation of pluripotent stem cells (PSCs) from panels of genetically diverse individuals is emerging as a powerful experimental system for characterizing the impact of natural genetic variation on developing cell types and tissues. Here, we establish new PSC lines and experimental approaches for modeling embryonic development in a genetically diverse, outbred mouse stock (Diversity Outbred mice). We show that a range of inbred and outbred PSC lines can be stably maintained in the primed pluripotent state (epiblast stem cells -- EpiSCs) and establish the contribution of genetic variation to phenotypic differences in gene regulation and directed differentiation. Using pooled in vitro fertilization, we generate and characterize a genetic reference panel of Diversity Outbred PSCs (n = 230). Finally, we demonstrate the feasibility of pooled culture of Diversity Outbred EpiSCs as "cell villages", which can facilitate the differentiation of large numbers of EpiSC lines for forward genetic screens. These data can complement and inform similar efforts within the stem cell biology and human genetics communities to model the impact of natural genetic variation on phenotypic variation and disease-risk.
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Affiliation(s)
- Rachel A. Glenn
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cell and Developmental Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Stephanie C. Do
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Emily K. Corrigan
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Present address: Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA and Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Laura Santini
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Medina-Cano
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarah Singer
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hyein Cho
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jing Liu
- Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karl Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI USA
| | | | | | - Richard Koche
- Center for Epigenetics Research, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yasuhide Furuta
- Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meik Kunz
- The Bioinformatics CRO, Sanford Florida, 32771 USA
| | - Thomas Vierbuchen
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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4
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Lounev V, Groppe JC, Brewer N, Wentworth KL, Smith V, Xu M, Schomburg L, Bhargava P, Al Mukaddam M, Hsiao EC, Shore EM, Pignolo RJ, Kaplan FS. Matrix metalloproteinase-9 deficiency confers resilience in fibrodysplasia ossificans progressiva in a man and mice. J Bone Miner Res 2024; 39:382-398. [PMID: 38477818 DOI: 10.1093/jbmr/zjae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 03/14/2024]
Abstract
Single case studies of extraordinary disease resilience may provide therapeutic insight into conditions for which no definitive treatments exist. An otherwise healthy 35-year-old man (patient-R) with the canonical pathogenic ACVR1R206H variant and the classic congenital great toe malformation of fibrodysplasia ossificans progressiva (FOP) had extreme paucity of post-natal heterotopic ossification (HO) and nearly normal mobility. We hypothesized that patient-R lacked a sufficient post-natal inflammatory trigger for HO. A plasma biomarker survey revealed a reduction in total matrix metalloproteinase-9 (MMP-9) compared to healthy controls and individuals with quiescent FOP. Whole exome sequencing identified compound heterozygous variants in MMP-9 (c.59C > T, p.A20V and c.493G > A, p.D165N). Structural analysis of the D165N variant predicted both decreased MMP-9 secretion and activity that were confirmed by enzyme-linked immunosorbent assay and gelatin zymography. Further, human proinflammatory M1-like macrophages expressing either MMP-9 variant produced significantly less Activin A, an obligate ligand for HO in FOP, compared to wildtype controls. Importantly, MMP-9 inhibition by genetic, biologic, or pharmacologic means in multiple FOP mouse models abrogated trauma-induced HO, sequestered Activin A in the extracellular matrix (ECM), and induced regeneration of injured skeletal muscle. Our data suggest that MMP-9 is a druggable node linking inflammation to HO, orchestrates an existential role in the pathogenesis of FOP, and illustrates that a single patient's clinical phenotype can reveal critical molecular mechanisms of disease that unveil novel treatment strategies.
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Affiliation(s)
- Vitali Lounev
- Department of Orthopaedic Surgery, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States
- The Center for Research in FOP and Related Disorders, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States
| | - Jay C Groppe
- Department of Biomedical Sciences, Texas A & M University College of Dentistry, Dallas, TX 75246-2013, United States
| | - Niambi Brewer
- Department of Orthopaedic Surgery, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States
- The Center for Research in FOP and Related Disorders, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States
| | - Kelly L Wentworth
- Department of Medicine, Division of Endocrinology and Metabolism, Zuckerberg San Francisco General Hospital, University of California, San Francisco, CA 94143-0794, United States
- Department of Medicine, University of California, San Francisco, CA 94143-0794, United States
| | | | - Meiqi Xu
- Department of Orthopaedic Surgery, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States
- The Center for Research in FOP and Related Disorders, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States
| | - Lutz Schomburg
- Institute for Experimental Endocrinology, Charite University Hospital, D-10115 Berlin, Germany
| | | | - Mona Al Mukaddam
- Department of Orthopaedic Surgery, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States
- The Center for Research in FOP and Related Disorders, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States
- Department of Medicine, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States
| | - Edward C Hsiao
- Department of Medicine, University of California, San Francisco, CA 94143-0794, United States
- Division of Endocrinology and Metabolism, The Institute for Human Genetics, the Program in Craniofacial Biology, University of California, San Francisco, CA 94143-0794, United States
| | - Eileen M Shore
- Department of Orthopaedic Surgery, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States
- The Center for Research in FOP and Related Disorders, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States
- Department of Genetics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States
| | - Robert J Pignolo
- Department of Medicine, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN 55905, United States
| | - Frederick S Kaplan
- Department of Orthopaedic Surgery, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States
- The Center for Research in FOP and Related Disorders, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States
- Department of Medicine, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States
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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 PMCID: PMC11050712 DOI: 10.3390/ijms25084217] [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: 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; (N.Y.F.); (D.A.); (K.M.); (C.A.W.); (N.X.C.)
| | - 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; (N.Y.F.); (D.A.); (K.M.); (C.A.W.); (N.X.C.)
| | - 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; (N.Y.F.); (D.A.); (K.M.); (C.A.W.); (N.X.C.)
| | - 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; (N.Y.F.); (D.A.); (K.M.); (C.A.W.); (N.X.C.)
| | - 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; (N.Y.F.); (D.A.); (K.M.); (C.A.W.); (N.X.C.)
| | - 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; (N.Y.F.); (D.A.); (K.M.); (C.A.W.); (N.X.C.)
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Dong X, Lu Y, Guo L, Li C, Ni Q, Wu B, Wang H, Yang L, Wu S, Sun Q, Zheng H, Zhou W, Wang S. PICOTEES: a privacy-preserving online service of phenotype exploration for genetic-diagnostic variants from Chinese children cohorts. J Genet Genomics 2024; 51:243-251. [PMID: 37714454 DOI: 10.1016/j.jgg.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/31/2023] [Accepted: 09/03/2023] [Indexed: 09/17/2023]
Abstract
The growth in biomedical data resources has raised potential privacy concerns and risks of genetic information leakage. For instance, exome sequencing aids clinical decisions by comparing data through web services, but it requires significant trust between users and providers. To alleviate privacy concerns, the most commonly used strategy is to anonymize sensitive data. Unfortunately, studies have shown that anonymization is insufficient to protect against reidentification attacks. Recently, privacy-preserving technologies have been applied to preserve application utility while protecting the privacy of biomedical data. We present the PICOTEES framework, a privacy-preserving online service of phenotype exploration for genetic-diagnostic variants (https://birthdefectlab.cn:3000/). PICOTEES enables privacy-preserving queries of the phenotype spectrum for a single variant by utilizing trusted execution environment technology, which can protect the privacy of the user's query information, backend models, and data, as well as the final results. We demonstrate the utility and performance of PICOTEES by exploring a bioinformatics dataset. The dataset is from a cohort containing 20,909 genetic testing patients with 3,152,508 variants from the Children's Hospital of Fudan University in China, dominated by the Chinese Han population (>99.9%). Our query results yield a large number of unreported diagnostic variants and previously reported pathogenicity.
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Affiliation(s)
- Xinran Dong
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Yulan Lu
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Lanting Guo
- Department of Bioinformatics, Hangzhou Nuowei Information Technology Co., Ltd, Hangzhou, Zhejiang 310000, China
| | - Chuan Li
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Qi Ni
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Huijun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Lin Yang
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Songyang Wu
- The Third Research Institute of the Ministry of Public Security, Shanghai 200031, China
| | - Qi Sun
- Department of Bioinformatics, Hangzhou Nuowei Information Technology Co., Ltd, Hangzhou, Zhejiang 310000, China
| | - Hao Zheng
- Department of Bioinformatics, Hangzhou Nuowei Information Technology Co., Ltd, Hangzhou, Zhejiang 310000, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Xiamen Campus of Children's Hospital of Fudan University, Xiamen, Fujian 361006, China.
| | - Shuang Wang
- Department of Bioinformatics, Hangzhou Nuowei Information Technology Co., Ltd, Hangzhou, Zhejiang 310000, China; Institutes for Systems Genetics, West China Hospital, Chengdu, Sichuan 610041, China; Shanghai Putuo People's Hospital, Tongji University, Shanghai 200060, China.
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7
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Leopold JA. Editorial commentary: Precision medicine based on personal phenotyping. Trends Cardiovasc Med 2024; 34:126-127. [PMID: 36717063 DOI: 10.1016/j.tcm.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/29/2023]
Affiliation(s)
- Jane A Leopold
- Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, NRB0630K, Boston, MA 02115, USA.
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8
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Auwerx C, Jõeloo M, Sadler MC, Tesio N, Ojavee S, Clark CJ, Mägi R, Reymond A, Kutalik Z. Rare copy-number variants as modulators of common disease susceptibility. Genome Med 2024; 16:5. [PMID: 38185688 PMCID: PMC10773105 DOI: 10.1186/s13073-023-01265-5] [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: 07/17/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
BACKGROUND Copy-number variations (CNVs) have been associated with rare and debilitating genomic disorders (GDs) but their impact on health later in life in the general population remains poorly described. METHODS Assessing four modes of CNV action, we performed genome-wide association scans (GWASs) between the copy-number of CNV-proxy probes and 60 curated ICD-10 based clinical diagnoses in 331,522 unrelated white British UK Biobank (UKBB) participants with replication in the Estonian Biobank. RESULTS We identified 73 signals involving 40 diseases, all of which indicating that CNVs increased disease risk and caused earlier onset. We estimated that 16% of these associations are indirect, acting by increasing body mass index (BMI). Signals mapped to 45 unique, non-overlapping regions, nine of which being linked to known GDs. Number and identity of genes affected by CNVs modulated their pathogenicity, with many associations being supported by colocalization with both common and rare single-nucleotide variant association signals. Dissection of association signals provided insights into the epidemiology of known gene-disease pairs (e.g., deletions in BRCA1 and LDLR increased risk for ovarian cancer and ischemic heart disease, respectively), clarified dosage mechanisms of action (e.g., both increased and decreased dosage of 17q12 impacted renal health), and identified putative causal genes (e.g., ABCC6 for kidney stones). Characterization of the pleiotropic pathological consequences of recurrent CNVs at 15q13, 16p13.11, 16p12.2, and 22q11.2 in adulthood indicated variable expressivity of these regions and the involvement of multiple genes. Finally, we show that while the total burden of rare CNVs-and especially deletions-strongly associated with disease risk, it only accounted for ~ 0.02% of the UKBB disease burden. These associations are mainly driven by CNVs at known GD CNV regions, whose pleiotropic effect on common diseases was broader than anticipated by our CNV-GWAS. CONCLUSIONS Our results shed light on the prominent role of rare CNVs in determining common disease susceptibility within the general population and provide actionable insights for anticipating later-onset comorbidities in carriers of recurrent CNVs.
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Affiliation(s)
- Chiara Auwerx
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland.
| | - Maarja Jõeloo
- Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Marie C Sadler
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland
| | - Nicolò Tesio
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
| | - Sven Ojavee
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Charlie J Clark
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland.
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9
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Derrick CJ, Szenker-Ravi E, Santos-Ledo A, Alqahtani A, Yusof A, Eley L, Coleman AHL, Tohari S, Ng AYJ, Venkatesh B, Alharby E, Mansard L, Bonnet-Dupeyron MN, Roux AF, Vaché C, Roume J, Bouvagnet P, Almontashiri NAM, Henderson DJ, Reversade B, Chaudhry B. Functional analysis of germline VANGL2 variants using rescue assays of vangl2 knockout zebrafish. Hum Mol Genet 2024; 33:150-169. [PMID: 37815931 PMCID: PMC10772043 DOI: 10.1093/hmg/ddad171] [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: 07/27/2023] [Revised: 09/11/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023] Open
Abstract
Developmental studies have shown that the evolutionarily conserved Wnt Planar Cell Polarity (PCP) pathway is essential for the development of a diverse range of tissues and organs including the brain, spinal cord, heart and sensory organs, as well as establishment of the left-right body axis. Germline mutations in the highly conserved PCP gene VANGL2 in humans have only been associated with central nervous system malformations, and functional testing to understand variant impact has not been performed. Here we report three new families with missense variants in VANGL2 associated with heterotaxy and congenital heart disease p.(Arg169His), non-syndromic hearing loss p.(Glu465Ala) and congenital heart disease with brain defects p.(Arg135Trp). To test the in vivo impact of these and previously described variants, we have established clinically-relevant assays using mRNA rescue of the vangl2 mutant zebrafish. We show that all variants disrupt Vangl2 function, although to different extents and depending on the developmental process. We also begin to identify that different VANGL2 missense variants may be haploinsufficient and discuss evidence in support of pathogenicity. Together, this study demonstrates that zebrafish present a suitable pipeline to investigate variants of unknown significance and suggests new avenues for investigation of the different developmental contexts of VANGL2 function that are clinically meaningful.
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Affiliation(s)
- Christopher J Derrick
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | | | - Adrian Santos-Ledo
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Ahlam Alqahtani
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Amirah Yusof
- Genome Institute of Singapore (GIS), A*STAR, 60 Biopolis St, 138672, Singapore
| | - Lorraine Eley
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Alistair H L Coleman
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Sumanty Tohari
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Dr, Proteos, 138673, Singapore
| | - Alvin Yu-Jin Ng
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Dr, Proteos, 138673, Singapore
- MGI Tech Singapore Pte Ltd, 21 Biopolis Rd, 138567, Singapore
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Dr, Proteos, 138673, Singapore
| | - Essa Alharby
- Center for Genetics and Inherited Diseases, Taibah University, 7534 Abdul Muhsin Ibn Abdul Aziz, Al Ihn, Al-Madinah al-Munawwarah 42318, Saudi Arabia
- Faculty of Applied Medical Sciences, Taibah University, Janadah Bin Umayyah Road, Tayba, Al-Madinah al-Munawwarah 42353, Saudi Arabia
| | - Luke Mansard
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, 80 Av. Augustin Fliche, 34000 Montpellier, France
| | | | - Anne-Francoise Roux
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, 80 Av. Augustin Fliche, 34000 Montpellier, France
| | - Christel Vaché
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, 80 Av. Augustin Fliche, 34000 Montpellier, France
| | - Joëlle Roume
- Département de Génétique, CHI Poissy, St Germain-en-Laye, 10 Rue du Champ Gaillard, 78300 Poissy, France
| | - Patrice Bouvagnet
- CPDPN, Hôpital MFME, CHU de Martinique, Fort de France, Fort-de-France 97261, Martinique, France
| | - Naif A M Almontashiri
- Center for Genetics and Inherited Diseases, Taibah University, 7534 Abdul Muhsin Ibn Abdul Aziz, Al Ihn, Al-Madinah al-Munawwarah 42318, Saudi Arabia
- Faculty of Applied Medical Sciences, Taibah University, Janadah Bin Umayyah Road, Tayba, Al-Madinah al-Munawwarah 42353, Saudi Arabia
| | - Deborah J Henderson
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Bruno Reversade
- Genome Institute of Singapore (GIS), A*STAR, 60 Biopolis St, 138672, Singapore
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Dr, Proteos, 138673, Singapore
- Smart-Health Initiative, BESE, KAUST, Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Medical Genetics Department, Koç Hospital Davutpaşa Caddesi 34010 Topkapı Istanbul, Istanbul, Turkey
| | - Bill Chaudhry
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
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10
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Pons C, van Leeuwen J. Meta-analysis of dispensable essential genes and their interactions with bypass suppressors. Life Sci Alliance 2024; 7:e202302192. [PMID: 37918966 PMCID: PMC10622647 DOI: 10.26508/lsa.202302192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023] Open
Abstract
Genes have been historically classified as essential or non-essential based on their requirement for viability. However, genomic mutations can sometimes bypass the requirement for an essential gene, challenging the binary classification of gene essentiality. Such dispensable essential genes represent a valuable model for understanding the incomplete penetrance of loss-of-function mutations often observed in natural populations. Here, we compiled data from multiple studies on essential gene dispensability in Saccharomyces cerevisiae to comprehensively characterize these genes. In analyses spanning different evolutionary timescales, dispensable essential genes exhibited distinct phylogenetic properties compared with other essential and non-essential genes. Integration of interactions with suppressor genes that can bypass the gene essentiality revealed the high functional modularity of the bypass suppression network. Furthermore, dispensable essential and bypass suppressor gene pairs reflected simultaneous changes in the mutational landscape of S. cerevisiae strains. Importantly, species in which dispensable essential genes were non-essential tended to carry bypass suppressor mutations in their genomes. Overall, our study offers a comprehensive view of dispensable essential genes and illustrates how their interactions with bypass suppressors reflect evolutionary outcomes.
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Affiliation(s)
- Carles Pons
- https://ror.org/01z1gye03 Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Jolanda van Leeuwen
- Center for Integrative Genomics, Bâtiment Génopode, University of Lausanne, Lausanne, Switzerland
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11
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Matkarimov BT, Saparbaev MK. Chargaff's second parity rule lies at the origin of additive genetic interactions in quantitative traits to make omnigenic selection possible. PeerJ 2023; 11:e16671. [PMID: 38107580 PMCID: PMC10725672 DOI: 10.7717/peerj.16671] [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: 07/21/2023] [Accepted: 11/22/2023] [Indexed: 12/19/2023] Open
Abstract
Background Francis Crick's central dogma provides a residue-by-residue mechanistic explanation of the flow of genetic information in living systems. However, this principle may not be sufficient for explaining how random mutations cause continuous variation of quantitative highly polygenic complex traits. Chargaff's second parity rule (CSPR), also referred to as intrastrand DNA symmetry, defined as near-exact equalities G ≈ C and A ≈ T within a single DNA strand, is a statistical property of cellular genomes. The phenomenon of intrastrand DNA symmetry was discovered more than 50 years ago; at present, it remains unclear what its biological role is, what the mechanisms are that force cellular genomes to comply strictly with CSPR, and why genomes of certain noncellular organisms have broken intrastrand DNA symmetry. The present work is aimed at studying a possible link between intrastrand DNA symmetry and the origin of genetic interactions in quantitative traits. Methods Computational analysis of single-nucleotide polymorphisms in human and mouse populations and of nucleotide composition biases at different codon positions in bacterial and human proteomes. Results The analysis of mutation spectra inferred from single-nucleotide polymorphisms observed in murine and human populations revealed near-exact equalities of numbers of reverse complementary mutations, indicating that random genetic variations obey CSPR. Furthermore, nucleotide compositions of coding sequences proved to be statistically interwoven via CSPR because pyrimidine bias at the 3rd codon position compensates purine bias at the 1st and 2nd positions. Conclusions According to Fisher's infinitesimal model, we propose that accumulation of reverse complementary mutations results in a continuous phenotypic variation due to small additive effects of statistically interwoven genetic variations. Therefore, additive genetic interactions can be inferred as a statistical entanglement of nucleotide compositions of separate genetic loci. CSPR challenges the neutral theory of molecular evolution-because all random mutations participate in variation of a trait-and provides an alternative solution to Haldane's dilemma by making a gene function diffuse. We propose that CSPR is symmetry of Fisher's infinitesimal model and that genetic information can be transferred in an implicit contactless manner.
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Affiliation(s)
- Bakhyt T. Matkarimov
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- L.N.Gumilev Eurasian National University, Astana, Kazakhstan
| | - Murat K. Saparbaev
- Groupe «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR9019, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
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12
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Abou Tayoun AN. Unequal global implementation of genomic newborn screening. Nat Rev Genet 2023; 24:801-802. [PMID: 37723349 DOI: 10.1038/s41576-023-00654-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Affiliation(s)
- Ahmad N Abou Tayoun
- Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates.
- Center for Genomic Discovery, Mohammed bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.
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13
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Maroilley T, Rahit KMTH, Chida AR, Cotra F, Rodrigues Alves Barbosa V, Tarailo-Graovac M. Model Organism Modifier (MOM): a user-friendly Galaxy workflow to detect modifiers from genome sequencing data using Caenorhabditis elegans. G3 (BETHESDA, MD.) 2023; 13:jkad184. [PMID: 37585487 PMCID: PMC10627290 DOI: 10.1093/g3journal/jkad184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 04/21/2023] [Accepted: 08/05/2023] [Indexed: 08/18/2023]
Abstract
Genetic modifiers are variants modulating phenotypic outcomes of a primary detrimental variant. They contribute to rare diseases phenotypic variability, but their identification is challenging. Genetic screening with model organisms is a widely used method for demystifying genetic modifiers. Forward genetics screening followed by whole genome sequencing allows the detection of variants throughout the genome but typically produces thousands of candidate variants making the interpretation and prioritization process very time-consuming and tedious. Despite whole genome sequencing is more time and cost-efficient, usage of computational pipelines specific to modifier identification remains a challenge for biological-experiment-focused laboratories doing research with model organisms. To facilitate a broader implementation of whole genome sequencing in genetic screens, we have developed Model Organism Modifier or MOM, a pipeline as a user-friendly Galaxy workflow. Model Organism Modifier analyses raw short-read whole genome sequencing data and implements tailored filtering to provide a Candidate Variant List short enough to be further manually curated. We provide a detailed tutorial to run the Galaxy workflow Model Organism Modifier and guidelines to manually curate the Candidate Variant Lists. We have tested Model Organism Modifier on published and validated Caenorhabditis elegans modifiers screening datasets. As whole genome sequencing facilitates high-throughput identification of genetic modifiers in model organisms, Model Organism Modifier provides a user-friendly solution to implement the bioinformatics analysis of the short-read datasets in laboratories without expertise or support in Bioinformatics.
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Affiliation(s)
- Tatiana Maroilley
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - K M Tahsin Hassan Rahit
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Afiya Razia Chida
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Filip Cotra
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Victoria Rodrigues Alves Barbosa
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Maja Tarailo-Graovac
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
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14
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Sproule TJ, Wilpan RY, Wilson JJ, Low BE, Kabata Y, Ushiki T, Abe R, Wiles MV, Roopenian DC, Sundberg JP. Dystonin modifiers of junctional epidermolysis bullosa and models of epidermolysis bullosa simplex without dystonia musculorum. PLoS One 2023; 18:e0293218. [PMID: 37883475 PMCID: PMC10602294 DOI: 10.1371/journal.pone.0293218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/07/2023] [Indexed: 10/28/2023] Open
Abstract
The Lamc2jeb junctional epidermolysis bullosa (EB) mouse model has been used to demonstrate that significant genetic modification of EB symptoms is possible, identifying as modifiers Col17a1 and six other quantitative trait loci, several with strong candidate genes including dystonin (Dst/Bpag1). Here, CRISPR/Cas9 was used to alter exon 23 in mouse skin specific isoform Dst-e (Ensembl GRCm38 transcript name Dst-213, transcript ID ENSMUST00000183302.5, protein size 2639AA) and validate a proposed arginine/glutamine difference at amino acid p1226 in B6 versus 129 mice as a modifier of EB. Frame shift deletions (FSD) in mouse Dst-e exon 23 (Dst-eFSD/FSD) were also identified that cause mice carrying wild-type Lamc2 to develop a phenotype similar to human EB simplex without dystonia musculorum. When combined, Dst-eFSD/FSD modifies Lamc2jeb/jeb (FSD+jeb) induced disease in unexpected ways implicating an altered balance between DST-e (BPAG1e) and a rarely reported rodless DST-eS (BPAG1eS) in epithelium as a possible mechanism. Further, FSD+jeb mice with pinnae removed are found to provide a test bed for studying internal epithelium EB disease and treatment without severe skin disease as a limiting factor while also revealing and accelerating significant nasopharynx symptoms present but not previously noted in Lamc2jeb/jeb mice.
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Affiliation(s)
| | - Robert Y. Wilpan
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | - John J. Wilson
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | - Benjamin E. Low
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | - Yudai Kabata
- Division of Dermatology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- Division of Microscopic Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Tatsuo Ushiki
- Division of Microscopic Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Riichiro Abe
- Division of Dermatology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Michael V. Wiles
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | | | - John P. Sundberg
- The Jackson Laboratory, Bar Harbor, ME, United States of America
- Department of Dermatology, Vanderbilt University Medical Center, Nashville, TN, United States of America
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15
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Keseroglu K, Zinani OQH, Keskin S, Seawall H, Alpay EE, Özbudak EM. Stochastic gene expression and environmental stressors trigger variable somite segmentation phenotypes. Nat Commun 2023; 14:6497. [PMID: 37838784 PMCID: PMC10576776 DOI: 10.1038/s41467-023-42220-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 10/04/2023] [Indexed: 10/16/2023] Open
Abstract
Mutations of several genes cause incomplete penetrance and variable expressivity of phenotypes, which are usually attributed to modifier genes or gene-environment interactions. Here, we show stochastic gene expression underlies the variability of somite segmentation defects in embryos mutant for segmentation clock genes her1 or her7. Phenotypic strength is further augmented by low temperature and hypoxia. By performing live imaging of the segmentation clock reporters, we further show that groups of cells with higher oscillation amplitudes successfully form somites while those with lower amplitudes fail to do so. In unfavorable environments, the number of cycles with high amplitude oscillations and the number of successful segmentations proportionally decrease. These results suggest that individual oscillation cycles stochastically fail to pass a threshold amplitude, resulting in segmentation defects in mutants. Our quantitative methodology is adaptable to investigate variable phenotypes of mutant genes in different tissues.
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Affiliation(s)
- Kemal Keseroglu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Oriana Q H Zinani
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Molecular and Developmental Biology Graduate Program, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Sevdenur Keskin
- Allergy and Immunology, University of Arkansas for Medical Science and Arkansas Children's Hospital, Little Rock, AR, 72202, USA
| | - Hannah Seawall
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Eslim E Alpay
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Ertuğrul M Özbudak
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA.
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16
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Lowther C, Valkanas E, Giordano JL, Wang HZ, Currall BB, O'Keefe K, Pierce-Hoffman E, Kurtas NE, Whelan CW, Hao SP, Weisburd B, Jalili V, Fu J, Wong I, Collins RL, Zhao X, Austin-Tse CA, Evangelista E, Lemire G, Aggarwal VS, Lucente D, Gauthier LD, Tolonen C, Sahakian N, Stevens C, An JY, Dong S, Norton ME, MacKenzie TC, Devlin B, Gilmore K, Powell BC, Brandt A, Vetrini F, DiVito M, Sanders SJ, MacArthur DG, Hodge JC, O'Donnell-Luria A, Rehm HL, Vora NL, Levy B, Brand H, Wapner RJ, Talkowski ME. Systematic evaluation of genome sequencing for the diagnostic assessment of autism spectrum disorder and fetal structural anomalies. Am J Hum Genet 2023; 110:1454-1469. [PMID: 37595579 PMCID: PMC10502737 DOI: 10.1016/j.ajhg.2023.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/25/2023] [Accepted: 07/25/2023] [Indexed: 08/20/2023] Open
Abstract
Short-read genome sequencing (GS) holds the promise of becoming the primary diagnostic approach for the assessment of autism spectrum disorder (ASD) and fetal structural anomalies (FSAs). However, few studies have comprehensively evaluated its performance against current standard-of-care diagnostic tests: karyotype, chromosomal microarray (CMA), and exome sequencing (ES). To assess the clinical utility of GS, we compared its diagnostic yield against these three tests in 1,612 quartet families including an individual with ASD and in 295 prenatal families. Our GS analytic framework identified a diagnostic variant in 7.8% of ASD probands, almost 2-fold more than CMA (4.3%) and 3-fold more than ES (2.7%). However, when we systematically captured copy-number variants (CNVs) from the exome data, the diagnostic yield of ES (7.4%) was brought much closer to, but did not surpass, GS. Similarly, we estimated that GS could achieve an overall diagnostic yield of 46.1% in unselected FSAs, representing a 17.2% increased yield over karyotype, 14.1% over CMA, and 4.1% over ES with CNV calling or 36.1% increase without CNV discovery. Overall, GS provided an added diagnostic yield of 0.4% and 0.8% beyond the combination of all three standard-of-care tests in ASD and FSAs, respectively. This corresponded to nine GS unique diagnostic variants, including sequence variants in exons not captured by ES, structural variants (SVs) inaccessible to existing standard-of-care tests, and SVs where the resolution of GS changed variant classification. Overall, this large-scale evaluation demonstrated that GS significantly outperforms each individual standard-of-care test while also outperforming the combination of all three tests, thus warranting consideration as the first-tier diagnostic approach for the assessment of ASD and FSAs.
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Affiliation(s)
- Chelsea Lowther
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Elise Valkanas
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Jessica L Giordano
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Harold Z Wang
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin B Currall
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Kathryn O'Keefe
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emma Pierce-Hoffman
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nehir E Kurtas
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Christopher W Whelan
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie P Hao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ben Weisburd
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vahid Jalili
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jack Fu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Isaac Wong
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Xuefang Zhao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Christina A Austin-Tse
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Emily Evangelista
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vimla S Aggarwal
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Diane Lucente
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Laura D Gauthier
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charlotte Tolonen
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nareh Sahakian
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christine Stevens
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joon-Yong An
- School of Biosystem and Biomedical Science, Korea University, Seoul, South Korea
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Mary E Norton
- Center for Maternal-Fetal Precision Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Tippi C MacKenzie
- Center for Maternal-Fetal Precision Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kelly Gilmore
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alicia Brandt
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Francesco Vetrini
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michelle DiVito
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel G MacArthur
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Centre for Population Genomics, Garvan Institute of Medical Research, and University of New South Wales Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Anne O'Donnell-Luria
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Heidi L Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neeta L Vora
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Ronald J Wapner
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA; Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA.
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17
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AlAbdi L, Maddirevula S, Shamseldin HE, Khouj E, Helaby R, Hamid H, Almulhim A, Hashem MO, Abdulwahab F, Abouyousef O, Alqahtani M, Altuwaijri N, Jaafar A, Alshidi T, Alzahrani F, Alkuraya FS. Diagnostic implications of pitfalls in causal variant identification based on 4577 molecularly characterized families. Nat Commun 2023; 14:5269. [PMID: 37644014 PMCID: PMC10465531 DOI: 10.1038/s41467-023-40909-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
Despite large sequencing and data sharing efforts, previously characterized pathogenic variants only account for a fraction of Mendelian disease patients, which highlights the need for accurate identification and interpretation of novel variants. In a large Mendelian cohort of 4577 molecularly characterized families, numerous scenarios in which variant identification and interpretation can be challenging are encountered. We describe categories of challenges that cover the phenotype (e.g. novel allelic disorders), pedigree structure (e.g. imprinting disorders masquerading as autosomal recessive phenotypes), positional mapping (e.g. double recombination events abrogating candidate autozygous intervals), gene (e.g. novel gene-disease assertion) and variant (e.g. complex compound inheritance). Overall, we estimate a probability of 34.3% for encountering at least one of these challenges. Importantly, our data show that by only addressing non-sequencing-based challenges, around 71% increase in the diagnostic yield can be expected. Indeed, by applying these lessons to a cohort of 314 cases with negative clinical exome or genome reports, we could identify the likely causal variant in 54.5%. Our work highlights the need to have a thorough approach to undiagnosed diseases by considering a wide range of challenges rather than a narrow focus on sequencing technologies. It is hoped that by sharing this experience, the yield of undiagnosed disease programs globally can be improved.
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Affiliation(s)
- Lama AlAbdi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ebtissal Khouj
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana Helaby
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Halima Hamid
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Aisha Almulhim
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Omar Abouyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Norah Altuwaijri
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amal Jaafar
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa Alshidi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fatema Alzahrani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.
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18
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Einson J, Glinos D, Boerwinkle E, Castaldi P, Darbar D, de Andrade M, Ellinor P, Fornage M, Gabriel S, Germer S, Gibbs R, Hersh CP, Johnsen J, Kaplan R, Konkle BA, Kooperberg C, Nassir R, Loos RJF, Meyers DA, Mitchell BD, Psaty B, Vasan RS, Rich SS, Rienstra M, Rotter JI, Saferali A, Shoemaker MB, Silverman E, Smith AV, Mohammadi P, Castel SE, Iossifov I, Lappalainen T. Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants. Genetics 2023; 224:iyad115. [PMID: 37348055 PMCID: PMC10411602 DOI: 10.1093/genetics/iyad115] [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: 02/02/2023] [Revised: 02/02/2023] [Accepted: 04/18/2023] [Indexed: 06/24/2023] Open
Abstract
Exonic variants present some of the strongest links between genotype and phenotype. However, these variants can have significant inter-individual pathogenicity differences, known as variable penetrance. In this study, we propose a model where genetically controlled mRNA splicing modulates the pathogenicity of exonic variants. By first cataloging exonic inclusion from RNA-sequencing data in GTEx V8, we find that pathogenic alleles are depleted on highly included exons. Using a large-scale phased whole genome sequencing data from the TOPMed consortium, we observe that this effect may be driven by common splice-regulatory genetic variants, and that natural selection acts on haplotype configurations that reduce the transcript inclusion of putatively pathogenic variants, especially when limiting to haploinsufficient genes. Finally, we test if this effect may be relevant for autism risk using families from the Simons Simplex Collection, but find that splicing of pathogenic alleles has a penetrance reducing effect here as well. Overall, our results indicate that common splice-regulatory variants may play a role in reducing the damaging effects of rare exonic variants.
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Affiliation(s)
- Jonah Einson
- Department of Biomedical Informatics, Columbia University, New York, NY 10027, USA
- New York Genome Center, New York, NY 10013, USA
| | | | - Eric Boerwinkle
- School of Public Health, University of Texas Health at Houston, Houston, TX 77030, USA
| | - Peter Castaldi
- Department of Medicine, Brigham & Women's Hospital, Boston, MA 02115, USA
| | - Dawood Darbar
- Department of Cardiology, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Mariza de Andrade
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Patrick Ellinor
- Corrigan Minehan Heart Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health at Houston, Houston, TX 77030, USA
| | | | | | - Richard Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine Human Genome Sequencing Center, Houston, TX 77030, USA
| | - Craig P Hersh
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jill Johnsen
- Department of Hematology, University of Washington, Seattle, WA 98195, USA
| | - Robert Kaplan
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Barbara A Konkle
- Department of Hematology, University of Washington, Seattle, WA 98195, USA
| | | | - Rami Nassir
- Department of Pathology, School of Medicine, Umm Al-Qura University, Mecca 24382, Saudi Arabia
| | - Ruth J F Loos
- Environmental Medicine & Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Deborah A Meyers
- Department of Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD 21201, USA
| | - Bruce Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA 98195, USA
| | | | - Stephen S Rich
- Public Health Sciences, University of Virginia, Charlottesville, VA 22903, USA
| | - Michael Rienstra
- Clinical Cardiology, UMCG Cardiology, Groningen 09713, the Netherlands
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Aabida Saferali
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | - Edwin Silverman
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham & Women's Hospital, Boston, MA 02115, USA
| | - Albert Vernon Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Stephane E Castel
- New York Genome Center, New York, NY 10013, USA
- Variant Bio, Seattle, WA 98102, USA
| | - Ivan Iossifov
- New York Genome Center, New York, NY 10013, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY 10013, USA
- Department of Systems Biology, Columbia University, New York, NY 10027, USA
- Department of Gene Technology, KTH Royal Institute of Technology, Stockholm 114 28, Sweden
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19
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Li M, Popovic N, Wang Y, Chen C, Polychronakos C. Incomplete penetrance and variable expressivity in monogenic diabetes; a challenge but also an opportunity. Rev Endocr Metab Disord 2023; 24:673-684. [PMID: 37165203 DOI: 10.1007/s11154-023-09809-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/01/2023] [Indexed: 05/12/2023]
Abstract
Monogenic Forms of Diabetes (MFD) account for about 3% of all diabetes, and their accurate diagnosis often results in life-changing therapeutic reassignment for the patients. Like other Mendelian diseases, reduced penetrance and variable expressivity are often seen in several different types of MFD, where symptoms develop only in a portion of the persons who carry the pathogenic variant or vary widely in symptom severity and age of onset. This complicates diagnosis and disease management in MFD. In addition to its clinical importance, knowledge of genetic modifiers that confer penetrance and expressivity variability opens possibilities to identify protective genetic variants which may help probe the mechanisms of more common forms of diabetes and shed light in new therapeutic strategies. In this review, we will mainly address penetrance and expressivity variation in different types of MFD, factors that confer such variations and opportunities that come with such knowledge. Related literature was searched in PubMed, Medline and Embase. Papers with publication year from 1974 to 2023 are included. Data are either sourced from literatures or from OMIM, Clinvar and 1000 genome browser.
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Affiliation(s)
- Meihang Li
- College of pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, Guangdong, China.
- Department of Emergency, Department of Endorinology, Maoming People's Hospital, 101 Weimin Road, Maoming, Guangdong, China.
- Montreal Children's Hospital and the Endocrine Genetics Laboratory, Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, China.
- MaiDa Gene Technology, Zhoushan, China.
| | - Natalija Popovic
- Montreal Children's Hospital and the Endocrine Genetics Laboratory, Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, China
| | - Ying Wang
- College of pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, Guangdong, China
| | - Chunbo Chen
- Department of Emergency, Department of Endorinology, Maoming People's Hospital, 101 Weimin Road, Maoming, Guangdong, China
- Department of Critical Care Medicine, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of South University of Science and Technology, Shenzhen, China
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Constantin Polychronakos
- Montreal Children's Hospital and the Endocrine Genetics Laboratory, Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, China
- MaiDa Gene Technology, Zhoushan, China
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20
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Sproule TJ, Philip VM, Chaudhry NA, Roopenian DC, Sundberg JP. Seven naturally variant loci serve as genetic modifiers of Lamc2jeb induced non-Herlitz junctional Epidermolysis Bullosa in mice. PLoS One 2023; 18:e0288263. [PMID: 37437067 DOI: 10.1371/journal.pone.0288263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/22/2023] [Indexed: 07/14/2023] Open
Abstract
Epidermolysis Bullosa (EB) is a group of rare genetic disorders that compromise the structural integrity of the skin such that blisters and subsequent erosions occur after minor trauma. While primary genetic risk of all subforms of EB adhere to Mendelian patterns of inheritance, their clinical presentations and severities can vary greatly, implying genetic modifiers. The Lamc2jeb mouse model of non-Herlitz junctional EB (JEB-nH) demonstrated that genetic modifiers can contribute substantially to the phenotypic variability of JEB and likely other forms of EB. The innocuous changes in an 'EB related gene', Col17a1, have shown it to be a dominant modifier of Lamc2jeb. This work identifies six additional Quantitative Trait Loci (QTL) that modify disease in Lamc2jeb/jeb mice. Three QTL include other known 'EB related genes', with the strongest modifier effect mapping to a region including the epidermal hemi-desmosomal structural gene dystonin (Dst-e/Bpag1-e). Three other QTL map to intervals devoid of known EB-associated genes. Of these, one contains the nuclear receptor coactivator Ppargc1a as its primary candidate and the others contain related genes Pparg and Igf1, suggesting modifier pathways. These results, demonstrating the potent disease modifying effects of normally innocuous genetic variants, greatly expand the landscape of genetic modifiers of EB and therapeutic approaches that may be applied.
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Affiliation(s)
- Thomas J Sproule
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Vivek M Philip
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Nabig A Chaudhry
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | | | - John P Sundberg
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- Department of Dermatology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
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21
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Rolland T, Cliquet F, Anney RJL, Moreau C, Traut N, Mathieu A, Huguet G, Duan J, Warrier V, Portalier S, Dry L, Leblond CS, Douard E, Amsellem F, Malesys S, Maruani A, Toro R, Børglum AD, Grove J, Baron-Cohen S, Packer A, Chung WK, Jacquemont S, Delorme R, Bourgeron T. Phenotypic effects of genetic variants associated with autism. Nat Med 2023; 29:1671-1680. [PMID: 37365347 PMCID: PMC10353945 DOI: 10.1038/s41591-023-02408-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/19/2023] [Indexed: 06/28/2023]
Abstract
While over 100 genes have been associated with autism, little is known about the prevalence of variants affecting them in individuals without a diagnosis of autism. Nor do we fully appreciate the phenotypic diversity beyond the formal autism diagnosis. Based on data from more than 13,000 individuals with autism and 210,000 undiagnosed individuals, we estimated the odds ratios for autism associated to rare loss-of-function (LoF) variants in 185 genes associated with autism, alongside 2,492 genes displaying intolerance to LoF variants. In contrast to autism-centric approaches, we investigated the correlates of these variants in individuals without a diagnosis of autism. We show that these variants are associated with a small but significant decrease in fluid intelligence, qualification level and income and an increase in metrics related to material deprivation. These effects were larger for autism-associated genes than in other LoF-intolerant genes. Using brain imaging data from 21,040 individuals from the UK Biobank, we could not detect significant differences in the overall brain anatomy between LoF carriers and non-carriers. Our results highlight the importance of studying the effect of the genetic variants beyond categorical diagnosis and the need for more research to understand the association between these variants and sociodemographic factors, to best support individuals carrying these variants.
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Affiliation(s)
- Thomas Rolland
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France.
| | - Freddy Cliquet
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Richard J L Anney
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Clara Moreau
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Nicolas Traut
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Center for Research and Interdisciplinarity (CRI), Université Paris Descartes, Paris, France
| | - Alexandre Mathieu
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Guillaume Huguet
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, Canada
| | - Jinjie Duan
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine and the iSEQ Centre, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Varun Warrier
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Swan Portalier
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Louise Dry
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Claire S Leblond
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Elise Douard
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, Canada
- Département de Pédiatrie, Université de Montréal, Montréal, Québec, Canada
| | - Frédérique Amsellem
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Department of Child and Adolescent Psychiatry, Robert Debré Hospital, APHP, Paris, France
| | - Simon Malesys
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
| | - Anna Maruani
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Department of Child and Adolescent Psychiatry, Robert Debré Hospital, APHP, Paris, France
| | - Roberto Toro
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Center for Research and Interdisciplinarity (CRI), Université Paris Descartes, Paris, France
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine and the iSEQ Centre, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine and the iSEQ Centre, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | | | - Wendy K Chung
- Simons Foundation, New York, NY, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Sébastien Jacquemont
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, Canada
- Département de Pédiatrie, Université de Montréal, Montréal, Québec, Canada
| | - Richard Delorme
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France
- Department of Child and Adolescent Psychiatry, Robert Debré Hospital, APHP, Paris, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, IUF, Université Paris Cité, Paris, France.
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22
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Zhu W, Lo CW. Insights into the genetic architecture of congenital heart disease from animal modeling. Zool Res 2023; 44:577-590. [PMID: 37147909 PMCID: PMC10236297 DOI: 10.24272/j.issn.2095-8137.2022.463] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/28/2023] [Indexed: 05/07/2023] Open
Abstract
Congenital heart disease (CHD) is observed in up to 1% of live births and is one of the leading causes of mortality from birth defects. While hundreds of genes have been implicated in the genetic etiology of CHD, their role in CHD pathogenesis is still poorly understood. This is largely a reflection of the sporadic nature of CHD, as well as its variable expressivity and incomplete penetrance. We reviewed the monogenic causes and evidence for oligogenic etiology of CHD, as well as the role of de novo mutations, common variants, and genetic modifiers. For further mechanistic insight, we leveraged single-cell data across species to investigate the cellular expression characteristics of genes implicated in CHD in developing human and mouse embryonic hearts. Understanding the genetic etiology of CHD may enable the application of precision medicine and prenatal diagnosis, thereby facilitating early intervention to improve outcomes for patients with CHD.
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Affiliation(s)
- Wenjuan Zhu
- Chinese University of Hong Kong, Hong Kong SAR, China
- Kunming Institute of Zoology-Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Hong Kong SAR, China
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201 USA. E-mail:
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23
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Ang RML, Chen SAA, Kern AF, Xie Y, Fraser HB. Widespread epistasis among beneficial genetic variants revealed by high-throughput genome editing. CELL GENOMICS 2023; 3:100260. [PMID: 37082144 PMCID: PMC10112194 DOI: 10.1016/j.xgen.2023.100260] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/27/2022] [Accepted: 01/06/2023] [Indexed: 04/22/2023]
Abstract
The phenotypic effect of any genetic variant can be altered by variation at other genomic loci. Known as epistasis, these genetic interactions shape the genotype-phenotype map of every species, yet their origins remain poorly understood. To investigate this, we employed high-throughput genome editing to measure the fitness effects of 1,826 naturally polymorphic variants in four strains of Saccharomyces cerevisiae. About 31% of variants affect fitness, of which 24% have strain-specific fitness effects indicative of epistasis. We found that beneficial variants are more likely to exhibit genetic interactions and that these interactions can be mediated by specific traits such as flocculation ability. This work suggests that adaptive evolution will often involve trade-offs where a variant is only beneficial in some genetic backgrounds, potentially explaining why many beneficial variants remain polymorphic. In sum, we provide a framework to understand the factors influencing epistasis with single-nucleotide resolution, revealing widespread epistasis among beneficial variants.
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Affiliation(s)
- Roy Moh Lik Ang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Shi-An A. Chen
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Alexander F. Kern
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Yihua Xie
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Hunter B. Fraser
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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24
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Ghosh AJ, Moll M, Hess J, Hobbs BD, Love A, Coyne L, Cho MH, Castaldi P, Middleton FA, Perl A, Silverman EK, Hersh CP, Glatt SJ. Clinical Features of Genetic Resilience in Chronic Obstructive Pulmonary Disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.06.23286843. [PMID: 36945553 PMCID: PMC10029040 DOI: 10.1101/2023.03.06.23286843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Introduction In the personalized risk quantification of chronic obstructive pulmonary disease (COPD), genome-wide association studies and polygenic risk scores (PRS) complement traditional risk factors, such as age and cigarette smoking. However, despite being at considerable levels of risk, some individuals do not develop COPD. Research on COPD resilience remains largely unexplored. Methods We applied the previously published COPD PRS to whole genome sequencing data from non-Hispanic white and African American individuals in the COPDGene study. We defined genetic resilience as individuals unaffected by COPD with a polygenic risk score above the 90 th percentile. We defined risk-matched case individuals as those with COPD (i.e., FEV 1 /FVC < 0.70) and a PRS above the 90 th percentile. We defined low risk individuals without COPD (i.e., FEV 1 /FVC > 0.70) as a polygenic risk score below the 10 th percentile. We compared genetically resilient individuals to risk-matched individuals with COPD and low risk individuals by demographics, lung function, respiratory symptoms, co-morbidities, and chest CT scan measurements. We also performed survival analyses, differential expression analysis, and matching for sensitivity analyses. Results We identified 211 resilient individuals without COPD, 605 genetic risk-matched individuals with COPD, and 527 low-risk individuals without COPD. Resilient individuals had higher FEV 1 % predicted and lower percent emphysema. In contrast, resilient individuals had higher airway wall thickness compared to low-risk unaffected individuals. While there was no difference in survival between low-risk and resilient individuals, resilient individuals had higher survival compared to risk matched cases. We also identified two genes that were differentially expressed between low-risk unaffected individuals and resilient individuals. Conclusion Genetically resilient individuals had a reduced burden of COPD disease-related measures compared to risk-matched cases but had subtly increased measures compared to low-risk unaffected individuals. Further genetic studies will be needed to illuminate the underlying pathobiology of our observations.
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Wagener R, Walter C, Surowy HM, Brandes D, Soura S, Alzoubi D, Yasin L, Fischer U, Dugas M, Borkhardt A, Brozou T. Noncancer-related Secondary Findings in a Cohort of 231 Children With Cancer and Their Parents. J Pediatr Hematol Oncol 2023; 45:e244-e248. [PMID: 35537032 DOI: 10.1097/mph.0000000000002475] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/30/2022] [Indexed: 11/26/2022]
Abstract
Application of next-generation sequencing may lead to the detection of secondary findings (SF) not related to the initially analyzed disease but to other severe medically actionable diseases. However, the analysis of SFs is not yet routinely performed. We mined whole-exome sequencing data of 231 pediatric cancer patients and their parents who had been treated in our center for the presence of SFs. By this approach, we identified in 6 children (2.6%) pathogenic germline variants in 5 of the noncancer-related genes on the American College of Medical Genetics and Genomics (ACMG) SF v3.0 list, of which the majority were related to cardiovascular diseases ( RYR2 , MYBPC3 , KCNQ1 ). Interestingly, only the patient harboring the KCNQ1 variant showed at the time point of the analysis signs of the related Long QT syndrome. Moreover, we report 3 variants of unknown significance which, although not classified as pathogenic, have been reported in the literature to occur in individuals with the respective disease. While the frequency of patients with SFs is low, the impact of such findings on the patients' life is enormous, with regard to the potential prevention of life-threatening diseases. Hence, we are convinced that such actionable SF should be routinely analyzed.
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Affiliation(s)
- Rabea Wagener
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Carolin Walter
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf
| | - Harald M Surowy
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf
| | - Danielle Brandes
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Stavrieta Soura
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Deya Alzoubi
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Layal Yasin
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster
- Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Triantafyllia Brozou
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
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26
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Long Y, Tang L, Zhou Y, Zhao S, Zhu H. Causal relationship between gut microbiota and cancers: a two-sample Mendelian randomisation study. BMC Med 2023; 21:66. [PMID: 36810112 PMCID: PMC9945666 DOI: 10.1186/s12916-023-02761-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 95.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Evidence from observational studies and clinical trials suggests that the gut microbiota is associated with cancer. However, the causal association between gut microbiota and cancer remains to be determined. METHODS We first identified two sets of gut microbiota based on phylum, class, order, family, and genus level information, and cancer data were obtained from the IEU Open GWAS project. We then performed two-sample Mendelian randomisation (MR) to determine whether the gut microbiota is causally associated with eight cancer types. Furthermore, we performed a bi-directional MR analysis to examine the direction of the causal relations. RESULTS We identified 11 causal relationships between genetic liability in the gut microbiome and cancer, including those involving the genus Bifidobacterium. We found 17 strong associations between genetic liability in the gut microbiome and cancer. Moreover, we found 24 associations between genetic liability in the gut microbiome and cancer using multiple datasets. CONCLUSIONS Our MR analysis revealed that the gut microbiota was causally associated with cancers and may be useful in providing new insights for further mechanistic and clinical studies of microbiota-mediated cancer.
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Affiliation(s)
- Yiwen Long
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Lanhua Tang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Yangying Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Shushan Zhao
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China. .,Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.
| | - Hong Zhu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.
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Reiner J, Rosenblum LS, Xin W, Zhou Z, Zhu H, Leach N. Incidental molecular diagnoses and heterozygous risk alleles in a carrier screening cohort. Genet Med 2023; 25:100317. [PMID: 36459106 DOI: 10.1016/j.gim.2022.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/30/2022] [Accepted: 10/02/2022] [Indexed: 12/05/2022] Open
Abstract
PURPOSE Expanded pan-ethnic carrier screening is an effective tool for the management of reproductive risk. However, growth in the number of conditions screened, in combination with increasingly more comprehensive test methodologies, can lead to the detection of genetic findings that may affect the health of the tested individual. The objective of this study was to investigate the frequency of pathogenic genotypes in a presumed healthy carrier screening cohort to facilitate broader discussions regarding disclosure of genetic information from carrier screening. METHODS A retrospective analysis of 73,755 targeted carrier screens was performed to identify individuals with pathogenic genotypes and heterozygous risk alleles. RESULTS In this study, we identified 79 individuals (0.11%) with pathogenic genotypes associated with moderate to profound autosomal recessive or X-linked conditions. In addition, 10 cases had chromosome X dosage abnormalities suggestive of a sex chromosome abnormality. Heterozygote risk alleles represented the majority of ancillary findings in this cohort, including 280 female carriers of FMR1 premutation alleles, 15 heterozygous females with pathogenic DMD variants, and 174 heterozygotes with pathogenic variants in genes that may confer increased risk for somatic malignancies in the heterozygous state. CONCLUSION These data suggest that nearly 1% of individuals undergoing carrier screening will have a finding that may require clinical evaluation or surveillance.
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28
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Einson J, Glinos D, Boerwinkle E, Castaldi P, Darbar D, de Andrade M, Ellinor P, Fornage M, Gabriel S, Germer S, Gibbs R, Hersh CP, Johnsen J, Kaplan R, Konkle BA, Kooperberg C, Nassir R, Loos RJF, Meyers DA, Mitchell BD, Psaty B, Vasan RS, Rich SS, Rienstra M, Rotter JI, Saferali A, Shoemaker MB, Silverman E, Smith AV, Mohammadi P, Castel SE, Iossifov I, Lappalainen T. Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526505. [PMID: 36778406 PMCID: PMC9915611 DOI: 10.1101/2023.01.31.526505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Exonic variants present some of the strongest links between genotype and phenotype. However, these variants can have significant inter-individual pathogenicity differences, known as variable penetrance. In this study, we propose a model where genetically controlled mRNA splicing modulates the pathogenicity of exonic variants. By first cataloging exonic inclusion from RNA-seq data in GTEx v8, we find that pathogenic alleles are depleted on highly included exons. Using a large-scale phased WGS data from the TOPMed consortium, we observe that this effect may be driven by common splice-regulatory genetic variants, and that natural selection acts on haplotype configurations that reduce the transcript inclusion of putatively pathogenic variants, especially when limiting to haploinsufficient genes. Finally, we test if this effect may be relevant for autism risk using families from the Simons Simplex Collection, but find that splicing of pathogenic alleles has a penetrance reducing effect here as well. Overall, our results indicate that common splice-regulatory variants may play a role in reducing the damaging effects of rare exonic variants.
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Affiliation(s)
- Jonah Einson
- Department of Biomedical Informatics, Columbia University
- New York Genome Center
| | | | | | | | - Dawood Darbar
- Department of Cardiology, University of Illinois at Chicago
| | | | - Patrick Ellinor
- Corrigan Minehan Heart Center, Massachusetts General Hospital
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health at Houston
| | | | | | - Richard Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine Human Genome Sequencing Center
| | - Craig P Hersh
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital
| | - Jill Johnsen
- Department of Hematology, University of Washington
| | - Robert Kaplan
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine
| | | | | | - Rami Nassir
- Department of Pathology, School of Medicine, Umm Al-Qura University
| | - Ruth J F Loos
- Environmental Medicine & Public Health, Icahn School of Medicine at Mount Sinai
| | | | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center
| | - Bruce Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington
| | | | | | | | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
| | - Aabida Saferali
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital
| | | | - Edwin Silverman
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham & Women's Hospital
| | | | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute
| | | | | | - Tuuli Lappalainen
- Department of Systems Biology, Columbia University
- Department of Gene Technology, KTH Royal Institute of Technology
- New York Genome Center
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29
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Ren M, Yang Y, Heng KHY, Ng LY, Chong CYY, Ng YT, Gorur-Shandilya S, Lee RMQ, Lim KL, Zhang J, Koh TW. MED13 and glycolysis are conserved modifiers of α-synuclein-associated neurodegeneration. Cell Rep 2022; 41:111852. [PMID: 36543134 DOI: 10.1016/j.celrep.2022.111852] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 10/04/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
α-Synuclein (α-syn) is important in synucleinopathies such as Parkinson's disease (PD). While genome-wide association studies (GWASs) of synucleinopathies have identified many risk loci, the underlying genes have not been shown for most loci. Using Drosophila, we screened 3,471 mutant chromosomes for genetic modifiers of α-synuclein and identified 12 genes. Eleven modifiers have human orthologs associated with diseases, including MED13 and CDC27, which lie within PD GWAS loci. Drosophila Skd/Med13 and glycolytic enzymes are co-upregulated by α-syn-associated neurodegeneration. While elevated α-syn compromises mitochondrial function, co-expressing skd/Med13 RNAi and α-syn synergistically increase the ratio of oxidized-to-reduced glutathione. The resulting neurodegeneration can be suppressed by overexpressing a glycolytic enzyme or treatment with deferoxamine, suggesting that compensatory glycolysis is neuroprotective. In addition, the functional relationship between α-synuclein, MED13, and glycolytic enzymes is conserved between flies and mice. We propose that hypoxia-inducible factor and MED13 are part of a druggable pathway for PD.
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Affiliation(s)
- Mengda Ren
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308207, Singapore; National Neuroscience Institute, Singapore 308433, Singapore
| | - Ying Yang
- Department of Pathology, Zhejiang University First Affiliated Hospital and School of Medicine, Hangzhou, Zhejiang 310002, China
| | | | - Lu Yi Ng
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | | | - Yan Ting Ng
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | | | - Rachel Min Qi Lee
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Kah Leong Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308207, Singapore; National Neuroscience Institute, Singapore 308433, Singapore
| | - Jing Zhang
- Department of Pathology, Zhejiang University First Affiliated Hospital and School of Medicine, Hangzhou, Zhejiang 310002, China; China National Health and Disease Human Brain Tissue Resource Center, Hangzhou, Zhejiang 310002, China
| | - Tong-Wey Koh
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore.
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30
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Ganesh S, Vemula A, Bhattacharjee S, Mathew K, Ithal D, Navin K, Nadella RK, Viswanath B, Sullivan PF, Jain S, Purushottam M. Whole exome sequencing in dense families suggests genetic pleiotropy amongst Mendelian and complex neuropsychiatric syndromes. Sci Rep 2022; 12:21128. [PMID: 36476812 PMCID: PMC9729597 DOI: 10.1038/s41598-022-25664-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
Whole Exome Sequencing (WES) studies provide important insights into the genetic architecture of serious mental illness (SMI). Genes that are central to the shared biology of SMIs may be identified by WES in families with multiple affected individuals with diverse SMI (F-SMI). We performed WES in 220 individuals from 75 F-SMI families and 60 unrelated controls. Within pedigree prioritization employed criteria of rarity, functional consequence, and sharing by ≥ 3 affected members. Across the sample, gene and gene-set-wide case-control association analysis was performed with Sequence Kernel Association Test (SKAT). In 14/16 families with ≥ 3 sequenced affected individuals, we identified a total of 78 rare predicted deleterious variants in 78 unique genes shared by ≥ 3 members with SMI. Twenty (25%) genes were implicated in monogenic CNS syndromes in OMIM (OMIM-CNS), a fraction that is a significant overrepresentation (Fisher's Exact test OR = 2.47, p = 0.001). In gene-set SKAT, statistically significant association was noted for OMIM-CNS gene-set (SKAT-p = 0.005) but not the synaptic gene-set (SKAT-p = 0.17). In this WES study in F-SMI, we identify private, rare, protein altering variants in genes previously implicated in Mendelian neuropsychiatric syndromes; suggesting pleiotropic influences in neurodevelopment between complex and Mendelian syndromes.
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Affiliation(s)
- Suhas Ganesh
- Central Institute of Psychiatry, Kanke, Ranchi, India
- Schizophrenia Neuropharmacology Research Group, Department of Psychiatry, Yale University School of Medicine, New Haven, USA
| | - Alekhya Vemula
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, India
| | | | - Kezia Mathew
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, India
| | - Dhruva Ithal
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, India
| | - Karthick Navin
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, India
| | - Ravi Kumar Nadella
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, India
- Department of Psychiatry, Varma Hospital, Bhimavaram, India
| | - Biju Viswanath
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, India
| | - Patrick F Sullivan
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics at Karolinska Institutet, Stockholm, Sweden
| | - Sanjeev Jain
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, India
| | - Meera Purushottam
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, India.
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Taylor HA, Finkel T, Gao Y, Ballinger SW, Campo R, Chen R, Chen SH, Davidson K, Iruela-Arispe ML, Jaquish C, LeBrasseur NK, Odden MC, Papanicolaou GJ, Picard M, Srinivas P, Tjurmina O, Wolz M, Galis ZS. Scientific opportunities in resilience research for cardiovascular health and wellness. Report from a National Heart, Lung, and Blood Institute workshop. FASEB J 2022; 36:e22639. [PMID: 36322029 PMCID: PMC9703084 DOI: 10.1096/fj.202201407r] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 11/07/2022]
Abstract
Exposure of biological systems to acute or chronic insults triggers a host of molecular and physiological responses to either tolerate, adapt, or fully restore homeostasis; these responses constitute the hallmarks of resilience. Given the many facets, dimensions, and discipline-specific focus, gaining a shared understanding of "resilience" has been identified as a priority for supporting advances in cardiovascular health. This report is based on the working definition: "Resilience is the ability of living systems to successfully maintain or return to homeostasis in response to physical, molecular, individual, social, societal, or environmental stressors or challenges," developed after considering many factors contributing to cardiovascular resilience through deliberations of multidisciplinary experts convened by the National Heart, Lung, and Blood Institute during a workshop entitled: "Enhancing Resilience for Cardiovascular Health and Wellness." Some of the main emerging themes that support the possibility of enhancing resilience for cardiovascular health include optimal energy management and substrate diversity, a robust immune system that safeguards tissue homeostasis, and social and community support. The report also highlights existing research challenges, along with immediate and long-term opportunities for resilience research. Certain immediate opportunities identified are based on leveraging existing high-dimensional data from longitudinal clinical studies to identify vascular resilience measures, create a 'resilience index,' and adopt a life-course approach. Long-term opportunities include developing quantitative cell/organ/system/community models to identify resilience factors and mechanisms at these various levels, designing experimental and clinical interventions that specifically assess resilience, adopting global sharing of resilience-related data, and cross-domain training of next-generation researchers in this field.
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Affiliation(s)
- Herman A. Taylor
- Cardiovascular Research Institute Morehouse School of Medicine, Atlanta, Georgia, USA
- Morehouse-Emory Cardiovascular Center for Health Equity, Atlanta, Georgia, USA
- Harvard Chan School of Public Health, Atlanta, Georgia, USA
- Emory School of Medicine, Atlanta, Georgia, USA
| | - Toren Finkel
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yunling Gao
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Scott W. Ballinger
- University of Alabama Heersink School of Medicine, Birmingham, Alabama, USA
| | - Rebecca Campo
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rong Chen
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Shu Hui Chen
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Karina Davidson
- Feinstein Institutes for Medical Research, Northwell Health, New York, New York, USA
| | | | - Cashell Jaquish
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | | | - George J. Papanicolaou
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Martin Picard
- Columbia University Irving Medical Center, New York, New York, USA
- New York State Psychiatric Institute, New York, New York, USA
| | - Pothur Srinivas
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Olga Tjurmina
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Wolz
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Zorina S. Galis
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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Tomas-Roca L, Qiu Z, Fransén E, Gokhale R, Bulovaite E, Price DJ, Komiyama NH, Grant SGN. Developmental disruption and restoration of brain synaptome architecture in the murine Pax6 neurodevelopmental disease model. Nat Commun 2022; 13:6836. [PMID: 36369219 PMCID: PMC9652404 DOI: 10.1038/s41467-022-34131-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/14/2022] [Indexed: 11/13/2022] Open
Abstract
Neurodevelopmental disorders of genetic origin delay the acquisition of normal abilities and cause disabling phenotypes. Nevertheless, spontaneous attenuation and even complete amelioration of symptoms in early childhood and adolescence can occur in many disorders, suggesting that brain circuits possess an intrinsic capacity to overcome the deficits arising from some germline mutations. We examined the molecular composition of almost a trillion excitatory synapses on a brain-wide scale between birth and adulthood in mice carrying a mutation in the homeobox transcription factor Pax6, a neurodevelopmental disorder model. Pax6 haploinsufficiency had no impact on total synapse number at any age. By contrast, the molecular composition of excitatory synapses, the postnatal expansion of synapse diversity and the acquisition of normal synaptome architecture were delayed in all brain regions, interfering with networks and electrophysiological simulations of cognitive functions. Specific excitatory synapse types and subtypes were affected in two key developmental age-windows. These phenotypes were reversed within 2-3 weeks of onset, restoring synapse diversity and synaptome architecture to the normal developmental trajectory. Synapse subtypes with rapid protein turnover mediated the synaptome remodeling. This brain-wide capacity for remodeling of synapse molecular composition to recover and maintain the developmental trajectory of synaptome architecture may help confer resilience to neurodevelopmental genetic disorders.
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Affiliation(s)
- Laura Tomas-Roca
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Zhen Qiu
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Erik Fransén
- Science for Life Laboratory, KTH Royal Institute of Technology, SE-171 65, Solna, Sweden
| | - Ragini Gokhale
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Edita Bulovaite
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - David J Price
- Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Noboru H Komiyama
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
- Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Seth G N Grant
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK.
- Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK.
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Pena SDJ, Tarazona-Santos E. Clinical genomics and precision medicine. Genet Mol Biol 2022; 45:e20220150. [PMID: 36218382 PMCID: PMC9555143 DOI: 10.1590/1678-4685-gmb-2022-0150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/12/2022] [Indexed: 11/04/2022] Open
Abstract
Precision Medicine emerges from the genomic paradigm of health and disease. For precise molecular diagnoses of genetic diseases, we must analyze the Whole Exome (WES) or the Whole Genome (WGS). By not needing exon capture, WGS is more powerful to detect single nucleotide variants and copy number variants. In healthy individuals, we can observe monogenic highly penetrant variants, which may be causally responsible for diseases, and also susceptibility variants, associated with common polygenic diseases. But there is the major problem of penetrance. Thus, there is the question of whether it is worthwhile to perform WGS in all healthy individuals as a step towards Precision Medicine. The genetic architecture of disease is consistent with the fact that they are all polygenic. Moreover, ancestry adds another layer of complexity. We are now capable of obtaining Polygenic Risk Scores for all complex diseases using only data from new generation sequencing. Yet, review of available evidence does not at present favor the idea that WGS analyses are sufficiently developed to allow reliable predictions of the risk components for monogenic and polygenic hereditary diseases in healthy individuals. Probably, it is still better for WGS to remain reserved for the diagnosis of pathogenic variants of Mendelian diseases.
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Affiliation(s)
- Sérgio D. J. Pena
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Bioquímica e Imunologia, Belo Horizonte, MG, Brazil. ,Núcleo de Genética Médica, Belo Horizonte, MG, Brazil
| | - Eduardo Tarazona-Santos
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Belo Horizonte, MG, Brazil
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Bailon-Zambrano R, Sucharov J, Mumme-Monheit A, Murry M, Stenzel A, Pulvino AT, Mitchell JM, Colborn KL, Nichols JT. Variable paralog expression underlies phenotype variation. eLife 2022; 11:e79247. [PMID: 36134886 PMCID: PMC9555865 DOI: 10.7554/elife.79247] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Human faces are variable; we look different from one another. Craniofacial disorders further increase facial variation. To understand craniofacial variation and how it can be buffered, we analyzed the zebrafish mef2ca mutant. When this transcription factor encoding gene is mutated, zebrafish develop dramatically variable craniofacial phenotypes. Years of selective breeding for low and high penetrance of mutant phenotypes produced strains that are either resilient or sensitive to the mef2ca mutation. Here, we compared gene expression between these strains, which revealed that selective breeding enriched for high and low mef2ca paralog expression in the low- and high-penetrance strains, respectively. We found that mef2ca paralog expression is variable in unselected wild-type zebrafish, motivating the hypothesis that heritable variation in paralog expression underlies mutant phenotype severity and variation. In support, mutagenizing the mef2ca paralogs, mef2aa, mef2b, mef2cb, and mef2d demonstrated modular buffering by paralogs. Specifically, some paralogs buffer severity while others buffer variability. We present a novel, mechanistic model for phenotypic variation where variable, vestigial paralog expression buffers development. These studies are a major step forward in understanding the mechanisms of facial variation, including how some genetically resilient individuals can overcome a deleterious mutation.
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Affiliation(s)
- Raisa Bailon-Zambrano
- Department of Craniofacial Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Juliana Sucharov
- Department of Craniofacial Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Abigail Mumme-Monheit
- Department of Craniofacial Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Matthew Murry
- Department of Craniofacial Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Amanda Stenzel
- Department of Craniofacial Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Anthony T Pulvino
- Department of Craniofacial Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Jennyfer M Mitchell
- Department of Craniofacial Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Kathryn L Colborn
- Department of Surgery, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - James T Nichols
- Department of Craniofacial Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
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Loss-of-function mutation survey revealed that genes with background-dependent fitness are rare and functionally related in yeast. Proc Natl Acad Sci U S A 2022; 119:e2204206119. [PMID: 36067306 PMCID: PMC9478683 DOI: 10.1073/pnas.2204206119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In different individuals, the same mutation can lead to different phenotypes due to genetic background effects. This is commonly observed in various systems, including many human diseases. While isolated examples of such background effects have been observed, a systematic view across a large number of individuals is still lacking. Here, we surveyed genetic background effects associated with gene loss-of-function mutations across a population of natural isolates of the yeast Saccharomyces cerevisiae. We found that ∼15% of genes can display a background-dependent fitness change. Genes related to mitochondrial functions are significantly overrepresented, and showed reversed patterns of fitness gain or loss with genes involved in transcription and chromatin remodeling as well as in nuclear–cytoplasmic transport, suggesting a potential functional rewiring. In natural populations, the same mutation can lead to different phenotypic outcomes due to the genetic variation that exists among individuals. Such genetic background effects are commonly observed, including in the context of many human diseases. However, systematic characterization of these effects at the species level is still lacking to date. Here, we sought to comprehensively survey background-dependent traits associated with gene loss-of-function (LoF) mutations in 39 natural isolates of Saccharomyces cerevisiae using a transposon saturation strategy. By analyzing the modeled fitness variability of a total of 4,469 genes, we found that 15% of them, when impacted by a LoF mutation, exhibited a significant gain- or loss-of-fitness phenotype in certain natural isolates compared with the reference strain S288C. Out of these 632 genes with predicted background-dependent fitness effects, around 2/3 impact multiple backgrounds with a gradient of predicted fitness change while 1/3 are specific to a single genetic background. Genes related to mitochondrial function are significantly overrepresented in the set of genes showing a continuous variation and display a potential functional rewiring with other genes involved in transcription and chromatin remodeling as well as in nuclear–cytoplasmic transport. Such rewiring effects are likely modulated by both the genetic background and the environment. While background-specific cases are rare and span diverse cellular processes, they can be functionally related at the individual level. All genes with background-dependent fitness effects tend to have an intermediate connectivity in the global genetic interaction network and have shown relaxed selection pressure at the population level, highlighting their potential evolutionary characteristics.
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Kingsmore SF, Smith LD, Kunard CM, Bainbridge M, Batalov S, Benson W, Blincow E, Caylor S, Chambers C, Del Angel G, Dimmock DP, Ding Y, Ellsworth K, Feigenbaum A, Frise E, Green RC, Guidugli L, Hall KP, Hansen C, Hobbs CA, Kahn SD, Kiel M, Van Der Kraan L, Krilow C, Kwon YH, Madhavrao L, Le J, Lefebvre S, Mardach R, Mowrey WR, Oh D, Owen MJ, Powley G, Scharer G, Shelnutt S, Tokita M, Mehtalia SS, Oriol A, Papadopoulos S, Perry J, Rosales E, Sanford E, Schwartz S, Tran D, Reese MG, Wright M, Veeraraghavan N, Wigby K, Willis MJ, Wolen AR, Defay T. A genome sequencing system for universal newborn screening, diagnosis, and precision medicine for severe genetic diseases. Am J Hum Genet 2022; 109:1605-1619. [PMID: 36007526 PMCID: PMC9502059 DOI: 10.1016/j.ajhg.2022.08.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/01/2022] [Indexed: 12/31/2022] Open
Abstract
Newborn screening (NBS) dramatically improves outcomes in severe childhood disorders by treatment before symptom onset. In many genetic diseases, however, outcomes remain poor because NBS has lagged behind drug development. Rapid whole-genome sequencing (rWGS) is attractive for comprehensive NBS because it concomitantly examines almost all genetic diseases and is gaining acceptance for genetic disease diagnosis in ill newborns. We describe prototypic methods for scalable, parentally consented, feedback-informed NBS and diagnosis of genetic diseases by rWGS and virtual, acute management guidance (NBS-rWGS). Using established criteria and the Delphi method, we reviewed 457 genetic diseases for NBS-rWGS, retaining 388 (85%) with effective treatments. Simulated NBS-rWGS in 454,707 UK Biobank subjects with 29,865 pathogenic or likely pathogenic variants associated with 388 disorders had a true negative rate (specificity) of 99.7% following root cause analysis. In 2,208 critically ill children with suspected genetic disorders and 2,168 of their parents, simulated NBS-rWGS for 388 disorders identified 104 (87%) of 119 diagnoses previously made by rWGS and 15 findings not previously reported (NBS-rWGS negative predictive value 99.6%, true positive rate [sensitivity] 88.8%). Retrospective NBS-rWGS diagnosed 15 children with disorders that had been undetected by conventional NBS. In 43 of the 104 children, had NBS-rWGS-based interventions been started on day of life 5, the Delphi consensus was that symptoms could have been avoided completely in seven critically ill children, mostly in 21, and partially in 13. We invite groups worldwide to refine these NBS-rWGS conditions and join us to prospectively examine clinical utility and cost effectiveness.
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Affiliation(s)
- Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA; Keck Graduate Institute, Claremont, CA 91711, USA.
| | - Laurie D Smith
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Matthew Bainbridge
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Wendy Benson
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Eric Blincow
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Sara Caylor
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Christina Chambers
- Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Katarzyna Ellsworth
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Annette Feigenbaum
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA; Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Erwin Frise
- Fabric Genomics, Inc., Oakland, CA 94612, USA
| | - Robert C Green
- Mass General Brigham, Broad Institute, Ariadne Labs and Harvard Medical School, Boston, MA 02115, USA
| | - Lucia Guidugli
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Christian Hansen
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Charlotte A Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Mark Kiel
- Genomenon Inc., Ann Arbor, MI 48108, USA
| | - Lucita Van Der Kraan
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Yong H Kwon
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Lakshminarasimha Madhavrao
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Jennie Le
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Rebecca Mardach
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA; Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - Danny Oh
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Mallory J Owen
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Gunter Scharer
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Mari Tokita
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Albert Oriol
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - James Perry
- Rady Children's Hospital, San Diego, CA 92123, USA; Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Edwin Rosales
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Erica Sanford
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Duke Tran
- Illumina, Inc., San Diego, CA 92122, USA
| | | | - Meredith Wright
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Narayanan Veeraraghavan
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Kristen Wigby
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA; Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Mary J Willis
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Thomas Defay
- Alexion, Astra Zeneca Rare Disease, Boston, MA 02210, USA
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Liu H, Dehestani M, Blauwendraat C, Makarious MB, Leonard H, Kim JJ, Schulte C, Noyce A, Jacobs BM, Foote I, Sharma M, Nalls M, Singleton A, Gasser T, Bandres‐Ciga S. Polygenic Resilience Modulates the Penetrance of Parkinson Disease Genetic Risk Factors. Ann Neurol 2022; 92:270-278. [PMID: 35599344 PMCID: PMC9329258 DOI: 10.1002/ana.26416] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 11/10/2022]
Abstract
OBJECTIVE The aim of the current study is to understand why some individuals avoid developing Parkinson disease (PD) despite being at relatively high genetic risk, using the largest datasets of individual-level genetic data available. METHODS We calculated polygenic risk score to identify controls and matched PD cases with the highest burden of genetic risk for PD in the discovery cohort (International Parkinson's Disease Genomics Consortium, 7,204 PD cases and 9,412 controls) and validation cohorts (Comprehensive Unbiased Risk Factor Assessment for Genetics and Environment in Parkinson's Disease, 8,968 cases and 7,598 controls; UK Biobank, 2,639 PD cases and 14,301 controls; Accelerating Medicines Partnership-Parkinson's Disease Initiative, 2,248 cases and 2,817 controls). A genome-wide association study meta-analysis was performed on these individuals to understand genetic variation associated with resistance to disease. We further constructed a polygenic resilience score, and performed multimarker analysis of genomic annotation (MAGMA) gene-based analyses and functional enrichment analyses. RESULTS A higher polygenic resilience score was associated with a lower risk for PD (β = -0.054, standard error [SE] = 0.022, p = 0.013). Although no single locus reached genome-wide significance, MAGMA gene-based analyses nominated TBCA as a putative gene. Furthermore, we estimated the narrow-sense heritability associated with resilience to PD (h2 = 0.081, SE = 0.035, p = 0.0003). Subsequent functional enrichment analysis highlighted histone methylation as a potential pathway harboring resilience alleles that could mitigate the effects of PD risk loci. INTERPRETATION The present study represents a novel and comprehensive assessment of heritable genetic variation contributing to PD resistance. We show that a genetic resilience score can modify the penetrance of PD genetic risk factors and therefore protect individuals carrying a high-risk genetic burden from developing PD. ANN NEUROL 2022;92:270-278.
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Affiliation(s)
- Hui Liu
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain ResearchUniversity of Tübingen and German Center of Neurodegenerative DiseasesTübingenGermany
| | - Mohammad Dehestani
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain ResearchUniversity of Tübingen and German Center of Neurodegenerative DiseasesTübingenGermany
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, Molecular Genetics Section, National Institute on AgingNational Institutes of HealthBethesdaMDUSA
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMDUSA
| | - Mary B. Makarious
- Laboratory of Neurogenetics, Molecular Genetics Section, National Institute on AgingNational Institutes of HealthBethesdaMDUSA
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMDUSA
- Data Tecnica InternationalGlen EchoMDUSA
- Department of Clinical and Movement NeurosciencesUCL Queen Square Institute of NeurologyLondonUK
| | - Hampton Leonard
- Data Tecnica InternationalGlen EchoMDUSA
- Department of Clinical and Movement NeurosciencesUCL Queen Square Institute of NeurologyLondonUK
| | - Jonggeol J. Kim
- Laboratory of Neurogenetics, Molecular Genetics Section, National Institute on AgingNational Institutes of HealthBethesdaMDUSA
- Preventive Neurology Unit, Wolfson Institute of Population HealthQueen Mary University of LondonLondonUK
| | - Claudia Schulte
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain ResearchUniversity of Tübingen and German Center of Neurodegenerative DiseasesTübingenGermany
| | - Alastair Noyce
- Preventive Neurology Unit, Wolfson Institute of Population HealthQueen Mary University of LondonLondonUK
| | - Benjamin M. Jacobs
- Preventive Neurology Unit, Wolfson Institute of Population HealthQueen Mary University of LondonLondonUK
| | - Isabelle Foote
- Preventive Neurology Unit, Wolfson Institute of Population HealthQueen Mary University of LondonLondonUK
| | - Manu Sharma
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain ResearchUniversity of Tübingen and German Center of Neurodegenerative DiseasesTübingenGermany
- Center for Genetic Epidemiology, Institute for Clinical Epidemiology and Functional BiometryUniversity of TübingenTübingenGermany
| | - Mike Nalls
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMDUSA
- Data Tecnica InternationalGlen EchoMDUSA
| | - Andrew Singleton
- Laboratory of Neurogenetics, Molecular Genetics Section, National Institute on AgingNational Institutes of HealthBethesdaMDUSA
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMDUSA
| | - Thomas Gasser
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain ResearchUniversity of Tübingen and German Center of Neurodegenerative DiseasesTübingenGermany
| | - Sara Bandres‐Ciga
- Laboratory of Neurogenetics, Molecular Genetics Section, National Institute on AgingNational Institutes of HealthBethesdaMDUSA
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMDUSA
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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: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [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)
| | - 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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Blair DR, Hoffmann TJ, Shieh JT. Common genetic variation associated with Mendelian disease severity revealed through cryptic phenotype analysis. Nat Commun 2022; 13:3675. [PMID: 35760791 PMCID: PMC9237040 DOI: 10.1038/s41467-022-31030-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 05/30/2022] [Indexed: 11/09/2022] Open
Abstract
Clinical heterogeneity is common in Mendelian disease, but small sample sizes make it difficult to identify specific contributing factors. However, if a disease represents the severely affected extreme of a spectrum of phenotypic variation, then modifier effects may be apparent within a larger subset of the population. Analyses that take advantage of this full spectrum could have substantially increased power. To test this, we developed cryptic phenotype analysis, a model-based approach that infers quantitative traits that capture disease-related phenotypic variability using qualitative symptom data. By applying this approach to 50 Mendelian diseases in two cohorts, we identify traits that reliably quantify disease severity. We then conduct genome-wide association analyses for five of the inferred cryptic phenotypes, uncovering common variation that is predictive of Mendelian disease-related diagnoses and outcomes. Overall, this study highlights the utility of computationally-derived phenotypes and biobank-scale cohorts for investigating the complex genetic architecture of Mendelian diseases.
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Affiliation(s)
- David R Blair
- Division of Medical Genetics, Department of Pediatrics, Benioff Children's Hospital, San Francisco, CA, USA.
| | - Thomas J Hoffmann
- Institute for Human Genetics, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Joseph T Shieh
- Division of Medical Genetics, Department of Pediatrics, Benioff Children's Hospital, San Francisco, CA, USA.
- Institute for Human Genetics, San Francisco, CA, USA.
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Inherited variants in CHD3 show variable expressivity in Snijders Blok-Campeau syndrome. Genet Med 2022; 24:1283-1296. [PMID: 35346573 DOI: 10.1016/j.gim.2022.02.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/22/2022] [Accepted: 02/22/2022] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Common diagnostic next-generation sequencing strategies are not optimized to identify inherited variants in genes associated with dominant neurodevelopmental disorders as causal when the transmitting parent is clinically unaffected, leaving a significant number of cases with neurodevelopmental disorders undiagnosed. METHODS We characterized 21 families with inherited heterozygous missense or protein-truncating variants in CHD3, a gene in which de novo variants cause Snijders Blok-Campeau syndrome. RESULTS Computational facial and Human Phenotype Ontology-based comparisons showed that the phenotype of probands with inherited CHD3 variants overlaps with the phenotype previously associated with de novo CHD3 variants, whereas heterozygote parents are mildly or not affected, suggesting variable expressivity. In addition, similarly reduced expression levels of CHD3 protein in cells of an affected proband and of healthy family members with a CHD3 protein-truncating variant suggested that compensation of expression from the wild-type allele is unlikely to be an underlying mechanism. Notably, most inherited CHD3 variants were maternally transmitted. CONCLUSION Our results point to a significant role of inherited variation in Snijders Blok-Campeau syndrome, a finding that is critical for correct variant interpretation and genetic counseling and warrants further investigation toward understanding the broader contributions of such variation to the landscape of human disease.
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Brennand KJ. Using Stem Cell Models to Explore the Genetics Underlying Psychiatric Disorders: Linking Risk Variants, Genes, and Biology in Brain Disease. Am J Psychiatry 2022; 179:322-328. [PMID: 35491564 DOI: 10.1176/appi.ajp.20220235] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There is an urgent and unmet need to advance our ability to translate genetic studies of psychiatric disorders into clinically actionable information, which could transform diagnostics and even one day lead to novel (and potentially presymptomatic) therapeutic interventions. Today, although there are hundreds of significant loci associated with psychiatric disorders, resolving the target gene(s) and pathway(s) impacted by each is a major challenge. Integrating human induced pluripotent stem cell-based approaches with CRISPR-mediated genomic engineering strategies makes it possible to study the impact of patient-specific variants within the cell types of the brain. As the scale and scope of functional genomic studies expands, so does our ability to resolve the complex interplay of the many risk variants linked to psychiatric disorders. In this review, the author discusses some of the technological advances that make it possible to ask exciting questions that are fundamental to our understanding of psychiatric disorders. How do distinct risk variants converge and interact with each other (and the environment) across the diverse cell types that comprise the human brain? Can clinical trajectories and/or therapeutic response be predicted from genetic profiles? Just as critically, by spreading the message that genetic risk for psychiatric disorders is biological and fundamentally no different than for other human conditions, we can dispel the stigma associated with mental illness.
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Affiliation(s)
- Kristen J Brennand
- Department of Psychiatry, Department of Genetics, Wu Tsai Institute at Yale, and Yale Stem Cell Center, Yale University School of Medicine, New Haven, Conn
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Auwerx C, Lepamets M, Sadler MC, Patxot M, Stojanov M, Baud D, Mägi R, Porcu E, Reymond A, Kutalik Z. The individual and global impact of copy-number variants on complex human traits. Am J Hum Genet 2022; 109:647-668. [PMID: 35240056 PMCID: PMC9069145 DOI: 10.1016/j.ajhg.2022.02.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/09/2022] [Indexed: 12/25/2022] Open
Abstract
The impact of copy-number variations (CNVs) on complex human traits remains understudied. We called CNVs in 331,522 UK Biobank participants and performed genome-wide association studies (GWASs) between the copy number of CNV-proxy probes and 57 continuous traits, revealing 131 signals spanning 47 phenotypes. Our analysis recapitulated well-known associations (e.g., 1q21 and height), revealed the pleiotropy of recurrent CNVs (e.g., 26 and 16 traits for 16p11.2-BP4-BP5 and 22q11.21, respectively), and suggested gene functionalities (e.g., MARF1 in female reproduction). Forty-eight CNV signals (38%) overlapped with single-nucleotide polymorphism (SNP)-GWASs signals for the same trait. For instance, deletion of PDZK1, which encodes a urate transporter scaffold protein, decreased serum urate levels, while deletion of RHD, which encodes the Rhesus blood group D antigen, associated with hematological traits. Other signals overlapped Mendelian disorder regions, suggesting variable expressivity and broad impact of these loci, as illustrated by signals mapping to Rotor syndrome (SLCO1B1/3), renal cysts and diabetes syndrome (HNF1B), or Charcot-Marie-Tooth (PMP22) loci. Total CNV burden negatively impacted 35 traits, leading to increased adiposity, liver/kidney damage, and decreased intelligence and physical capacity. Thirty traits remained burden associated after correcting for CNV-GWAS signals, pointing to a polygenic CNV architecture. The burden negatively correlated with socio-economic indicators, parental lifespan, and age (survivorship proxy), suggesting a contribution to decreased longevity. Together, our results showcase how studying CNVs can expand biological insights, emphasizing the critical role of this mutational class in shaping human traits and arguing in favor of a continuum between Mendelian and complex diseases.
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Affiliation(s)
- Chiara Auwerx
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland; Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; University Center for Primary Care and Public Health, Lausanne 1010, Switzerland
| | - Maarja Lepamets
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia; Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Marie C Sadler
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; University Center for Primary Care and Public Health, Lausanne 1010, Switzerland
| | - Marion Patxot
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Miloš Stojanov
- Materno-fetal and Obstetrics Research Unit, Department Woman-Mother-Child, CHUV, Lausanne 1011, Switzerland
| | - David Baud
- Materno-fetal and Obstetrics Research Unit, Department Woman-Mother-Child, CHUV, Lausanne 1011, Switzerland
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Eleonora Porcu
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; University Center for Primary Care and Public Health, Lausanne 1010, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland.
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; University Center for Primary Care and Public Health, Lausanne 1010, Switzerland.
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Complex Changes in the Efficiency of the Expression of Many Genes in Monogenic Diseases, Mucopolysaccharidoses, May Arise from Significant Disturbances in the Levels of Factors Involved in the Gene Expression Regulation Processes. Genes (Basel) 2022; 13:genes13040593. [PMID: 35456399 PMCID: PMC9029754 DOI: 10.3390/genes13040593] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 01/27/2023] Open
Abstract
Monogenic diseases are primarily caused by mutations in a single gene; thus, they are commonly recognized as genetic disorders with the simplest mechanisms. However, recent studies have indicated that the molecular mechanisms of monogenic diseases can be unexpectedly complicated, and their understanding requires complex studies at the molecular level. Previously, we have demonstrated that in mucopolysaccharidoses (MPS), a group of monogenic lysosomal storage diseases, several hundreds of genes reveal significant changes in the expression of various genes. Although the secondary effects of the primary biochemical defect and the inefficient degradation of glycosaminoglycans (GAGs) might be considered, the scale of the changes in the expression of a large fraction of genes cannot be explained by a block in one biochemical pathway. Here, we demonstrate that in cellular models of 11 types of MPS, the expression of genes coding for proteins involved in the regulation of the expression of many other genes at various stages (such as signal transduction, transcription, splicing, RNA degradation, translation, and others) is significantly disturbed relative to the control cells. This conclusion was based on transcriptomic studies, supported by biochemical analyses of levels of selected proteins encoded by genes revealing an especially high level of dysregulation in MPS (EXOSC9, SRSF10, RPL23, and NOTCH3 proteins were investigated). Interestingly, the reduction in GAGs levels, through the inhibition of their synthesis normalized the amounts of EXOSC9, RPL23, and NOTCH3 in some (but not all) MPS types, while the levels of SRSF10 could not be corrected in this way. These results indicate that different mechanisms are involved in the dysregulation of the expression of various genes in MPS, pointing to a potential explanation for the inability of some therapies (such as enzyme replacement therapy or substrate reduction therapy) to fully correct the physiology of MPS patients. We suggest that the disturbed expression of some genes, which appears as secondary or tertiary effects of GAG storage, might not be reversible, even after a reduction in the amounts of the storage material.
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Whole-genome sequencing of 1,171 elderly admixed individuals from São Paulo, Brazil. Nat Commun 2022; 13:1004. [PMID: 35246524 PMCID: PMC8897431 DOI: 10.1038/s41467-022-28648-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/21/2022] [Indexed: 02/07/2023] Open
Abstract
As whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics and medical applications, data on diverse non-European and admixed individuals are still scarce. Here, we present a high-coverage WGS dataset of 1,171 highly admixed elderly Brazilians from a census-based cohort, providing over 76 million variants, of which ~2 million are absent from large public databases. WGS enables identification of ~2,000 previously undescribed mobile element insertions without previous description, nearly 5 Mb of genomic segments absent from the human genome reference, and over 140 alleles from HLA genes absent from public resources. We reclassify and curate pathogenicity assertions for nearly four hundred variants in genes associated with dominantly-inherited Mendelian disorders and calculate the incidence for selected recessive disorders, demonstrating the clinical usefulness of the present study. Finally, we observe that whole-genome and HLA imputation could be significantly improved compared to available datasets since rare variation represents the largest proportion of input from WGS. These results demonstrate that even smaller sample sizes of underrepresented populations bring relevant data for genomic studies, especially when exploring analyses allowed only by WGS. Whole genome sequencing (WGS) data on non-European and admixed individuals remains scarce. Here, the authors analyse WGS data from 1,171 admixed elderly Brazilians from a census cohort, characterising population-specific genetic variation and exploring the clinical utility of this expanded dataset.
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45
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Teekakirikul P, Zhu W, Xu X, Young CB, Tan T, Smith AM, Wang C, Peterson KA, Gabriel GC, Ho S, Sheng Y, Moreau de Bellaing A, Sonnenberg DA, Lin JH, Fotiou E, Tenin G, Wang MX, Wu YL, Feinstein T, Devine W, Gou H, Bais AS, Glennon BJ, Zahid M, Wong TC, Ahmad F, Rynkiewicz MJ, Lehman WJ, Keavney B, Alastalo TP, Freckmann ML, Orwig K, Murray S, Ware SM, Zhao H, Feingold B, Lo CW. Genetic resiliency associated with dominant lethal TPM1 mutation causing atrial septal defect with high heritability. Cell Rep Med 2022; 3:100501. [PMID: 35243414 PMCID: PMC8861813 DOI: 10.1016/j.xcrm.2021.100501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 10/24/2021] [Accepted: 12/17/2021] [Indexed: 11/22/2022]
Abstract
Analysis of large-scale human genomic data has yielded unexplained mutations known to cause severe disease in healthy individuals. Here, we report the unexpected recovery of a rare dominant lethal mutation in TPM1, a sarcomeric actin-binding protein, in eight individuals with large atrial septal defect (ASD) in a five-generation pedigree. Mice with Tpm1 mutation exhibit early embryonic lethality with disrupted myofibril assembly and no heartbeat. However, patient-induced pluripotent-stem-cell-derived cardiomyocytes show normal beating with mild myofilament defect, indicating disease suppression. A variant in TLN2, another myofilament actin-binding protein, is identified as a candidate suppressor. Mouse CRISPR knock-in (KI) of both the TLN2 and TPM1 variants rescues heart beating, with near-term fetuses exhibiting large ASD. Thus, the role of TPM1 in ASD pathogenesis unfolds with suppression of its embryonic lethality by protective TLN2 variant. These findings provide evidence that genetic resiliency can arise with genetic suppression of a deleterious mutation.
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Affiliation(s)
- Polakit Teekakirikul
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Division of Cardiology, Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Centre for Cardiovascular Genomics & Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wenjuan Zhu
- Centre for Cardiovascular Genomics & Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Division of Medical Sciences, Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xinxiu Xu
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Cullen B. Young
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Tuantuan Tan
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amanda M. Smith
- Department of Pediatrics and Department of Medical and Molecular Genetics, and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Chengdong Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | | | - George C. Gabriel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sebastian Ho
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yi Sheng
- Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anne Moreau de Bellaing
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Daniel A. Sonnenberg
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jiuann-huey Lin
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Elisavet Fotiou
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Gennadiy Tenin
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Michael X. Wang
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yijen L. Wu
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Timothy Feinstein
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - William Devine
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Abha S. Bais
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Benjamin J. Glennon
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Maliha Zahid
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Timothy C. Wong
- UPMC Heart and Vascular Institute and Division of Cardiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ferhaan Ahmad
- Division of Cardiovascular Medicine, Department of Internal Medicine, The University of Iowa, Iowa City, IA, USA
| | - Michael J. Rynkiewicz
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - William J. Lehman
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Bernard Keavney
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | | | - Kyle Orwig
- Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Stephanie M. Ware
- Department of Pediatrics and Department of Medical and Molecular Genetics, and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Hui Zhao
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Brian Feingold
- Heart Institute and Division of Pediatric Cardiology, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Cecilia W. Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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46
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Narasimhan U, Janakiraman A, Puskur D, Anitha FS, Paul SFD, Koshy T. Case Report: A Disease Phenotype of Rett Syndrome and Neurofibromatosis Resulting from A Bilocus Variant Combination. J Autism Dev Disord 2022; 53:2138-2142. [PMID: 35122187 DOI: 10.1007/s10803-022-05458-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2022] [Indexed: 10/19/2022]
Affiliation(s)
- Udayakumar Narasimhan
- Department of Pediatrics, Karthikeyan Child Development Unit, Sri Ramachandra Institute of Higher Education and Research, #1, Ramachandra Nagar, Porur, Chennai, 600116, Tamil Nadu, India
| | - Abhinayaa Janakiraman
- Department of Pediatrics, Karthikeyan Child Development Unit, Sri Ramachandra Institute of Higher Education and Research, #1, Ramachandra Nagar, Porur, Chennai, 600116, Tamil Nadu, India
| | - Dedeepya Puskur
- Department of Pediatrics, Karthikeyan Child Development Unit, Sri Ramachandra Institute of Higher Education and Research, #1, Ramachandra Nagar, Porur, Chennai, 600116, Tamil Nadu, India
| | - Fatima Shirly Anitha
- Department of Pediatrics, Karthikeyan Child Development Unit, Sri Ramachandra Institute of Higher Education and Research, #1, Ramachandra Nagar, Porur, Chennai, 600116, Tamil Nadu, India
| | - Solomon Franklin Durairaj Paul
- Department of Human Genetics, Faculty of Biomedical Science and Technology, Sri Ramachandra Institute of Higher Education and Research, #1, Ramachandra Nagar, Porur, Chennai, 600116, Tamil Nadu, India
| | - Teena Koshy
- Department of Human Genetics, Faculty of Biomedical Science and Technology, Sri Ramachandra Institute of Higher Education and Research, #1, Ramachandra Nagar, Porur, Chennai, 600116, Tamil Nadu, India.
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Schell R, Hale JJ, Mullis MN, Matsui T, Foree R, Ehrenreich IM. Genetic basis of a spontaneous mutation’s expressivity. Genetics 2022; 220:6515283. [PMID: 35078232 PMCID: PMC8893249 DOI: 10.1093/genetics/iyac013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/19/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Genetic background often influences the phenotypic consequences of mutations, resulting in variable expressivity. How standing genetic variants collectively cause this phenomenon is not fully understood. Here, we comprehensively identify loci in a budding yeast cross that impact the growth of individuals carrying a spontaneous missense mutation in the nuclear-encoded mitochondrial ribosomal gene MRP20. Initial results suggested that a single large effect locus influences the mutation’s expressivity, with one allele causing inviability in mutants. However, further experiments revealed this simplicity was an illusion. In fact, many additional loci shape the mutation’s expressivity, collectively leading to a wide spectrum of mutational responses. These results exemplify how complex combinations of alleles can produce a diversity of qualitative and quantitative responses to the same mutation.
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Affiliation(s)
- Rachel Schell
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Joseph J Hale
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Martin N Mullis
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Takeshi Matsui
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Ryan Foree
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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Zug R. Developmental disorders caused by haploinsufficiency of transcriptional regulators: a perspective based on cell fate determination. Biol Open 2022; 11:bio058896. [PMID: 35089335 PMCID: PMC8801891 DOI: 10.1242/bio.058896] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Many human birth defects and neurodevelopmental disorders are caused by loss-of-function mutations in a single copy of transcription factor (TF) and chromatin regulator genes. Although this dosage sensitivity has long been known, how and why haploinsufficiency (HI) of transcriptional regulators leads to developmental disorders (DDs) is unclear. Here I propose the hypothesis that such DDs result from defects in cell fate determination that are based on disrupted bistability in the underlying gene regulatory network (GRN). Bistability, a crucial systems biology concept to model binary choices such as cell fate decisions, requires both positive feedback and ultrasensitivity, the latter often achieved through TF cooperativity. The hypothesis explains why dosage sensitivity of transcriptional regulators is an inherent property of fate decisions, and why disruption of either positive feedback or cooperativity in the underlying GRN is sufficient to cause disease. I present empirical and theoretical evidence in support of this hypothesis and discuss several issues for which it increases our understanding of disease, such as incomplete penetrance. The proposed framework provides a mechanistic, systems-level explanation of HI of transcriptional regulators, thus unifying existing theories, and offers new insights into outstanding issues of human disease. This article has an associated Future Leader to Watch interview with the author of the paper.
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Affiliation(s)
- Roman Zug
- Department of Biology, Lund University, 22362 Lund, Sweden
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49
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Gold NB, Harrison SM, Rowe JH, Gold J, Furutani E, Biffi A, Duncan CN, Shimamura A, Lehmann LE, Green RC. Low frequency of treatable pediatric disease alleles in gnomAD: An opportunity for future genomic screening of newborns. HGG ADVANCES 2022; 3:100059. [PMID: 35047849 PMCID: PMC8756496 DOI: 10.1016/j.xhgg.2021.100059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 09/20/2021] [Indexed: 01/18/2023] Open
Abstract
Hematopoietic stem cell transplant (HSCT) can prevent progression of several genetic disorders. Although a subset of these disorders are identified on newborn screening panels, others are not identified until irreversible symptoms develop. Genetic testing is an efficient methodology to ascertain pre-symptomatic children, but the penetrance of risk-associated variants in the general population is not well understood. We developed a list of 127 genes associated with disorders treatable with HSCT. We identified likely pathogenic or pathogenic (LP/P) and loss-of-function (LoF) variants in these genes in the Genome Aggregation Database (gnomAD), a dataset containing exome and genome sequencing data from 141,456 healthy adults. Within gnomAD, we identified 59 individuals with a LP/P or LoF variant in 15 genes. Genes were associated with bone marrow failure syndromes, bleeding disorders, primary immunodeficiencies, osteopetrosis, metabolic disorders, and epidermolysis bullosa. In conclusion, few ostensibly healthy adults had genotypes associated with pediatric disorders treatable with HSCTs. Given that most of these disorders do not have biomarkers that could be cheaply and universally assessed on a standard newborn screen, our data suggest that genetic testing may be a complementary approach to traditional newborn screening methodology that has the potential to improve mortality and is not expected to lead to a high burden of false-positive results.
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Affiliation(s)
- Nina B. Gold
- Massachusetts General Hospital for Children, Division of Medical Genetics and Metabolism, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Jared H. Rowe
- Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Division of Hematology and Oncology, Boston, MA, USA
- Dana-Farber Cancer Institute Division of Pediatric Oncology, Boston, MA, USA
| | - Jessica Gold
- Department of Pediatrics, Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elissa Furutani
- Boston Children’s Hospital, Division of Hematology and Oncology, Boston, MA, USA
| | - Alessandra Biffi
- Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Division of Hematology and Oncology, Boston, MA, USA
- Dana-Farber Cancer Institute Division of Pediatric Oncology, Boston, MA, USA
| | - Christine N. Duncan
- Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Division of Hematology and Oncology, Boston, MA, USA
- Dana-Farber Cancer Institute Division of Pediatric Oncology, Boston, MA, USA
| | - Akiko Shimamura
- Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Division of Hematology and Oncology, Boston, MA, USA
- Dana-Farber Cancer Institute Division of Pediatric Oncology, Boston, MA, USA
| | - Leslie E. Lehmann
- Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Division of Hematology and Oncology, Boston, MA, USA
- Dana-Farber Cancer Institute Division of Pediatric Oncology, Boston, MA, USA
| | - Robert C. Green
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Brigham and Women’s Hospital, Boston, MA, USA
- Ariadne Labs, Boston, MA, USA
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50
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Avramović V, Frederiksen SD, Brkić M, Tarailo-Graovac M. Driving mosaicism: somatic variants in reference population databases and effect on variant interpretation in rare genetic disease. Hum Genomics 2021; 15:71. [PMID: 34906245 PMCID: PMC8670043 DOI: 10.1186/s40246-021-00371-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/29/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Genetic variation databases provide invaluable information on the presence and frequency of genetic variants in the 'untargeted' human population, aggregated with the primary goal to facilitate the interpretation of clinically important variants. The presence of somatic variants in such databases can affect variant assessment in undiagnosed rare disease (RD) patients. Previously, the impact of somatic mosaicism was only considered in relation to two Mendelian disease-associated genes. Here, we expand the analyses to identify additional mosaicism-prone genes in blood-derived reference population databases. RESULTS To identify additional mosaicism-prone genes relevant to RDs, we focused on known/previously established ClinVar pathogenic and likely pathogenic single-nucleotide variants, residing in genes associated with early onset, severe autosomal dominant diseases. We asked whether any of these variants are present in a higher-than-expected frequency in the reference population databases and whether there is evidence of somatic origin (i.e., allelic imbalance) rather than germline heterozygosity (~ half of the reads supporting alternative allele). The mosaicism-prone genes identified were further categorized according to the processes they are involved in. Beyond the previously reported ASXL1 and DNMT3A, we identified 7 additional autosomal dominant RD-associated genes with known pathogenic single-nucleotide variants present in the reference population databases and good evidence of allelic imbalance: BRAF, CBL, FGFR3, IDH2, KRAS, PTPN11 and SETBP1. From this group of 9 genes, the majority (n = 7) was important for hematopoiesis. In addition, 4 of these genes were involved in cell proliferation. Further assessment of the known 156 hematopoietic genes led to identification of 48 genes (21 not yet associated with RDs) with at least some evidence of mosaicism detectable in reference population databases. CONCLUSIONS These results stress the importance of considering genes involved in hematopoiesis and cell proliferation when interpreting the presence and frequency of genetic variants in blood-derived reference population databases, both public and private. This is especially important when considering new variants of uncertain significance in known hematopoietic/cell proliferation RD genes and future novel gene-disease associations involving this class of genes.
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Affiliation(s)
- Vladimir Avramović
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Simona Denise Frederiksen
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Marjana Brkić
- Department of Neurobiology, Institute for Biological Research, University of Belgrade, 11060, Belgrade, Republic of Serbia.,VIB Center for Inflammation Research, Ghent University, 9052, Ghent, Belgium
| | - Maja Tarailo-Graovac
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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