1
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Capp JP, Catania F, Thomas F. From genetic mosaicism to tumorigenesis through indirect genetic effects. Bioessays 2024; 46:e2300238. [PMID: 38736323 DOI: 10.1002/bies.202300238] [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: 12/13/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024]
Abstract
Genetic mosaicism has long been linked to aging, and several hypotheses have been proposed to explain the potential connections between mosaicism and susceptibility to cancer. It has been proposed that mosaicism may disrupt tissue homeostasis by affecting intercellular communications and releasing microenvironmental constraints within tissues. The underlying mechanisms driving these tissue-level influences remain unidentified, however. Here, we present an evolutionary perspective on the interplay between mosaicism and cancer, suggesting that the tissue-level impacts of genetic mosaicism can be attributed to Indirect Genetic Effects (IGEs). IGEs can increase the level of cellular stochasticity and phenotypic instability among adjacent cells, thereby elevating the risk of cancer development within the tissue. Moreover, as cells experience phenotypic changes in response to challenging microenvironmental conditions, these changes can initiate a cascade of nongenetic alterations, referred to as Indirect non-Genetic Effects (InGEs), which in turn catalyze IGEs among surrounding cells. We argue that incorporating both InGEs and IGEs into our understanding of the process of oncogenic transformation could trigger a major paradigm shift in cancer research with far-reaching implications for practical applications.
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Affiliation(s)
- Jean-Pascal Capp
- Toulouse Biotechnology Institute, INSA/University of Toulouse, CNRS, INRAE, Toulouse, France
| | - Francesco Catania
- Institute of Environmental Radioactivity, Fukushima University, Kanayagawa, Fukushima, Japan
| | - Frédéric Thomas
- CREEC, UMR IRD 224-CNRS 5290-University of Montpellier, Montpellier, France
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2
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Nathan DI, Brander T, Gold J, Paul D, Klein P, Cheng K, Liu JM, Marcellino BK. Diagnostic and Practical Challenges in Applying National Comprehensive Cancer Network Guidelines for Suspected Pathogenic TP53 Mosaicism. JCO Precis Oncol 2024; 8:e2400006. [PMID: 38991177 PMCID: PMC11285011 DOI: 10.1200/po.24.00006] [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: 01/03/2024] [Revised: 04/12/2024] [Accepted: 05/08/2024] [Indexed: 07/13/2024] Open
Abstract
Benefits and limitations in using NCCN guidelines to distinguish TP53 CH from mosaic LFS.
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Affiliation(s)
- Daniel I. Nathan
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Tehilla Brander
- Division of Medical Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Julie Gold
- Division of Medical Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Deborah Paul
- Department of Breast Services, The Blavatnik Family Chelsea Medical Center, Mount Sinai Beth Israel, New York, NY
| | - Paula Klein
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kit Cheng
- Division of Medical Oncology and Hematology, Zuckerberg Cancer Center, New Hyde Park, NY
| | - Johnson M. Liu
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Bridget K. Marcellino
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
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3
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Parsons BL, Beal MA, Dearfield KL, Douglas GR, Gi M, Gollapudi BB, Heflich RH, Horibata K, Kenyon M, Long AS, Lovell DP, Lynch AM, Myers MB, Pfuhler S, Vespa A, Zeller A, Johnson GE, White PA. Severity of effect considerations regarding the use of mutation as a toxicological endpoint for risk assessment: A report from the 8th International Workshop on Genotoxicity Testing (IWGT). ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024. [PMID: 38828778 DOI: 10.1002/em.22599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/13/2024] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
Exposure levels without appreciable human health risk may be determined by dividing a point of departure on a dose-response curve (e.g., benchmark dose) by a composite adjustment factor (AF). An "effect severity" AF (ESAF) is employed in some regulatory contexts. An ESAF of 10 may be incorporated in the derivation of a health-based guidance value (HBGV) when a "severe" toxicological endpoint, such as teratogenicity, irreversible reproductive effects, neurotoxicity, or cancer was observed in the reference study. Although mutation data have been used historically for hazard identification, this endpoint is suitable for quantitative dose-response modeling and risk assessment. As part of the 8th International Workshops on Genotoxicity Testing, a sub-group of the Quantitative Analysis Work Group (WG) explored how the concept of effect severity could be applied to mutation. To approach this question, the WG reviewed the prevailing regulatory guidance on how an ESAF is incorporated into risk assessments, evaluated current knowledge of associations between germline or somatic mutation and severe disease risk, and mined available data on the fraction of human germline mutations expected to cause severe disease. Based on this review and given that mutations are irreversible and some cause severe human disease, in regulatory settings where an ESAF is used, a majority of the WG recommends applying an ESAF value between 2 and 10 when deriving a HBGV from mutation data. This recommendation may need to be revisited in the future if direct measurement of disease-causing mutations by error-corrected next generation sequencing clarifies selection of ESAF values.
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Affiliation(s)
- Barbara L Parsons
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Marc A Beal
- Bureau of Chemical Safety, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Kerry L Dearfield
- U.S. Environmental Protection Agency and U.S. Department of Agriculture, Washington, DC, USA
| | - George R Douglas
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Min Gi
- Department of Environmental Risk Assessment, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | | | - Robert H Heflich
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Michelle Kenyon
- Portfolio and Regulatory Strategy, Drug Safety Research and Development, Pfizer, Groton, Connecticut, USA
| | - Alexandra S Long
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - David P Lovell
- Population Health Research Institute, St George's Medical School, University of London, London, UK
| | | | - Meagan B Myers
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Alisa Vespa
- Pharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Andreas Zeller
- Pharmaceutical Sciences, pRED Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - George E Johnson
- Swansea University Medical School, Swansea University, Swansea, Wales, UK
| | - Paul A White
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
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4
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Graham JH, Schlachetzki JCM, Yang X, Breuss MW. Genomic Mosaicism of the Brain: Origin, Impact, and Utility. Neurosci Bull 2024; 40:759-776. [PMID: 37898991 PMCID: PMC11178748 DOI: 10.1007/s12264-023-01124-8] [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: 05/04/2023] [Accepted: 07/16/2023] [Indexed: 10/31/2023] Open
Abstract
Genomic mosaicism describes the phenomenon where some but not all cells within a tissue harbor unique genetic mutations. Traditionally, research focused on the impact of genomic mosaicism on clinical phenotype-motivated by its involvement in cancers and overgrowth syndromes. More recently, we increasingly shifted towards the plethora of neutral mosaic variants that can act as recorders of cellular lineage and environmental exposures. Here, we summarize the current state of the field of genomic mosaicism research with a special emphasis on our current understanding of this phenomenon in brain development and homeostasis. Although the field of genomic mosaicism has a rich history, technological advances in the last decade have changed our approaches and greatly improved our knowledge. We will provide current definitions and an overview of contemporary detection approaches for genomic mosaicism. Finally, we will discuss the impact and utility of genomic mosaicism.
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Affiliation(s)
- Jared H Graham
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, 92123, CA, USA
| | - Martin W Breuss
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA.
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5
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Parentelli AS, Boursier G, Cuisset L, Georgin-Lavialle S. [Genetic mosaicism in Systemic Auto-Inflammatory Diseases: A review of the literature]. Rev Med Interne 2024:S0248-8663(24)00566-6. [PMID: 38762439 DOI: 10.1016/j.revmed.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/07/2024] [Accepted: 05/02/2024] [Indexed: 05/20/2024]
Abstract
Systemic auto-inflammatory diseases (SAIDs) are disorders associated with deregulation of innate immunity in which patients present classically with systemic inflammatory manifestations, in particular fever, skin-mucosal rashes, arthromyalgia and abdominal pain, with an increase in blood biomarkers of inflammation. At the time of their discovery, these diseases were associated with constitutional mutations in genes encoding proteins involved in innate immunity, and it was then considered that they had to begin in childhood. This dogma of constitutional mutations in SAIDs is no longer so unquestionable, since 2005 several cases of mosaicism have been reported in the literature, initially in cryopyrinopathies, but also in other SAIDs in patients with obvious clinical phenotypes and late onset of disease expression, in particular in the VEXAS syndrome (Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic Syndrome) and very recently in MEVF gene. Next-generation sequencing techniques are more sensitive than Sanger for detecting mosaicisms. So, when a clinical diagnosis seems obvious but no constitutional mutation is found by low-depth genetic analysis, it is useful to discuss with expert geneticists whether to consider another genetic approach in a child or an adult. This modifies the situations in which clinicians can evoke these diseases. This review provides an update on mosaicism in SAIDs.
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Affiliation(s)
- A-S Parentelli
- Service de pédiatrie, CHU Félix-Guyon, allée des Topazes, 97400 Saint-Denis, Réunion.
| | - G Boursier
- Service de génétique moléculaire et cytogénomique, laboratoire de génétique des maladies rares et auto-inflammatoires, CHU de Montpellier, université de Montpellier, 371, avenue du Doyen-Gaston-Giraud, 34295 Montpellier cedex 5, France; Centre de référence des maladies auto-inflammatoires rares et de l'amylose inflammatoire (CEREMAIA), hôpital Tenon, Assistance publique-Hôpitaux de Paris, 4, rue de la Chine, 75020 Paris, France
| | - L Cuisset
- Service de médecine génomique des maladies de système et d'organe, hôpital Cochin, Assistance publique-Hôpitaux de Paris, université Paris Cité, 27, rue du Faubourg-Saint-Jacques, 75014 Paris, France
| | - S Georgin-Lavialle
- Service de médecine interne, hôpital Tenon, Assistance publique-Hôpitaux de Paris, Sorbonne université, 4, rue de la Chine, 75020 Paris, France; Centre de référence des maladies auto-inflammatoires rares et de l'amylose inflammatoire (CEREMAIA), hôpital Tenon, Assistance publique-Hôpitaux de Paris, 4, rue de la Chine, 75020 Paris, France
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6
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Waldvogel SM, Posey JE, Goodell MA. Human embryonic genetic mosaicism and its effects on development and disease. Nat Rev Genet 2024:10.1038/s41576-024-00715-z. [PMID: 38605218 DOI: 10.1038/s41576-024-00715-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2024] [Indexed: 04/13/2024]
Abstract
Nearly every mammalian cell division is accompanied by a mutational event that becomes fixed in a daughter cell. When carried forward to additional cell progeny, a clone of variant cells can emerge. As a result, mammals are complex mosaics of clones that are genetically distinct from one another. Recent high-throughput sequencing studies have revealed that mosaicism is common, clone sizes often increase with age and specific variants can affect tissue function and disease development. Variants that are acquired during early embryogenesis are shared by multiple cell types and can affect numerous tissues. Within tissues, variant clones compete, which can result in their expansion or elimination. Embryonic mosaicism has clinical implications for genetic disease severity and transmission but is likely an under-recognized phenomenon. To better understand its implications for mosaic individuals, it is essential to leverage research tools that can elucidate the mechanisms by which expanded embryonic variants influence development and disease.
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Affiliation(s)
- Sarah M Waldvogel
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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7
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Ansari M, Faour KNW, Shimamura A, Grimes G, Kao EM, Denhoff ER, Blatnik A, Ben-Isvy D, Wang L, Helm BM, Firth H, Breman AM, Bijlsma EK, Iwata-Otsubo A, de Ravel TJL, Fusaro V, Fryer A, Nykamp K, Stühn LG, Haack TB, Korenke GC, Constantinou P, Bujakowska KM, Low KJ, Place E, Humberson J, Napier MP, Hoffman J, Juusola J, Deardorff MA, Shao W, Rockowitz S, Krantz I, Kaur M, Raible S, Dortenzio V, Kliesch S, Singer-Berk M, Groopman E, DiTroia S, Ballal S, Srivastava S, Rothfelder K, Biskup S, Rzasa J, Kerkhof J, McConkey H, Sadikovic B, Hilton S, Banka S, Tüttelmann F, Conrad DF, O'Donnell-Luria A, Talkowski ME, FitzPatrick DR, Boone PM. Heterozygous loss-of-function SMC3 variants are associated with variable growth and developmental features. HGG ADVANCES 2024; 5:100273. [PMID: 38297832 PMCID: PMC10876629 DOI: 10.1016/j.xhgg.2024.100273] [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: 11/08/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 14 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism, reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated an overall milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, and some had alternative symptomatologies with rational biological links to SMC3. Analyses of tumor and model system transcriptomic data and epigenetic data in a subset of cases suggest that SMC3 pLoF variants reduce SMC3 expression but do not strongly support clustering with functional genomic signatures of typical CdLS. Our finding of substantial population-scale LoF intolerance in concert with variable growth and developmental features in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multilayered genomic data paired with careful phenotyping.
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Affiliation(s)
- Morad Ansari
- South East Scotland Genetic Service, Western General Hospital, Edinburgh, UK; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kamli N W Faour
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, USA
| | - Akiko Shimamura
- Division of Hematology and Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Graeme Grimes
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Emeline M Kao
- Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, MA, USA
| | - Erica R Denhoff
- Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, MA, USA
| | - Ana Blatnik
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK; Department of Clinical Cancer Genetics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Daniel Ben-Isvy
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Lily Wang
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Benjamin M Helm
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Helen Firth
- Clinical Genetics, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK
| | - Amy M Breman
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Aiko Iwata-Otsubo
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Thomy J L de Ravel
- Centre for Human Genetics, UZ Leuven/Leuven University Hospitals, Leuven, Belgium
| | | | - Alan Fryer
- Department of Clinical Genetics, Alder Hey Children's Hospital Liverpool, Liverpool, UK
| | | | - Lara G Stühn
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - G Christoph Korenke
- Department of Neuropaediatric and Metabolic Diseases, University Children's Hospital Oldenburg, Oldenburg, Germany
| | - Panayiotis Constantinou
- West of Scotland Centre for Genomic Medicine, Queen Elizabeth University Hospital, Glasgow, UK
| | | | - Karen J Low
- University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK; University of Bristol, Bristol, UK
| | - Emily Place
- Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | | | | | | | | | - Matthew A Deardorff
- Departments of Pathology and Pediatrics, Children's Hospital Los Angeles and University of Southern California, Los Angeles, CA, USA
| | - Wanqing Shao
- Research Computing, Information Technology, Boston Children's Hospital, Boston, MA, USA
| | - Shira Rockowitz
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Research Computing, Information Technology, Boston Children's Hospital, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Ian Krantz
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maninder Kaur
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah Raible
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Sabine Kliesch
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - Moriel Singer-Berk
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emily Groopman
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie DiTroia
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sonia Ballal
- Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, USA; Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
| | - Siddharth Srivastava
- Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, USA; Divison of Neurology, Boston Children's Hospital, Boston, MA, USA
| | | | - Saskia Biskup
- Zentrum für Humangenetik, Tübingen, Germany; Center for Genomics and Transcriptomics (CeGaT), Tübingen, Germany
| | - Jessica Rzasa
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Jennifer Kerkhof
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Haley McConkey
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Bekim Sadikovic
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Sarah Hilton
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Division of Evolution, Infection, and Genomics, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, UK
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Donald F Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Portland, OR, USA; Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland, OR, USA
| | - Anne O'Donnell-Luria
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael E Talkowski
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Philip M Boone
- Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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8
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Moustakli E, Zikopoulos A, Skentou C, Bouba I, Dafopoulos K, Georgiou I. Evolution of Minimally Invasive and Non-Invasive Preimplantation Genetic Testing: An Overview. J Clin Med 2024; 13:2160. [PMID: 38673433 PMCID: PMC11050362 DOI: 10.3390/jcm13082160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/27/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
Preimplantation genetic testing (PGT) has become a common supplementary diagnοstic/testing tοol for in vitro fertilization (ΙVF) cycles due to a significant increase in cases of PGT fοr mοnogenic cοnditions (ΡGT-M) and de novο aneuplοidies (ΡGT-A) over the last ten years. This tendency is mostly attributable to the advancement and application of novel cytogenetic and molecular techniques in clinical practice that are capable of providing an efficient evaluation of the embryonic chromosomal complement and leading to better IVF/ICSI results. Although PGT is widely used, it requires invasive biopsy of the blastocyst, which may harm the embryo. Non-invasive approaches, like cell-free DNA (cfDNA) testing, have lower risks but have drawbacks in consistency and sensitivity. This review discusses new developments and opportunities in the field of preimplantation genetic testing, enhancing the overall effectiveness and accessibility of preimplantation testing in the framework of developments in genomic sequencing, bioinformatics, and the integration of artificial intelligence in the interpretation of genetic data.
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Affiliation(s)
- Efthalia Moustakli
- Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (E.M.); (I.B.)
| | - Athanasios Zikopoulos
- Obstetrics and Gynecology, Royal Devon and Exeter Hospital Barrack Rd, Exeter EX2 5DW, UK;
| | - Charikleia Skentou
- Department of Obstetrics and Gynecology, Medical School of Ioannina, University General Hospital, 45110 Ioannina, Greece;
| | - Ioanna Bouba
- Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (E.M.); (I.B.)
| | - Konstantinos Dafopoulos
- IVF Unit, Department of Obstetrics and Gynecology, Faculty of Medicine, School of Health Sciences University of Thessaly, 41500 Larissa, Greece;
| | - Ioannis Georgiou
- Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (E.M.); (I.B.)
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9
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Bai T, Shen Y, Yang Y, Dai S, Liu H. Maternal CHD7 gonosomal mosaicism in a fetus with CHARGE syndrome. Am J Med Genet A 2024; 194:e63491. [PMID: 38057991 DOI: 10.1002/ajmg.a.63491] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023]
Abstract
Parental mosaicism is important in families with de novo mutations. Herein, we report a case of fetal CHARGE syndrome (CS) with a CHD7 variant inherited from maternal CHD7 gonosomal mosaicism. The variant was detected through trio-based whole-exome sequencing and Sanger sequencing. High-depth whole-exome sequencing was performed for the identification of parental mosaicism. A novel heterozygous CHD7 nonsense mutation (c.5794G>T/ p.E1932*) was detected in the tissue from the aborted fetus. The parents were wild-type, indicating that the mutation was a de novo variant. The mutation was suspected to be the cause of the fetal CS. However, high-depth whole-exome sequencing revealed maternal gonosomal mosaicism at a variant allele frequency of 3.2%-23.3%. The variant was identified in various tissues (peripheral blood, hair follicles, buccal epithelia, and pharyngeal epithelia) from the asymptomatic mother. We confirmed maternal CHD7 gonosomal mosaicism as a genetic cause of fetal CS. Our results emphasize the importance of clinical analysis in accurately determining the parents' status in detecting the CHD7 de novo variant in fetal CS, as this analysis has vital implications for evaluating the recurrence risk for genetic counseling.
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Affiliation(s)
- Ting Bai
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Ying Shen
- Department of Obstetrics/Gynecology, Joint Laboratory of Reproductive Medicine (SCU-CUHK), Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yanting Yang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Siyu Dai
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Hongqian Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
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10
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Ma JY, Xia TJ, Li S, Yin S, Luo SM, Li G. Germline cell de novo mutations and potential effects of inflammation on germline cell genome stability. Semin Cell Dev Biol 2024; 154:316-327. [PMID: 36376195 DOI: 10.1016/j.semcdb.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/05/2022] [Accepted: 11/06/2022] [Indexed: 11/13/2022]
Abstract
Uncontrolled pathogenic genome mutations in germline cells might impair adult fertility, lead to birth defects or even affect the adaptability of a species. Understanding the sources of DNA damage, as well as the features of damage response in germline cells are the overarching tasks to reduce the mutations in germline cells. With the accumulation of human genome data and genetic reports, genome variants formed in germline cells are being extensively explored. However, the sources of DNA damage, the damage repair mechanisms, and the effects of DNA damage or mutations on the development of germline cells are still unclear. Besides exogenous triggers of DNA damage such as irradiation and genotoxic chemicals, endogenous exposure to inflammation may also contribute to the genome instability of germline cells. In this review, we summarized the features of de novo mutations and the specific DNA damage responses in germline cells and explored the possible roles of inflammation on the genome stability of germline cells.
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Affiliation(s)
- Jun-Yu Ma
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China.
| | - Tian-Jin Xia
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China; College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Shuai Li
- Center for Clinical Epidemiology and Methodology, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Shen Yin
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.
| | - Shi-Ming Luo
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China.
| | - Guowei Li
- Center for Clinical Epidemiology and Methodology, Guangdong Second Provincial General Hospital, Guangzhou, China.
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11
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Woodis KM, Garlisi Torales LD, Wolf A, Britt A, Sheppard SE. Updates in Genetic Testing for Head and Neck Vascular Anomalies. Oral Maxillofac Surg Clin North Am 2024; 36:1-17. [PMID: 37867039 PMCID: PMC11092895 DOI: 10.1016/j.coms.2023.09.001] [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] [Indexed: 10/24/2023]
Abstract
Vascular anomalies include benign or malignant tumors or benign malformations of the arteries, veins, capillaries, or lymphatic vasculature. The genetic etiology of the lesion is essential to define the lesion and can help navigate choice of therapy. . In the United States, about 1.2% of the population has a vascular anomaly, which may be underestimating the true prevalence as genetic testing for these conditions continues to evolve.
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Affiliation(s)
- Kristina M Woodis
- Unit on Vascular Malformations, Division of Intramural Research, Eunice Kennedy Shriver National Institute for Child Health and Human Development, 10 Center Drive, MSC 1103, Bethesda, MD 20892-1103, USA
| | - Luciana Daniela Garlisi Torales
- Unit on Vascular Malformations, Division of Intramural Research, Eunice Kennedy Shriver National Institute for Child Health and Human Development, 10 Center Drive, MSC 1103, Bethesda, MD 20892-1103, USA
| | - Alejandro Wolf
- Department of Pathology and ARUP Laboratories, University of Utah, 2000 Circle of Hope, Room 3100, Salt Lake City, UT 84112, USA
| | - Allison Britt
- Comprehensive Vascular Anomalies Program, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah E Sheppard
- Unit on Vascular Malformations, Division of Intramural Research, Eunice Kennedy Shriver National Institute for Child Health and Human Development, 10 Center Drive, MSC 1103, Bethesda, MD 20892-1103, USA.
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12
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Grippa M, Graziano C. Landscape of Constitutional SOX4 Variation in Human Disorders. Genes (Basel) 2024; 15:158. [PMID: 38397148 PMCID: PMC10887744 DOI: 10.3390/genes15020158] [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: 12/30/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
SOX proteins are transcription factors which play a role in regulating the development of progenitor cells and tissue differentiation. Twenty members are known, clustered in eight groups named A through H and sharing a common DNA-binding domain called the HMG (high-mobility-group) box. Eleven of the SOX genes have been associated with genetic disorders so far, covering a broad spectrum of developmental diseases. SOX4 is a single-exon gene and belongs to the SOXC group, together with SOX11 and SOX12. SOX4 variants have been recently described to cause a highly penetrant but heterogeneous disorder, with a phenotypic spectrum ranging from mild developmental delays and learning difficulties to intellectual disabilities with congenital anomalies. Nineteen pathogenic variants have been reported to date, generally de novo, heterozygous, and inactivating, either stop-gain or missense, the latter ones primarily targeting the HMG domain. Further, a bi-allelic variant was reported in a single consanguineous family. Copy number variants leading to whole gene deletion or duplication are rare and not clearly associated with any neurodevelopmental disorder. Many open questions remain regarding the definition of variants of unknown significance, a possible role of missense variants outside the HMG domain, genotype-phenotype correlation, the range of phenotypic spectrum and modifying factors, and treatment options.
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Affiliation(s)
- Mina Grippa
- SSD Genetica Medica, Dipartimento Materno Infantile, AOU Policlinico Modena, 41125 Modena, Italy;
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13
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Chen YH, van Zon S, Adams A, Schmidt-Arras D, Laurence ADJ, Uhlig HH. The Human GP130 Cytokine Receptor and Its Expression-an Atlas and Functional Taxonomy of Genetic Variants. J Clin Immunol 2023; 44:30. [PMID: 38133879 PMCID: PMC10746620 DOI: 10.1007/s10875-023-01603-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/30/2023] [Indexed: 12/23/2023]
Abstract
Genetic variants in IL6ST encoding the shared cytokine receptor for the IL-6 cytokine family GP130 have been associated with a diverse number of clinical phenotypes and disorders. We provide a molecular classification for 59 reported rare IL6ST pathogenic or likely pathogenic variants and additional polymorphisms. Based on loss- or gain-of-function, cytokine selectivity, mono- and biallelic associations, and variable cellular mosaicism, we grade six classes of IL6ST variants and explore the potential for additional variants. We classify variants according to the American College of Medical Genetics and Genomics criteria. Loss-of-function variants with (i) biallelic complete loss of GP130 function that presents with extended Stüve-Wiedemann Syndrome; (ii) autosomal recessive hyper-IgE syndrome (HIES) caused by biallelic; and (iii) autosomal dominant HIES caused by monoallelic IL6ST variants both causing selective IL-6 and IL-11 cytokine loss-of-function defects; (iv) a biallelic cytokine-specific variant that exclusively impairs IL-11 signaling, associated with craniosynostosis and tooth abnormalities; (v) somatic monoallelic mosaic constitutively active gain-of-function variants in hepatocytes that present with inflammatory hepatocellular adenoma; and (vi) mosaic constitutively active gain-of-function variants in hematopoietic and non-hematopoietic cells that are associated with an immune dysregulation syndrome. In addition to Mendelian IL6ST coding variants, there are common non-coding cis-acting variants that modify gene expression, which are associated with an increased risk of complex immune-mediated disorders and trans-acting variants that affect GP130 protein function. Our taxonomy highlights IL6ST as a gene with particularly strong functional and phenotypic diversity due to the combinatorial biology of the IL-6 cytokine family and predicts additional genotype-phenotype associations.
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Affiliation(s)
- Yin-Huai Chen
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Sarah van Zon
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Alex Adams
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Dirk Schmidt-Arras
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | | | - Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.
- Biomedical Research Centre, University of Oxford, Oxford, UK.
- Department of Paediatrics, University of Oxford, Oxford, UK.
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14
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Hallermayr A, Keßler T, Steinke-Lange V, Heitzer E, Holinski-Feder E, Speicher M. The utility of liquid biopsy in clinical genetic diagnosis of cancer and monogenic mosaic disorders. MED GENET-BERLIN 2023; 35:275-284. [PMID: 38835734 PMCID: PMC11006364 DOI: 10.1515/medgen-2023-2066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Liquid biopsy for minimally invasive diagnosis and monitoring of cancer patients is progressing toward routine clinical practice. With the implementation of highly sensitive next-generation sequencing (NGS) based assays for the analysis of cfDNA, however, consideration of the utility of liquid biopsy for clinical genetic testing is critical. While the focus of liquid biopsy for cancer diagnosis is the detection of circulating tumor DNA (ctDNA) as a fraction of total cell-free DNA (cfDNA), cfDNA analysis reveals both somatic mosaic tumor and germline variants and clonal hematopoiesis. Here we outline advantages and limitations of mosaic and germline variant detection as well as the impact of clonal hematopoiesis on liquid biopsy in cancer diagnosis. We also evaluate the potential of cfDNA analysis for the molecular diagnosis of monogenic mosaic disorders.
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Affiliation(s)
| | - Thomas Keßler
- MGZ - Medizinisch Genetisches Zentrum München Germany
| | | | - Ellen Heitzer
- Medical University of Graz Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine (Austria) Graz Austria
| | | | - Michael Speicher
- Medical University of Graz Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine (Austria), Neue Stiftingtalstraße 2 Graz Austria
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15
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Kleyner R, Ung N, Arif M, Marchi E, Amble K, Gavin M, Madrid R, Lyon G. ITPR1-associated spinocerebellar ataxia with craniofacial features-additional evidence for germline mosaicism. Cold Spring Harb Mol Case Stud 2023; 9:a006303. [PMID: 37821226 PMCID: PMC10815276 DOI: 10.1101/mcs.a006303] [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: 07/05/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023] Open
Abstract
Inositol 1,4,5-triphosphate receptor type 1 (ITPR1) is an endoplasmic reticulum-bound intracellular inositol triphosphate receptor involved in the regulation of intracellular calcium. Pathogenic variants in ITPR1 are associated with spinocerebellar ataxia (SCA) types 15/16 and 29 and have recently been implicated in a facial microsomia syndrome. In this report, we present a family with three affected individuals found to have a heterozygous missense c.800C > T (predicted p.Thr267Met) who present clinically with a SCA29-like syndrome. All three individuals presented with varying degrees of ataxia, developmental delay, and apparent intellectual disability, as well as craniofacial involvement-an uncommon finding in patients with SCA29. The variant was identified using clinical exome sequencing and validated with Sanger sequencing. It is presumed to be inherited via parental germline mosaicism. We present our findings to provide additional evidence for germline mosaic inheritance of SCA29, as well as to expand the clinical phenotype of the syndrome.
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Affiliation(s)
- Robert Kleyner
- Department of Human Genetics, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA
- Department of Neurological Surgery, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York 11794-8122, USA
| | - Nathaniel Ung
- Department of Human Genetics, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA
| | - Mohammad Arif
- Department of Human Genetics, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA
- Division of Cytogenetics and Molecular Pathology, North Shore University Hospital, Manhasset, New York 11030, USA
| | - Elaine Marchi
- Department of Human Genetics, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA
| | - Karen Amble
- George A. Jervis Clinic, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA
| | - Maureen Gavin
- George A. Jervis Clinic, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA
| | - Ricardo Madrid
- George A. Jervis Clinic, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA
| | - Gholson Lyon
- Department of Human Genetics, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA;
- George A. Jervis Clinic, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA
- Biology PhD Program, The Graduate Center, The City University of New York, New York, New York 10016, USA
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16
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Minow MAA, Marand AP, Schmitz RJ. Leveraging Single-Cell Populations to Uncover the Genetic Basis of Complex Traits. Annu Rev Genet 2023; 57:297-319. [PMID: 37562412 PMCID: PMC10775913 DOI: 10.1146/annurev-genet-022123-110824] [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] [Indexed: 08/12/2023]
Abstract
The ease and throughput of single-cell genomics have steadily improved, and its current trajectory suggests that surveying single-cell populations will become routine. We discuss the merger of quantitative genetics with single-cell genomics and emphasize how this synergizes with advantages intrinsic to plants. Single-cell population genomics provides increased detection resolution when mapping variants that control molecular traits, including gene expression or chromatin accessibility. Additionally, single-cell population genomics reveals the cell types in which variants act and, when combined with organism-level phenotype measurements, unveils which cellular contexts impact higher-order traits. Emerging technologies, notably multiomics, can facilitate the measurement of both genetic changes and genomic traits in single cells, enabling single-cell genetic experiments. The implementation of single-cell genetics will advance the investigation of the genetic architecture of complex molecular traits and provide new experimental paradigms to study eukaryotic genetics.
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Affiliation(s)
- Mark A A Minow
- Department of Genetics, University of Georgia, Athens, Georgia, USA;
| | | | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, USA;
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17
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De Mazancourt P, Mazoyer E, Hormi M, Hanss M. Absence of Missense Variant Detection in Inherited Dysfibrinogenemia May Result from a Poor Raw Data Analysis Algorithm or Mosaicism. Int J Mol Sci 2023; 24:16551. [PMID: 38068874 PMCID: PMC10706790 DOI: 10.3390/ijms242316551] [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: 10/27/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Variant identification underlying inherited dysfibrinogenemia quite exceptionally fails. We report on two dysfibrinogenemia cases whose underlying DNA variant could not be identified by Sanger analysis. These failures result from two distinct mechanisms. The first case involved raw signal overcorrection by a built-in software, and the second constituted the first description of mosaicism for one of the fibrinogen genes. This mosaicism was subsequently identified by next-generation sequencing reanalysis of the sample.
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Affiliation(s)
- Philippe De Mazancourt
- UMR1179, Université de Versailles-Saint-Quentin, 1 Rue de la Source de la Bièvre, 78180 Montigny le Bretonneux, France
- Laboratoire de Biologie Moléculaire, Hôpital A. Paré, GHU APHP Paris-Saclay, 9 Avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France
- Département d’Hématologie, Hôpital Européen Georges Pompidou, GHU AP-HP Centre—Université Paris Cité, 20 Rue Leblanc, 75015 Paris, France
| | - Elisabeth Mazoyer
- Service d’Hématologie Biologique, GHU APHP Paris-Seine-St-Denis, Site Avicenne, 125 Rue de Stalingrad, 93000 Bobigny, France; (E.M.); (M.H.)
| | - Myriam Hormi
- Service d’Hématologie Biologique, GHU APHP Paris-Seine-St-Denis, Site Avicenne, 125 Rue de Stalingrad, 93000 Bobigny, France; (E.M.); (M.H.)
| | - Michel Hanss
- Laboratoire d’Hématologie, Centre de Biologie et Pathologie Est, CHU de Lyon HCL—GH Est, 59 Boulevard Pinel, 69677 Bron, France;
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Maier S, Nickel K, Lange T, Oeltzschner G, Dacko M, Endres D, Runge K, Schumann A, Domschke K, Rousos M, Tebartz van Elst L. Increased cerebral lactate levels in adults with autism spectrum disorders compared to non-autistic controls: a magnetic resonance spectroscopy study. Mol Autism 2023; 14:44. [PMID: 37978557 PMCID: PMC10655272 DOI: 10.1186/s13229-023-00577-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023] Open
Abstract
INTRODUCTION Autism spectrum disorder (ASD) encompasses a heterogeneous group with varied phenotypes and etiologies. Identifying pathogenic subgroups could facilitate targeted treatments. One promising avenue is investigating energy metabolism, as mitochondrial dysfunction has been implicated in a subgroup of ASD. Lactate, an indicator of energy metabolic anomalies, may serve as a potential biomarker for this subgroup. This study aimed to examine cerebral lactate (Lac+) levels in high-functioning adults with ASD, hypothesizing elevated mean Lac+ concentrations in contrast to neurotypical controls (NTCs). MATERIALS AND METHODS Magnetic resonance spectroscopy (MRS) was used to study cerebral Lac+ in 71 adults with ASD and NTC, focusing on the posterior cingulate cortex (PCC). After quality control, 64 ASD and 58 NTC participants remained. Lac+ levels two standard deviations above the mean of the control group were considered elevated. RESULTS Mean PCC Lac+ levels were significantly higher in the ASD group than in the NTC group (p = 0.028; Cohen's d = 0.404), and 9.4% of the ASD group had elevated levels as compared to 0% of the NTCs (p = 0.029). No significant correlation was found between blood serum lactate levels and MRS-derived Lac+ levels. LIMITATIONS A cautious interpretation of our results is warranted due to a p value of 0.028. In addition, a higher than anticipated proportion of data sets had to be excluded due to poor spectral quality. CONCLUSION This study confirms the presence of elevated cerebral Lac+ levels in a subgroup of adults with ASD, suggesting the potential of lactate as a biomarker for mitochondrial dysfunction in a subgroup of ASD. The lower-than-expected prevalence (20% was expected) and moderate increase require further investigation to elucidate the underlying mechanisms and relationships with mitochondrial function.
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Affiliation(s)
- Simon Maier
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104, Freiburg, Germany.
| | - Kathrin Nickel
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104, Freiburg, Germany
| | - Thomas Lange
- Medical Physics, Department of Radiology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Georg Oeltzschner
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Michael Dacko
- Medical Physics, Department of Radiology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dominique Endres
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104, Freiburg, Germany
| | - Kimon Runge
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104, Freiburg, Germany
| | - Anke Schumann
- Department of General Paediatrics, Adolescent Medicine and Neonatology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104, Freiburg, Germany
| | - Michalis Rousos
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104, Freiburg, Germany
| | - Ludger Tebartz van Elst
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104, Freiburg, Germany
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19
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Nardelli A, Laskoski LV, Luiz AF, Silveira MAD, d'Arce LPG. Occurrence of mosaic trisomy 22 and pericentric inversion of chromosome 9 in a patient with a good prognosis. BMC Med Genomics 2023; 16:286. [PMID: 37957608 PMCID: PMC10644605 DOI: 10.1186/s12920-023-01709-2] [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: 02/16/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023] Open
Abstract
Complete trisomy 22 is a rare chromosomal condition that is incompatible with life. However, mosaic trisomy 22 usually has prolonged survival compatibility and may present a good prognosis depending on the tissues affected. Herein, we described a male patient with the occurrence of mosaic trisomy 22 associated with the inversion of chromosome 9, with karyotype 47, XY, inv (9) (p11q13), + 22 [5] / 46, XY, inv(9) (p11q13) [45] and arr 22q11.1 ~ q13.33(16,417008-51,219,009)x2 ~ 3. It is not possible to infer, in general, the clinical characteristics associated with mosaic trisomy 22. However, the patient presented common clinical features observed in reported cases (in parentheses the percentage observed comparing all reported cases): facial dysmorphia (100%), delay in motor development/growth (82%), cardiac abnormalities (73%), ear abnormalities (55%) and facial and/or body asymmetry (55%), in addition to hypotonia, skin spots, hypoplastic nails. Given the survival and quality of life associated with multidisciplinary treatment, it can be concluded that the patient has a good prognosis. Conclusively, we're presenting the occurrence of mosaic trisomy 22 and chromosome 9 inversion in the patient with favorable prognosis. Thus, this study proposed a guide which should be inserted in databases of rare genetic conditions to help genetic counselors define mosaic trisomy 22 diagnosis.
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Affiliation(s)
- Aline Nardelli
- Hospital Universitário do Oeste do Paraná, Western Parana State University, Avenida Tancredo Neves 3224, Santo Onofre, Cascavel, Paraná, Brazil.
| | - Larissa Valéria Laskoski
- Hospital Universitário do Oeste do Paraná, Western Parana State University, Avenida Tancredo Neves 3224, Santo Onofre, Cascavel, Paraná, Brazil
| | - Andressa Fernanda Luiz
- Hospital Universitário do Oeste do Paraná, Western Parana State University, Avenida Tancredo Neves 3224, Santo Onofre, Cascavel, Paraná, Brazil
| | | | - Luciana Paula Grégio d'Arce
- Hospital Universitário do Oeste do Paraná, Western Parana State University, Avenida Tancredo Neves 3224, Santo Onofre, Cascavel, Paraná, Brazil
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20
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Bayanbold K, Younger G, Darbro B, Sidhu A. Mosaicism in BRPF1-Related Neurodevelopmental Disorder: Report of Two Sisters and Literature Review. Case Rep Genet 2023; 2023:1692422. [PMID: 37946714 PMCID: PMC10632058 DOI: 10.1155/2023/1692422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 04/28/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023] Open
Abstract
Bromodomain and PHD finger containing 1 (BRPF1)-related neurodevelopmental disorder is characterized by intellectual disability, developmental delay, hypotonia, dysmorphic facial features, ptosis, and blepharophimosis. Both de novo and inherited pathogenic variants have been previously reported in association with this disorder. We report two affected female siblings with a novel variant in BRPF1 c.2420_2433del (p.Q807Lfs∗27) identified through whole-exome sequencing. Their history of mild intellectual disability, speech delay, attention deficient hyperactivity disorder (ADHD), and ptosis align with the features previously reported in the literature. The absence of the BRPF1 variant in parental buccal samples provides evidence of a de novo frameshift pathogenic variant, most likely as a result of parental gonadal mosaicism, which has not been previously reported. The frameshift pathogenic variant reported here lends further support to haploinsufficiency as the underlying mechanism of disease. We review the literature, compare the clinical features seen in our patients with others reported, and explore the possibility of genotype-phenotype correlation based on the location of pathogenic variants in BRPF1. Our study helps to summarize available knowledge and report the first case of a de novo frameshift pathogenic variant in BRPF1 in two siblings with this neurodevelopmental disorder.
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Affiliation(s)
- Khaliunaa Bayanbold
- Free Radical Radiation Biology, Department of Radiation Oncology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Georgianne Younger
- Division of Medical Genetics and Genomics, The Stead Family Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Benjamin Darbro
- Division of Medical Genetics and Genomics, The Stead Family Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Alpa Sidhu
- Division of Medical Genetics and Genomics, The Stead Family Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
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21
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Lee M, Lui ACY, Chan JCK, Doong PHL, Kwong AKY, Mak CCY, Li RHW, Kan ASY, Chung BHY. Revealing parental mosaicism: the hidden answer to the recurrence of apparent de novo variants. Hum Genomics 2023; 17:91. [PMID: 37798624 PMCID: PMC10557286 DOI: 10.1186/s40246-023-00535-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
Mosaicism refers to the presence of two or more populations of genetically distinct cells within an individual, all of which originate from a single zygote. Previous literature estimated the percentage of parental mosaicism ranged from 0.33 to 25.9%. In this study, parents whose children had previously been diagnosed with developmental disorders with an apparent de novo variant were recruited. Peripheral blood, buccal and semen samples were collected from these parents if available for the detection of potential parental mosaicism using droplet digital PCR, complemented with the method of blocker displacement amplification. Among the 20 families being analyzed, we report four families with parental mosaicism (4/20, 20%). Two families have maternal gonosomal mosaicism (EYA1 and EBF3) and one family has paternal gonadal mosaicism (CHD7) with a pathogenic/ likely pathogenic variant. One family has a paternal gonosomal mosaicism with a variant of uncertain significance (FLNC) with high clinical relevance. The detectable variant allele frequency in our cohort ranged from 8.7-35.9%, limit of detection 0.08-0.16% based on our in-house EBF3 assay. Detecting parental mosaicism not only informs family with a more accurate recurrence risk, but also facilitates medical teams to create appropriate plans for pregnancy and delivery, offering the most suitable care.
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Affiliation(s)
- Mianne Lee
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Adrian C Y Lui
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Joshua C K Chan
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Anna K Y Kwong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Christopher C Y Mak
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Raymond H W Li
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong SAR, China
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Anita S Y Kan
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong SAR, China
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- Prenatal Diagnostic Laboratory, Department of Obstetrics and Gynaecology, Tsan Yuk Hospital, Sai Wan Ho, Hong Kong SAR, China
| | - Brian H Y Chung
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China.
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Ngau Tau Kok, Hong Kong SAR, China.
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22
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Ansari M, Faour KNW, Shimamura A, Grimes G, Kao EM, Denhoff ER, Blatnik A, Ben-Isvy D, Wang L, Helm BM, Firth H, Breman AM, Bijlsma EK, Iwata-Otsubo A, de Ravel TJL, Fusaro V, Fryer A, Nykamp K, Stühn LG, Haack TB, Korenke GC, Constantinou P, Bujakowska KM, Low KJ, Place E, Humberson J, Napier MP, Hoffman J, Juusola J, Deardorff MA, Shao W, Rockowitz S, Krantz I, Kaur M, Raible S, Kliesch S, Singer-Berk M, Groopman E, DiTroia S, Ballal S, Srivastava S, Rothfelder K, Biskup S, Rzasa J, Kerkhof J, McConkey H, O'Donnell-Luria A, Sadikovic B, Hilton S, Banka S, Tüttelmann F, Conrad D, Talkowski ME, FitzPatrick DR, Boone PM. Heterozygous loss-of-function SMC3 variants are associated with variable and incompletely penetrant growth and developmental features. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.27.23294269. [PMID: 37808847 PMCID: PMC10557843 DOI: 10.1101/2023.09.27.23294269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 13 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated a milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, some instead having intriguing symptomatologies with rational biological links to SMC3 including bone marrow failure, acute myeloid leukemia, and Coats retinal vasculopathy. Analyses of transcriptomic and epigenetic data suggest that SMC3 pLoF variants reduce SMC3 expression but do not result in a blood DNA methylation signature clustering with that of CdLS, and that the global transcriptional signature of SMC3 loss is model-dependent. Our finding of substantial population-scale LoF intolerance in concert with variable penetrance in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multi-layered genomic data paired with careful phenotyping.
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Affiliation(s)
- Morad Ansari
- South East Scotland Genetic Service, Western General Hospital, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- These authors contributed equally
| | - Kamli N W Faour
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, US
- Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, US
- These authors contributed equally
| | - Akiko Shimamura
- Division of Hematology and Oncology, Boston Children's Hospital, Boston, MA, US
| | - Graeme Grimes
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Emeline M Kao
- Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, MA, US
| | - Erica R Denhoff
- Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, MA, US
| | - Ana Blatnik
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Clinical Cancer Genetics, Institute of Oncology Ljubljana, Ljubljana, SI
| | - Daniel Ben-Isvy
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, US
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, US
- Division of Medical Sciences, Harvard Medical School, Boston, MA, US
| | - Lily Wang
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, US
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, US
- Division of Medical Sciences, Harvard Medical School, Boston, MA, US
| | - Benjamin M Helm
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, US
| | - Helen Firth
- Clinical Genetics, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK
| | - Amy M Breman
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, US
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, NL
| | - Aiko Iwata-Otsubo
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, US
| | - Thomy J L de Ravel
- Centre for Human Genetics, UZ Leuven/ Leuven University Hospitals, Leuven, BE
| | | | - Alan Fryer
- Department of Clinical Genetics, Alder Hey Children's Hospital Liverpool, Liverpool, UK
| | | | - Lara G Stühn
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, DE
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, DE
| | - G Christoph Korenke
- University Children's Hospital Oldenburg, Department of Neuropaediatric and Metabolic Diseases, University Children's Hospital Oldenburg, Oldenburg, DE
| | - Panayiotis Constantinou
- West of Scotland Centre for Genomic Medicine, Queen Elizabeth University Hospital, Glasgow, UK
| | | | - Karen J Low
- University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
- University of Bristol, Bristol, UK
| | - Emily Place
- Massachusetts Eye and Ear Infirmary, Boston, MA, US
| | | | | | | | | | - Matthew A Deardorff
- Departments of Pathology and Pediatrics, Children's Hospital Los Angeles and University of Southern California, Los Angeles, CA, US
| | - Wanqing Shao
- Research Computing, Information Technology, Boston Children's Hospital, Boston, MA, US
| | - Shira Rockowitz
- Research Computing, Information Technology, Boston Children's Hospital, Boston, MA, US
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, US
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, US
| | - Ian Krantz
- Children's Hospital of Philadelphia, Philadelphia, PA, US
| | - Maninder Kaur
- Children's Hospital of Philadelphia, Philadelphia, PA, US
| | - Sarah Raible
- Children's Hospital of Philadelphia, Philadelphia, PA, US
| | - Sabine Kliesch
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, DE
| | - Moriel Singer-Berk
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, US
| | - Emily Groopman
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, US
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, US
| | - Stephanie DiTroia
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, US
| | - Sonia Ballal
- Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, US
- Division of Gastroenterology, Boston Children's Hospital, Boston, MA, US
| | - Siddharth Srivastava
- Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, US
- Divison of Neurology, Boston Children's Hospital, Boston, MA, US
| | | | - Saskia Biskup
- Zentrum für Humangenetik, Tübingen, DE
- Center for Genomics and Transcriptomics (CeGaT), Tübingen, DE
| | - Jessica Rzasa
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, LHSC, London, CA
| | - Jennifer Kerkhof
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, LHSC, London, CA
| | - Haley McConkey
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, LHSC, London, CA
| | - Anne O'Donnell-Luria
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, US
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, US
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, US
| | - Bekim Sadikovic
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, LHSC, London, CA
| | | | | | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, DE
| | - Donald Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Portland, OR, US
- Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland, OR, US
| | - Michael E Talkowski
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, US
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, US
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- These authors contributed equally
| | - Philip M Boone
- Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, US
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, US
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, US
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, US
- These authors contributed equally
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23
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Qian N, Weinstein JA. Volumetric imaging of an intact organism by a distributed molecular network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.553025. [PMID: 37645933 PMCID: PMC10462061 DOI: 10.1101/2023.08.11.553025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Lymphatic, nervous, and tumoral tissues, among others, exhibit physiology that emerges from three-dimensional interactions between genetically unique cells. A technology capable of volumetrically imaging transcriptomes, genotypes, and morphologies in a single de novo measurement would therefore provide a critical view into the biological complexity of living systems. Here we achieve this by extending DNA microscopy, an imaging modality that encodes a spatio-genetic map of a specimen via a massive distributed network of DNA molecules inside it, to three dimensions and multiple length scales in developing zebrafish embryos.
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Affiliation(s)
- Nianchao Qian
- Department of Medicine, Section of Genetic Medicine, University of Chicago
| | - Joshua A. Weinstein
- Department of Medicine, Section of Genetic Medicine, University of Chicago
- Pritzker School of Molecular Engineering, University of Chicago
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24
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Leal Reis I, Lopes B, Sousa P, Sousa AC, Branquinho M, Caseiro AR, Pedrosa SS, Rêma A, Oliveira C, Porto B, Atayde L, Amorim I, Alvites R, Santos JM, Maurício AC. Allogenic Synovia-Derived Mesenchymal Stem Cells for Treatment of Equine Tendinopathies and Desmopathies-Proof of Concept. Animals (Basel) 2023; 13:ani13081312. [PMID: 37106875 PMCID: PMC10135243 DOI: 10.3390/ani13081312] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Tendon and ligament injuries are frequent in sport horses and humans, and such injuries represent a significant therapeutic challenge. Tissue regeneration and function recovery are the paramount goals of tendon and ligament lesion management. Nowadays, several regenerative treatments are being developed, based on the use of stem cell and stem cell-based therapies. In the present study, the preparation of equine synovial membrane mesenchymal stem cells (eSM-MSCs) is described for clinical use, collection, transport, isolation, differentiation, characterization, and application. These cells are fibroblast-like and grow in clusters. They retain osteogenic, chondrogenic, and adipogenic differentiation potential. We present 16 clinical cases of tendonitis and desmitis, treated with allogenic eSM-MSCs and autologous serum, and we also include their evaluation, treatment, and follow-up. The concerns associated with the use of autologous serum as a vehicle are related to a reduced immunogenic response after the administration of this therapeutic combination, as well as the pro-regenerative effects from the growth factors and immunoglobulins that are part of its constitution. Most of the cases (14/16) healed in 30 days and presented good outcomes. Treatment of tendon and ligament lesions with a mixture of eSM-MSCs and autologous serum appears to be a promising clinical option for this category of lesions in equine patients.
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Affiliation(s)
- Inês Leal Reis
- Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto (ICETA), Rua D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 1300-477 Lisboa, Portugal
- Cooperativa de Ensino Superior Politécnico e Universitário (CESPU), Avenida Central de Gandra 1317, 4585-116 Gandra, Portugal
| | - Bruna Lopes
- Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto (ICETA), Rua D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Patrícia Sousa
- Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto (ICETA), Rua D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Ana Catarina Sousa
- Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto (ICETA), Rua D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Mariana Branquinho
- Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto (ICETA), Rua D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Ana Rita Caseiro
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto (ICETA), Rua D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 1300-477 Lisboa, Portugal
- University School Vasco da Gama (EUVG), Avenida José R. Sousa Fernandes, 3020-210 Coimbra, Portugal
- Vasco da Gama Research Center (CIVG), University School Vasco da Gama (EUVG), Avenida José R. Sousa Fernandes, 3020-210 Coimbra, Portugal
| | - Sílvia Santos Pedrosa
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto (ICETA), Rua D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 1300-477 Lisboa, Portugal
- Centro de Biotecnologia e Química Fina (CBQF), Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua de Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Alexandra Rêma
- Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto (ICETA), Rua D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Cláudia Oliveira
- Laboratório de Citogenética, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal
| | - Beatriz Porto
- Laboratório de Citogenética, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal
| | - Luís Atayde
- Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto (ICETA), Rua D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Irina Amorim
- Departamento de Patologia e Imunologia Molecular, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto (UP), Rua Alfredo Allen, 4200-135 Porto, Portugal
| | - Rui Alvites
- Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto (ICETA), Rua D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 1300-477 Lisboa, Portugal
- Cooperativa de Ensino Superior Politécnico e Universitário (CESPU), Avenida Central de Gandra 1317, 4585-116 Gandra, Portugal
| | - Jorge Miguel Santos
- Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto (ICETA), Rua D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Ana Colette Maurício
- Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto (UP), Rua de Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal
- Centro de Estudos de Ciência Animal (CECA), Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto (ICETA), Rua D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 1300-477 Lisboa, Portugal
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25
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Limitations of gene editing assessments in human preimplantation embryos. Nat Commun 2023; 14:1219. [PMID: 36882397 PMCID: PMC9992379 DOI: 10.1038/s41467-023-36820-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 02/17/2023] [Indexed: 03/09/2023] Open
Abstract
Range of DNA repair in response to double-strand breaks induced in human preimplantation embryos remains uncertain due to the complexity of analyzing single- or few-cell samples. Sequencing of such minute DNA input requires a whole genome amplification that can introduce artifacts, including coverage nonuniformity, amplification biases, and allelic dropouts at the target site. We show here that, on average, 26.6% of preexisting heterozygous loci in control single blastomere samples appear as homozygous after whole genome amplification indicative of allelic dropouts. To overcome these limitations, we validate on-target modifications seen in gene edited human embryos in embryonic stem cells. We show that, in addition to frequent indel mutations, biallelic double-strand breaks can also produce large deletions at the target site. Moreover, some embryonic stem cells show copy-neutral loss of heterozygosity at the cleavage site which is likely caused by interallelic gene conversion. However, the frequency of loss of heterozygosity in embryonic stem cells is lower than in blastomeres, suggesting that allelic dropouts is a common whole genome amplification outcome limiting genotyping accuracy in human preimplantation embryos.
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Phenotype, genotype, and management of congenital fibrosis of extraocular muscles type 1 in 16 Chinese families. Graefes Arch Clin Exp Ophthalmol 2023; 261:879-889. [PMID: 36138147 PMCID: PMC9988770 DOI: 10.1007/s00417-022-05830-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/18/2022] [Accepted: 09/07/2022] [Indexed: 11/04/2022] Open
Abstract
PURPOSE Congenital fibrosis of extraocular muscles type 1 (CFEOM1), a classical subtype of CFEOM, is characterized by restrictive ophthalmoplegia and ptosis. It is mainly caused by aberrant neural innervation of the extraocular muscles. This study aimed to investigate the genetic characteristics and clinical manifestations of CFEOM1 in Chinese families. METHODS The clinical data, including ocular examinations, magnetic resonance imaging (MRI), and surgical procedures of affected individuals from 16 Chinese CFEOM1 families, were collected. The genomic DNA of 16 probands and their family members were sequenced for causative KIF21A gene mutations. Linkage analysis using microsatellite markers across KIF21A was also conducted. RESULTS Affected individuals were presented with bilateral non-progressive ptosis, restricted horizontal eye movement, fixed infraduction of both eyes, compensatory chin-up head position, and neuromuscular abnormalities. Three heterozygous KIF21A mutations, c.2860C > T (p.R954W) (in eight families), c.2861G > T (p.R954L) (in two families), and c.2861G > A (p.R954Q) (in two families) were identified, which implied that hotspot mutations were common in Chinese CFEOM1 families. Germline Mosaicism was likely to be the cause of affected individuals with asymptomatic parents without KIF21A mutations presented in the eight families. Two affected individuals underwent modified levator muscle complex suspension surgery and achieved a good result without any complications. CONCLUSION Instead of evaluating the whole CFEOM1 gene variant, hotspot mutations could be given priority for screening. The occurrence of germline mosaicism has to be taken into account in genetic counseling. Patients with CFEOM1 who have ptosis may benefit from an innovative surgical procedure called modified levator muscle complex suspension.
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Grave-to-cradle: human embryonic lineage tracing from the postmortem body. Exp Mol Med 2023; 55:13-21. [PMID: 36599930 PMCID: PMC9898511 DOI: 10.1038/s12276-022-00912-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/02/2022] [Accepted: 10/13/2022] [Indexed: 01/06/2023] Open
Abstract
Curiosity concerning the process of human creation has been around for a long time. Relevant questions seemed to be resolved with the knowledge of how cells divide after fertilization obtained through in vitro fertilization experiments. However, we still do not know how human life is created at the cellular level. Recently, the value of cadavers as a resource from which to obtain "normal" cells and tissues has been established, and human research using postmortem bodies has attracted growing scientific attention. As the human genome can be analyzed at the level of nucleotides through whole-genome sequencing, individual cells in a postmortem body can be traced back to determine what developmental processes have transpired from fertilization. These retrospective lineage tracing studies have answered several unsolved questions on how humans are created. This review covers the methodologies utilized in lineage tracing research in a historical context and the conceptual basis for reconstructing the division history of cells in a retrospective manner using postzygotic somatic variants in postmortem tissue. We further highlight answers that postmortem research could potentially address and discuss issues that wait to be solved in the future.
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Martínez-Hernández A, Martínez-Anaya D, Durán-McKinster C, Del Castillo-Ruiz V, Navarrete-Meneses P, Córdova EJ, Villegas-Torres BE, Ruiz-Herrera A, Juárez-Velázquez R, Yokoyama-Rebollar E, Cervantes-Barragán D, Pedraza-Meléndez A, Orozco L, Pérez-Vera P, Salas-Labadía C. Pigmentary mosaicism as a recurrent clinical manifestation in three new patients with mosaic trisomy 12 diagnosed postnatally: cases report and literature review. BMC Med Genomics 2022; 15:224. [PMCID: PMC9620619 DOI: 10.1186/s12920-022-01382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/22/2022] [Indexed: 11/10/2022] Open
Abstract
Background To date, only twenty-one cases diagnosed postnatally with mosaic trisomy 12 have been reported. The most frequent phenotypic manifestations are developmental delay, dysmorphic facial features, congenital heart defects, digital alterations, and pigmentary disorders. In the present report, detailed clinical and genetic profiles of three unrelated new patients with mosaic trisomy 12 are described and compared with previously reported cases. Case presentation In the present report, we include the clinical, cytogenetic, and molecular description of three Mexican patients diagnosed postnatally with mosaic trisomy 12. At phenotypic level, the three patients present with developmental delay, dysmorphic facial features, congenital heart defects and skin pigmentary anomalies. Particularly, patient 1 showed unique eye alterations as bilateral distichiasis, triple rows of upper lashes, and digital abnormalities. In patient 2 redundant skin, severe hearing loss, and hypotonia were observed, and patient 3 presented with hypertelorism and telecanthus. Hyperpigmentation with disseminated pigmentary anomalies is a common trait in all of them. The cytogenetic study was carried out under the strict criteria of analysis, screening 50–100 metaphases from three different tissues, showing trisomy 12 mosaicism in at least one of the three different tissues analyzed. With SNParray, the presence of low-level mosaic copy number variants not previously detected by cytogenetics, and uniparental disomy of chromosome 12, was excluded. STR markers allowed to confirm the absence of uniparental disomy as well as to know the parental origin of supernumerary chromosome 12. Conclusions The detailed clinical, cytogenetic, and molecular description of these three new patients, contributes with relevant information to delineate more accurately a group of patients that show a heterogeneous phenotype, although sharing the same chromosomal alteration. The possibility of detecting mosaic trisomy 12 is directly associated with the sensitivity of the methodology applied to reveal the low-level chromosomal mosaicism, as well as with the possibility to perform the analysis in a suitable tissue.
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Affiliation(s)
- A. Martínez-Hernández
- grid.452651.10000 0004 0627 7633Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica SS, Ciudad de Mexico, México
| | - D. Martínez-Anaya
- grid.419216.90000 0004 1773 4473Laboratorio de Genética y Cáncer, Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, 04530 México
| | - C. Durán-McKinster
- grid.419216.90000 0004 1773 4473Departamento de Dermatología, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - V. Del Castillo-Ruiz
- grid.419216.90000 0004 1773 4473Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - P. Navarrete-Meneses
- grid.419216.90000 0004 1773 4473Laboratorio de Genética y Cáncer, Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, 04530 México
| | - E. J. Córdova
- grid.452651.10000 0004 0627 7633Consorcio de Oncogenómica, Instituto Nacional de Medicina Genómica SS, Ciudad de Mexico, México
| | - B. E. Villegas-Torres
- grid.452651.10000 0004 0627 7633Instituto Nacional de Medicina Genómica SS, Ciudad de Mexico, México
| | - A. Ruiz-Herrera
- grid.414465.6Hospital de Especialidades Pediátrico de León, León, Guanajuato, México
| | - R. Juárez-Velázquez
- grid.419216.90000 0004 1773 4473Laboratorio de Genética y Cáncer, Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, 04530 México
| | - E. Yokoyama-Rebollar
- grid.419216.90000 0004 1773 4473Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - D. Cervantes-Barragán
- grid.502779.e0000 0004 0633 6373Hospital Central Sur de Alta Especialidad, PEMEX, Ciudad de Mexico, México
| | - A. Pedraza-Meléndez
- grid.9486.30000 0001 2159 0001Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de Mexico, México
| | - L. Orozco
- grid.452651.10000 0004 0627 7633Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica SS, Ciudad de Mexico, México
| | - P. Pérez-Vera
- grid.419216.90000 0004 1773 4473Laboratorio de Genética y Cáncer, Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, 04530 México
| | - C. Salas-Labadía
- grid.419216.90000 0004 1773 4473Laboratorio de Genética y Cáncer, Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, 04530 México
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Feresin A, Stampalija T, Cappellani S, Bussani R, Faletra F, Murru F, Ulivi S, Suergiu S, Savarese P, Pedicini A, Policicchio M, Ruggiero R, Bosio B, Savarese G, Ardisia C. Case Report: Two cases of apparent discordance between non-invasive prenatal testing (NIPT) and amniocentesis resulting in feto-placental mosaicism of trisomy 21. Issues in diagnosis, investigation and counselling. Front Genet 2022; 13:982508. [PMID: 36386832 PMCID: PMC9642548 DOI: 10.3389/fgene.2022.982508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022] Open
Abstract
The sequencing of cell-free fetal DNA in the maternal plasma through non-invasive prenatal testing (NIPT) is an accurate genetic screening test to detect the most common fetal aneuploidies during pregnancy. The extensive use of NIPT, as a screening method, has highlighted the limits of the technique, including false positive and negative results. Feto-placental mosaicism is a challenging biological issue and is the most frequent cause of false positive and negative results in NIPT screening, and of discrepancy between NIPT and invasive test results. We are reporting on two cases of feto-placental mosaicism of trisomy 21, both with a low-risk NIPT result, identified by ultrasound signs and a subsequent amniocentesis consistent with a trisomy 21. In both cases, after the pregnancy termination, cytogenetic and/or cytogenomic analyses were performed on the placenta and fetal tissues, showing in the first case a mosaicism of trisomy 21 in both the placenta and the fetus, but a mosaicism in the placenta and a complete trisomy 21 in the fetus in the second case. These cases emphasize the need for accurate and complete pre-test NIPT counselling, as well as to identify situations at risk for a possible false negative NIPT result, which may underestimate a potential pathological condition, such as feto-placental mosaicism or fetal trisomy. Post-mortem molecular autopsy may discriminate between placental, fetal and feto-placental mosaicism, and between complete or mosaic fetal chromosomal anomalies. A multidisciplinary approach in counselling, as well as in the interpretation of biological events, is essential for the clarification of complex cases, such as feto-placental mosaicisms.
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Affiliation(s)
- Agnese Feresin
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Tamara Stampalija
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Stefania Cappellani
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Rossana Bussani
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
- Unit of Pathologic Anatomy and Histology, Asugi, Trieste, Italy
| | - Flavio Faletra
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Flora Murru
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Sheila Ulivi
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Sarah Suergiu
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | | | | | | | | | - Barbara Bosio
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | | | - Carmela Ardisia
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
- *Correspondence: Carmela Ardisia,
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Sherer DM, Hsieh V, Hall A, Gerren A, Walters E, Dalloul M. Current Perspectives of Prenatal Cell-free DNA Screening in Clinical Management of First-Trimester Septated Cystic Hygroma. Int J Womens Health 2022; 14:1499-1518. [PMID: 36325393 PMCID: PMC9621220 DOI: 10.2147/ijwh.s328201] [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: 04/28/2022] [Accepted: 08/08/2022] [Indexed: 11/07/2022] Open
Abstract
First-trimester septated cystic hygroma occurs in approximately 1 in 268 pregnancies and has long been associated with a markedly increased risk of fetal aneuploidy and, among euploid fetuses, an increased risk of structural anomalies primarily affecting the cardiac and skeletal systems. Invasive prenatal diagnosis – chorionic villus sampling and/or amniocentesis – encompasses the time-honored clinical tools for the next step in management following prenatal sonographic diagnosis of first-trimester septated cystic hygroma. Currently, prenatal cell-free DNA (cfDNA) screening for fetal aneuploidy with select microdeletions is gradually replacing the considerably less sensitive, and labor-intensive combined first-trimester screening. These new technologies have opened potential new venues in the clinical management of this ominous late first-trimester sonographic diagnosis. Advances in cfDNA technologies are now permitting detection of chromosomal copy number variants (CNV) larger than 7Mb across genome and select serious single-gene disorders (mainly impacting skeletal and neurological development), affecting quality of life and may benefit from medical and/or surgical management. This commentary will address the available non-invasive prenatal screening technologies, which clearly enhance immediate genetic analysis modalities applicable in the presence of the complex sonographic finding of first-trimester septated cystic hygroma.
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Affiliation(s)
- David M Sherer
- The Division of Maternal Fetal Medicine, the Department of Obstetrics and Gynecology, State University of New York (SUNY), Downstate Health Sciences University, Brooklyn, New York, USA,Correspondence: David M Sherer, Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, State University of New York (SUNY), Downstate Health Sciences University, 450 Clarkson Avenue, Box 24, Brooklyn, NY, 11203, USA, Tel +001-718-270-2081, Fax +001-718-270-4122, Email
| | - Vicky Hsieh
- The Division of Maternal Fetal Medicine, the Department of Obstetrics and Gynecology, State University of New York (SUNY), Downstate Health Sciences University, Brooklyn, New York, USA
| | - Anika Hall
- The Division of Maternal Fetal Medicine, the Department of Obstetrics and Gynecology, State University of New York (SUNY), Downstate Health Sciences University, Brooklyn, New York, USA
| | - Allison Gerren
- The Division of Maternal Fetal Medicine, the Department of Obstetrics and Gynecology, State University of New York (SUNY), Downstate Health Sciences University, Brooklyn, New York, USA
| | - Erin Walters
- The Division of Maternal Fetal Medicine, the Department of Obstetrics and Gynecology, State University of New York (SUNY), Downstate Health Sciences University, Brooklyn, New York, USA
| | - Mudar Dalloul
- The Division of Maternal Fetal Medicine, the Department of Obstetrics and Gynecology, State University of New York (SUNY), Downstate Health Sciences University, Brooklyn, New York, USA
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Bai H, Li X, Liu X, Shi W, He B, Wei R, Shi J. Preimplantation genetic testing for recurrent autosomal dominant osteogenesis imperfecta associated with paternal gonosomal mosaicism. Front Genet 2022; 13:1011833. [PMID: 36276971 PMCID: PMC9579439 DOI: 10.3389/fgene.2022.1011833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/22/2022] [Indexed: 11/22/2022] Open
Abstract
Research Question: How to prevent the transfer of a mutation causing osteogenesis imperfecta (OI) to offspring in a couple with recurrent adverse pregnancy outcomes, when the male partner is a gonosomal mosaic carrier. Design: High-throughput sequencing and first-generation DNA sequencing were performed using the tissues from an aborted fetus and its parents. Regions 2 Mb upstream and downstream of the COL1A1 gene were subjected to multiplex PCR to identify single nucleotide polymorphisms (SNPs) and family haplotypes associated with the disease-causing mutation. Single-cell whole-genome amplification and sequencing were performed on trophoblasts cultured in vitro for 5–6 days to construct embryonic SNP haplotypes, and first-generation sequencing was used for pathogenic locus verification and aneuploidy screening. Preimplantation genetic testing for monogenic disorders (PGT-M) was also performed. Results: The aborted fetus was heterozygous for the COL1A1 mutation c.1454G>A (chr17-48272089, p.Gly485Asp) suspected to cause OI. The variant was also detected in the peripheral blood cells and sperm of the male partner, who appeared to be a gonosomal mosaic carrier of the mutation. Three morphologically usable blastocysts were obtained in vitro and successfully expanded after a trophectoderm biopsy. Two blastocysts were unusable owing to aneuploidy; however, one was euploid and did not carry the paternal mutation. Post-transfer gestation was confirmed by systematic B-scan ultrasound, and amniocentesis findings were consistent with the PGT-M results. Conclusion: Parental gonadal mosaicism was the cause of recurrent terminated pregnancies due to fetal skeletal dysplasia. Using PGT-M to select embryos without the paternal pathogenic mutation prevented the vertical transmission of OI in this family, and a successful pregnancy was achieved.
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Affiliation(s)
- Haiyan Bai
- The ART Center, Northwest Women’s and Children’s Hospital, Xi’an, China
| | - Xiaofang Li
- The ART Center, Northwest Women’s and Children’s Hospital, Xi’an, China
| | - Xitong Liu
- The ART Center, Northwest Women’s and Children’s Hospital, Xi’an, China
| | - Wenhao Shi
- The ART Center, Northwest Women’s and Children’s Hospital, Xi’an, China
| | - Bin He
- Genetic Medical Center, Xi’an, Jiangsu, China
| | | | - Juanzi Shi
- The ART Center, Northwest Women’s and Children’s Hospital, Xi’an, China
- *Correspondence: Juanzi Shi,
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Bi W, Yuan B, Liu P, Murry JB, Qin X, Xia F, Quach T, Cooper LM, Wiszniewska J, Hixson P, Peacock S, Tonk VS, Huff RW, Ortega V, Lupski JR, Scherer SE, Littlejohn RO, Velagaleti GVN, Roeder ER, Cheung SW. Recurring germline mosaicism in a family due to reversion of an inherited derivative chromosome 8 from an 8;21 translocation with interstitial telomeric sequences. J Med Genet 2022; 60:547-556. [PMID: 36150828 DOI: 10.1136/jmg-2022-108586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/14/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Mosaicism for chromosomal structural abnormalities, other than marker or ring chromosomes, is rarely inherited. METHODS We performed cytogenetics studies and breakpoint analyses on a family with transmission of mosaicism for a derivative chromosome 8 (der(8)), resulting from an unbalanced translocation between the long arms of chromosomes 8 and 21 over three generations. RESULTS The proband and his maternal half-sister had mosaicism for a der(8) cell line leading to trisomy of the distal 21q, and both had Down syndrome phenotypic features. Mosaicism for a cell line with the der(8) and a normal cell line was also detected in a maternal half-cousin. The der(8) was inherited from the maternal grandmother who had four abnormal cell lines containing the der(8), in addition to a normal cell line. One maternal half-aunt had the der(8) and an isodicentric chromosome 21 (idic(21)). Sequencing studies revealed microhomologies at the junctures of the der(8) and idic(21) in the half-aunt, suggesting a replicative mechanism in the rearrangement formation. Furthermore, interstitial telomeric sequences (ITS) were identified in the juncture between chromosomes 8 and 21 in the der(8). CONCLUSION Mosaicism in the proband, his half-sister and half-cousin resulting from loss of chromosome 21 material from the der(8) appears to be a postzygotic event due to the genomic instability of ITS and associated with selective growth advantage of normal cells. The reversion of the inherited der(8) to a normal chromosome 8 in this family resembles revertant mosaicism of point mutations. We propose that ITS could mediate recurring revertant mosaicism for some constitutional chromosomal structural abnormalities.
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Affiliation(s)
- Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - Jaclyn B Murry
- Baylor Genetics, Houston, Texas, USA.,Department of Pathology, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | | | | | - Joanna Wiszniewska
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pathology and Laboratory Medicine, Oregon Health and Science University, Portland, Oregon, USA
| | | | - Sandra Peacock
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - Vijay S Tonk
- Departments of Pediatrics, Obstetrics and Gynecology, Pathology, Texas Tech University Health Science Centers, Lubbock, Texas, USA
| | - Robert W Huff
- Department of Obstetrics and Gynecology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Veronica Ortega
- Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Steven E Scherer
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Rebecca Okashah Littlejohn
- Department of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, San Antonio, Texas, USA
| | - Gopalrao V N Velagaleti
- Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Elizabeth R Roeder
- Department of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, San Antonio, Texas, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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Huang SJ, Amendola LM, Sternen DL. Variation among DNA banking consent forms: points for clinicians to bank on. J Community Genet 2022; 13:389-397. [PMID: 35834113 DOI: 10.1007/s12687-022-00601-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/07/2022] [Indexed: 11/24/2022] Open
Abstract
Deoxyribonucleic acid (DNA) banking is an important laboratory service that preserves the option of future genetic testing. DNA bank consent forms are a critical tool to facilitate thorough and valid informed consent. The objectives of this study were to assess the level of consistency of current clinical DNA banking consent forms with the American Society of Human Genetics (ASHG) and the American College of Medical Genetics and Genomics (ACMG) guidance and to explore variation among the forms. The content analysis matrix included key points identified from the ASHG and ACMG documents (including benefits/risks, sample storage, access, disposition, and communication) and additional points beyond the ASHG and ACMG documents identified from the consent forms themselves during the analysis process. Forms were assessed for language addressing each point. Five consent forms were identified and analyzed for twelve key points and eight additional points. The average consistency for key points was 10.8/12 (range 8/12 to 12/12). The range for additional points was 1/8 to 5/8. There was variation across forms in the details provided related to key and additional points. Gaps in clinical DNA banking consent forms are barriers to achieving informed consent. Clinicians can consider the consent key and additional points discussed here to supplement and enrich their clinical DNA banking informed consent discussions, promote stewardship, and maximize downstream utility of banked DNA. The identification of multiple additional points beyond the ASHG and ACMG documents' key points indicates a need for this guidance to be updated.
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Affiliation(s)
- Samuel J Huang
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA.
| | - Laura M Amendola
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Darci L Sternen
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA, USA
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Wasilewska K, Gambin T, Rydzanicz M, Szczałuba K, Płoski R. Postzygotic mutations and where to find them - Recent advances and future implications in the field of non-neoplastic somatic mosaicism. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108426. [PMID: 35690331 DOI: 10.1016/j.mrrev.2022.108426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/05/2022] [Accepted: 06/03/2022] [Indexed: 01/01/2023]
Abstract
The technological progress of massively parallel sequencing (MPS) has triggered a remarkable development in the research on postzygotic mutations. Although the overwhelming majority of studies in the field focus on oncogenesis, non-neoplastic diseases are attracting more and more attention. The aim of this review was to summarize some of the most recent findings in the field of somatic mosaicism in diseases other than neoplastic events. We discuss the abundance and role of postzygotic mutations, with a special emphasis on disorders which occur only in a mosaic form (obligatory mosaic diseases; OMDs). Based on the list of OMDs compiled from the published literature and three databases (OMIM, Orphanet and MosaicBase), we demonstrate the prevalence of cancer-related genes across OMDs and suggest other sources to further explore OMDs and OMD-related genes. Additionally, we comment on some practical aspects related to mosaic diseases, such as approaches to tissue sampling, the MPS coverage required to detect variants at a very low frequency, as well as on bioinformatic and molecular tools dedicated to detect somatic mutations in MPS data.
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Affiliation(s)
- Krystyna Wasilewska
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Nowowiejska 15/19, 00-665 Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland.
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Abstract
Genetic studies of human traits have revolutionized our understanding of the variation between individuals, and yet, the genetics of most traits is still poorly understood. In this review, we highlight the major open problems that need to be solved, and by discussing these challenges provide a primer to the field. We cover general issues such as population structure, epistasis and gene-environment interactions, data-related issues such as ancestry diversity and rare genetic variants, and specific challenges related to heritability estimates, genetic association studies, and polygenic risk scores. We emphasize the interconnectedness of these problems and suggest promising avenues to address them.
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Affiliation(s)
- Nadav Brandes
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Omer Weissbrod
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Michal Linial
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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Xiao M, Shi H, Rao J, Xi Y, Zhang S, Wu J, Zhu S, Zhou J, Xu H, Lei C, Sun X. Combined Preimplantation Genetic Testing for Genetic Kidney Disease: Genetic Risk Identification, Assisted Reproductive Cycle, and Pregnancy Outcome Analysis. Front Med (Lausanne) 2022; 9:936578. [PMID: 35783601 PMCID: PMC9247246 DOI: 10.3389/fmed.2022.936578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Background Genetic kidney disease is a major cause of morbidity and mortality in neonates and end-stage renal disease (ESRD) in children and adolescents. Genetic diagnosis provides key information for early identification of congenital kidney disease and reproductive risk counseling. Preimplantation genetic testing for monogenic disease (PGT-M) as a reproductive technology helps prospective parents to prevent passing on disease-causing mutations to their offspring. Materials and Methods A retrospective cohort of couples counseled on PGT who had a risk to given birth to a child with genetic kidney disease or had a history of prenatal fetal kidney and urinary system development abnormalities from 2011 to 2021. Through a combination of simultaneously screening for aneuploidy and monogenic kidney disease, we achieved reproductive genetic intervention. Results A total of 64 couples counseled on PGT for monogenic kidney disease in a single reproductive center during the past 10 years, of whom 38 different genetic kidney diseases were identified. The most frequent indications for referral were autosomal recessive disease (54.7%), then autosomal dominant disease (29.7%), and X-linked disease (15.6%). Polycystic kidney disease was the most common diseases counted for 34.4%. After oocyte-retrieval in all of 64 females, a total of 339 embryos were diagnosed and 63 embryos were transferred in succession. Among 61 cycles of frozen-embryo transfer (FET), ongoing pregnancy/live birth rate (OP/LBR) reached 57.38%. The cumulative OP/LBR in our cohort for the 64 couples was 54.69%. In addition, we have carried out expanded carrier screening (ECS) in all the in vitro fertilization (IVF) couples performed PGT covering 7,311 individuals. The carrier frequency of the candidate genes for monogenic kidney diseases accounted for 12.19%. Conclusion Overall, the customization PGT-M plan in our IVF center is pivotal to decreasing the morbidity and implementing reproductive genetic intervention of genetic kidney disease.
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Affiliation(s)
- Min Xiao
- Shanghai Ji Ai Genetics and IVF Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Hua Shi
- Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China
| | - Jia Rao
- Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China
| | - Yanping Xi
- Shanghai Ji Ai Genetics and IVF Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Shuo Zhang
- Shanghai Ji Ai Genetics and IVF Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Junping Wu
- Shanghai Ji Ai Genetics and IVF Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Saijuan Zhu
- Shanghai Ji Ai Genetics and IVF Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Jing Zhou
- Shanghai Ji Ai Genetics and IVF Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Hong Xu
- Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China
| | - Caixia Lei
- Shanghai Ji Ai Genetics and IVF Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics and IVF Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
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Zhu W, Deo RC, MacRae CA. Single Cell Biology: Exploring Somatic Cell Behaviors, Competition and Selection in Chronic Disease. Front Pharmacol 2022; 13:867431. [PMID: 35656307 PMCID: PMC9152313 DOI: 10.3389/fphar.2022.867431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
The full range of cell functions is under-determined in most human diseases. The evidence that somatic cell competition and clonal imbalance play a role in non-neoplastic chronic disease reveal a need for a dedicated effort to explore single cell function if we are to understand the mechanisms by which cell population behaviors influence disease. It will be vital to document not only the prevalent pathologic behaviors but also those beneficial functions eliminated or suppressed by competition. An improved mechanistic understanding of the role of somatic cell biology will help to stratify chronic disease, define more precisely at an individual level the role of environmental factors and establish principles for prevention and potential intervention throughout the life course and across the trajectory from wellness to disease.
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Affiliation(s)
- Wandi Zhu
- Cardiovascular Medicine Division and Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Rahul C Deo
- Cardiovascular Medicine Division and Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Calum A MacRae
- Cardiovascular Medicine Division and Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
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38
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Lehmann U, Stenzinger A. [The molecular pathological breviary: allele frequencies in NGS analysis]. DER PATHOLOGE 2022; 43:154-156. [PMID: 34643753 DOI: 10.1007/s00292-021-01003-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Ulrich Lehmann
- Molekularpathologie, Institut für Pathologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, OE 5110, 30625, Hannover, Deutschland.
| | - Albrecht Stenzinger
- Molekularpathologisches Zentrum, Pathologisches Institut, Universität Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Deutschland
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Parada CA, El‐Ghazali FM, Toglia D, Ruzevick J, McAvoy M, Emerson S, Karasozen Y, Busald T, Nazem AA, Suranowitz SM, Shalhub S, Marshall DA, Gonzalez‐Cuyar LF, Dorschner MO, Ferreira M. Somatic Mosaicism of a PDGFRB Activating Variant in Aneurysms of the Intracranial, Coronary, Aortic, and Radial Artery Vascular Beds. J Am Heart Assoc 2022; 11:e024289. [PMID: 35156398 PMCID: PMC9245804 DOI: 10.1161/jaha.121.024289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background Activating variants in platelet‐derived growth factor receptor beta (PDGFRB), including a variant we have previously described (p.Tyr562Cys [g.149505130T>C [GRCh37/hg19]; c.1685A>G]), are associated with development of multiorgan pathology, including aneurysm formation. To investigate the association between the allele fraction genotype and histopathologic phenotype, we performed an expanded evaluation of post‐mortem normal and aneurysmal tissue specimens from the previously published index patient. Methods and Results Following death due to diffuse subarachnoid hemorrhage in a patient with mosaic expression of the above PDGFRB variant, specimens from the intracranial, coronary, radial and aortic arteries were harvested. DNA was extracted and alternate allele fractions (AAF) of PDGFRB were determined using digital droplet PCR. Radiographic and histopathologic findings, together with genotype expression of PDGFRB were then correlated in aneurysmal tissue and compared to non‐aneurysmal tissue. The PDGFRB variant was identified in the vertebral artery, basilar artery, and P1 segment aneurysms (AAF: 28.7%, 16.4%, and 17.8%, respectively). It was also identified in the coronary and radial artery aneurysms (AAF: 22.3% and 20.6%, respectively). In phenotypically normal intracranial and coronary artery tissues, the PDGFRB variant was not present. The PDGFRB variant was absent from lymphocyte DNA and normal tissue, confirming it to be a non‐germline somatic variant. Primary cell cultures from a radial artery aneurysm localized the PDGFRB variant to CD31‐, non‐endothelial cells. Conclusions Constitutive expression of PDGFRB within the arterial wall is associated with the development of human fusiform aneurysms. The role of targeted therapy with tyrosine kinase inhibitors in fusiform aneurysms with PDGFRB mutations should be further studied.
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Affiliation(s)
- Carolina A. Parada
- Departments of Neurosurgery University of Washington School of MedicineUniversity of Washington Medical Center Seattle WA
| | - Fatima M. El‐Ghazali
- Departments of Neurosurgery University of Washington School of MedicineUniversity of Washington Medical Center Seattle WA
| | - Daphne Toglia
- Departments of Neurosurgery University of Washington School of MedicineUniversity of Washington Medical Center Seattle WA
| | - Jacob Ruzevick
- Departments of Neurosurgery University of Washington School of MedicineUniversity of Washington Medical Center Seattle WA
| | - Malia McAvoy
- Departments of Neurosurgery University of Washington School of MedicineUniversity of Washington Medical Center Seattle WA
| | - Samuel Emerson
- Departments of Neurosurgery University of Washington School of MedicineUniversity of Washington Medical Center Seattle WA
| | - Yigit Karasozen
- Departments of Neurosurgery University of Washington School of MedicineUniversity of Washington Medical Center Seattle WA
| | - Tina Busald
- Departments of Neurosurgery University of Washington School of MedicineUniversity of Washington Medical Center Seattle WA
| | - Ahmad A. Nazem
- Departments of Neurosurgery University of Washington School of MedicineUniversity of Washington Medical Center Seattle WA
| | - Shaun M. Suranowitz
- Departments of Neurosurgery University of Washington School of MedicineUniversity of Washington Medical Center Seattle WA
| | - Sherene Shalhub
- Division of Vascular Surgery University of Washington School of MedicineUniversity of Washington Medical Center Seattle WA
| | - Desiree A. Marshall
- Division of Neuropathology Department of Laboratory Medicine and Pathology University of Washington School of MedicineHarborview Medical Center Seattle WA
| | - Luis F. Gonzalez‐Cuyar
- Division of Neuropathology Department of Laboratory Medicine and Pathology University of Washington School of MedicineHarborview Medical Center Seattle WA
| | - Michael O. Dorschner
- Departments of Genome Sciences University of Washington School of MedicineUniversity of Washington Medical Center Seattle WA
| | - Manuel Ferreira
- Departments of Neurosurgery University of Washington School of MedicineUniversity of Washington Medical Center Seattle WA
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Establishment of reference standards for multifaceted mosaic variant analysis. Sci Data 2022; 9:35. [PMID: 35115554 PMCID: PMC8813952 DOI: 10.1038/s41597-022-01133-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/20/2021] [Indexed: 11/21/2022] Open
Abstract
Detection of somatic mosaicism in non-proliferative cells is a new challenge in genome research, however, the accuracy of current detection strategies remains uncertain due to the lack of a ground truth. Herein, we sought to present a set of ultra-deep sequenced WES data based on reference standards generated by cell line mixtures, providing a total of 386,613 mosaic single-nucleotide variants (SNVs) and insertion-deletion mutations (INDELs) with variant allele frequencies (VAFs) ranging from 0.5% to 56%, as well as 35,113,417 non-variant and 19,936 germline variant sites as a negative control. The whole reference standard set mimics the cumulative aspect of mosaic variant acquisition such as in the early developmental stage owing to the progressive mixing of cell lines with established genotypes, ultimately unveiling 741 possible inter-sample relationships with respect to variant sharing and asymmetry in VAFs. We expect that our reference data will be essential for optimizing the current use of mosaic variant detection strategies and for developing algorithms to enable future improvements. Measurement(s) | genotype | Technology Type(s) | DNA sequencing | Factor Type(s) | genotyping | Sample Characteristic - Organism | Homo sapiens | Sample Characteristic - Environment | cell line |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.16970041
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Datta S, Patel M, Kashyap S, Patel D, Singh U. Chimeric chromosome landscapes of human somatic cell cultures show dependence on stress and regulation of genomic repeats by CGGBP1. Oncotarget 2022; 13:136-155. [PMID: 35070079 PMCID: PMC8765472 DOI: 10.18632/oncotarget.28174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/20/2021] [Indexed: 11/25/2022] Open
Abstract
Genomes of somatic cells in culture are prone to spontaneous mutations due to errors in replication and DNA repair. Some of these errors, such as chromosomal fusions, are not rectifiable and subject to selection or elimination in growing cultures. Somatic cell cultures are thus expected to generate background levels of potentially stable chromosomal chimeras. A description of the landscape of such spontaneously generated chromosomal chimeras in cultured cells will help understand the factors affecting somatic mosaicism. Here we show that short homology-associated non-homologous chromosomal chimeras occur in normal human fibroblasts and HEK293T cells at genomic repeats. The occurrence of chromosomal chimeras is enhanced by heat stress and depletion of a repeat regulatory protein CGGBP1. We also present evidence of homologous chromosomal chimeras between allelic copies in repeat-rich DNA obtained by methylcytosine immunoprecipitation. The formation of homologous chromosomal chimeras at Alu and L1 repeats increases upon depletion of CGGBP1. Our data are derived from de novo sequencing from three different cell lines under different experimental conditions and our chromosomal chimera detection pipeline is applicable to long as well as short read sequencing platforms. These findings present significant information about the generation, sensitivity and regulation of somatic mosaicism in human cell cultures.
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Affiliation(s)
- Subhamoy Datta
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
| | - Manthan Patel
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AD, UK
| | - Sukesh Kashyap
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
| | - Divyesh Patel
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
- Current address: Research Programs Unit, Applied Tumor Genomics Program, Faculty of Medicine, University of Helsinki, Biomedicum, Helsinki 00290, Finland
| | - Umashankar Singh
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
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Oliveira Netto AB, Brusius-Facchin AC, Leistner-Segal S, Kubaski F, Josahkian J, Giugliani R. Detection of Mosaic Variants in Mothers of MPS II Patients by Next Generation Sequencing. Front Mol Biosci 2021; 8:789350. [PMID: 34805285 PMCID: PMC8602069 DOI: 10.3389/fmolb.2021.789350] [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: 10/04/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
Mucopolysaccharidosis type II is an X-linked lysosomal storage disorder caused by mutations in the IDS gene that encodes the iduronate-2-sulfatase enzyme. The IDS gene is located on the long arm of the X-chromosome, comprising 9 exons, spanning approximately 24 kb. The analysis of carriers, in addition to detecting mutations in patients, is essential for genetic counseling, since the risk of recurrence for male children is 50%. Mosaicism is a well-known phenomenon described in many genetic disorders caused by a variety of mechanisms that occur when a mutation arises in the early development of an embryo. Sanger sequencing is limited in detecting somatic mosaicism and sequence change levels of less than 20% may be missed. The Next Generation Sequencing (NGS) has been increasingly used in diagnosis. It is a sensitive and fast method for the detection of somatic mosaicism. Compared to Sanger sequencing, which represents a cumulative signal, NGS technology analyzes the sequence of each DNA read in a sample. NGS might therefore facilitate the detection of mosaicism in mothers of MPS II patients. The aim of this study was to reanalyze, by NGS, all MPS II mothers that showed to be non-carriers by Sanger analysis. Twelve non-carriers were selected for the reanalysis on the Ion PGM and Ion Torrent S5 platform, using a custom panel that includes the IDS gene. Results were visualized in the Integrative Genomics Viewer (IGV). We were able to detected the presence of the variant previously found in the index case in three of the mothers, with frequencies ranging between 13 and 49% of the reads. These results suggest the possibility of mosaicism in the mothers. The use of a more sensitive technology for detecting low-level mosaic mutations is essential for accurate recurrence-risk estimates. In our study, the NGS analysis showed to be an effective methodology to detect the mosaic event.
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Affiliation(s)
- Alice Brinckmann Oliveira Netto
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre, Brazil
| | - Ana Carolina Brusius-Facchin
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Brazil.,BioDiscovery Laboratory, Experimental Research Center, HCPA, Porto Alegre, Brazil
| | - Sandra Leistner-Segal
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil
| | - Francyne Kubaski
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Brazil.,BioDiscovery Laboratory, Experimental Research Center, HCPA, Porto Alegre, Brazil
| | - Juliana Josahkian
- Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre, Brazil.,Department of Clinical Medicine, Hospital Universitario de Santa Maria (HUSM), Santa Maria, Brazil
| | - Roberto Giugliani
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Brazil.,BioDiscovery Laboratory, Experimental Research Center, HCPA, Porto Alegre, Brazil.,Department of Genetics, UFRGS, Porto Alegre, Brazil
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Swiatczak B. Struggle within: evolution and ecology of somatic cell populations. Cell Mol Life Sci 2021; 78:6797-6806. [PMID: 34477897 PMCID: PMC11073125 DOI: 10.1007/s00018-021-03931-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/31/2021] [Accepted: 08/25/2021] [Indexed: 12/19/2022]
Abstract
The extent to which normal (nonmalignant) cells of the body can evolve through mutation and selection during the lifetime of the organism has been a major unresolved issue in evolutionary and developmental studies. On the one hand, stable multicellular individuality seems to depend on genetic homogeneity and suppression of evolutionary conflicts at the cellular level. On the other hand, the example of clonal selection of lymphocytes indicates that certain forms of somatic mutation and selection are concordant with the organism-level fitness. Recent DNA sequencing and tissue physiology studies suggest that in addition to adaptive immune cells also neurons, epithelial cells, epidermal cells, hematopoietic stem cells and functional cells in solid bodily organs are subject to evolutionary forces during the lifetime of an organism. Here we refer to these recent studies and suggest that the expanding list of somatically evolving cells modifies idealized views of biological individuals as radically different from collectives.
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Affiliation(s)
- Bartlomiej Swiatczak
- Department of History of Science and Scientific Archeology, University of Science and Technology of China, 96 Jinzhai Rd., Hefei, 230026, China.
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44
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Mouse models of aneuploidy to understand chromosome disorders. Mamm Genome 2021; 33:157-168. [PMID: 34719726 PMCID: PMC8913467 DOI: 10.1007/s00335-021-09930-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/20/2021] [Indexed: 12/04/2022]
Abstract
An organism or cell carrying a number of chromosomes that is not a multiple of the haploid count is in a state of aneuploidy. This condition results in significant changes in the level of expression of genes that are gained or lost from the aneuploid chromosome(s) and most cases in humans are not compatible with life. However, a few aneuploidies can lead to live births, typically associated with deleterious phenotypes. We do not understand why phenotypes arise from aneuploid syndromes in humans. Animal models have the potential to provide great insight, but less than a handful of mouse models of aneuploidy have been made, and no ideal system exists in which to study the effects of aneuploidy per se versus those of raised gene dosage. Here, we give an overview of human aneuploid syndromes, the effects on physiology of having an altered number of chromosomes and we present the currently available mouse models of aneuploidy, focusing on models of trisomy 21 (which causes Down syndrome) because this is the most common, and therefore, the most studied autosomal aneuploidy. Finally, we discuss the potential role of carrying an extra chromosome on aneuploid phenotypes, independent of changes in gene dosage, and methods by which this could be investigated further.
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Abstract
Over the past decade, genomic analyses of single cells-the fundamental units of life-have become possible. Single-cell DNA sequencing has shed light on biological questions that were previously inaccessible across diverse fields of research, including somatic mutagenesis, organismal development, genome function, and microbiology. Single-cell DNA sequencing also promises significant future biomedical and clinical impact, spanning oncology, fertility, and beyond. While single-cell approaches that profile RNA and protein have greatly expanded our understanding of cellular diversity, many fundamental questions in biology and important biomedical applications require analysis of the DNA of single cells. Here, we review the applications and biological questions for which single-cell DNA sequencing is uniquely suited or required. We include a discussion of the fields that will be impacted by single-cell DNA sequencing as the technology continues to advance.
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Affiliation(s)
- Gilad D Evrony
- Center for Human Genetics and Genomics, Grossman School of Medicine, New York University, New York, NY 10016, USA;
| | - Anjali Gupta Hinch
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom;
| | - Chongyuan Luo
- Department of Human Genetics, University of California, Los Angeles, California 90095, USA;
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Hamada M, Nagasawa H, Muramatsu KI, Jitsuiki K, Yanagawa Y. Asymmetry of Edema Formation: The Possibility of a Somatic Mosaic. Cureus 2021; 13:e15335. [PMID: 34235014 PMCID: PMC8240916 DOI: 10.7759/cureus.15335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2021] [Indexed: 11/16/2022] Open
Abstract
A 57-year-old woman experienced an abnormal feeling on the left side of her neck and difficulty breathing 90 minutes after eating Chinese noodles. She had a history of removal of a left sphenoid ridge meningioma one year earlier. She had experienced rigidity of her left neck and peripheral cold sensation on her left side in winter since approximately 10 years of age. She had experienced peripheral swelling of her left side and lower back pain of unknown origin on her left side several times. She had suffered for oral allergy syndrome since she was young. She sometimes experienced a tingling sensation on her lips and an unpleasant feeling in her throat after eating some types of fruit. On arrival, 180 minutes after eating the noodles, she had clear consciousness and stable vital signs. She had left neck and chest swelling without color change. Her difficulty breathing subsided spontaneously. A blood analysis revealed an increased level of immunoglobulin E. Neck computed tomography (CT) with contrast medium and magnetic resonance imaging (MRI) revealed left-side-limited edema in the subcutaneous area and surrounding esophagus and bronchus. These radiological findings denied hemorrhaging or pseudoaneurysmal formation. She underwent observational admission. After her edema improved, she was discharged on the third hospital day. A follow-up examination one week later showed the complete resolution of the neck and chest edema. A blood allergen test did not reveal the cause of the edema. The mechanism underlying the asymmetric transient edema after eating in the present case may involve somatic mosaic.
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Affiliation(s)
- Michika Hamada
- Acute Critical Care Medicine, Juntendo University Shizuoka Hospital, Izunokuni, JPN
| | - Hiroki Nagasawa
- Acute Critical Care Medicine, Juntendo University Shizuoka Hospital, Izunokuni, JPN
| | - Ken-Ichi Muramatsu
- Acute Critical Care Medicine, Juntendo University Shizuoka Hospital, Izunokuni, JPN
| | - Kei Jitsuiki
- Acute Critical Care Medicine, Juntendo University Shizuoka Hospital, Izunokuni, JPN
| | - Youichi Yanagawa
- Acute Critical Care Medicine, Juntendo University Shizuoka Hospital, Izunokuni, JPN
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Iourov IY, Yurov YB, Vorsanova SG, Kutsev SI. Chromosome Instability, Aging and Brain Diseases. Cells 2021; 10:cells10051256. [PMID: 34069648 PMCID: PMC8161106 DOI: 10.3390/cells10051256] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 02/07/2023] Open
Abstract
Chromosome instability (CIN) has been repeatedly associated with aging and progeroid phenotypes. Moreover, brain-specific CIN seems to be an important element of pathogenic cascades leading to neurodegeneration in late adulthood. Alternatively, CIN and aneuploidy (chromosomal loss/gain) syndromes exhibit accelerated aging phenotypes. Molecularly, cellular senescence, which seems to be mediated by CIN and aneuploidy, is likely to contribute to brain aging in health and disease. However, there is no consensus about the occurrence of CIN in the aging brain. As a result, the role of CIN/somatic aneuploidy in normal and pathological brain aging is a matter of debate. Still, taking into account the effects of CIN on cellular homeostasis, the possibility of involvement in brain aging is highly likely. More importantly, the CIN contribution to neuronal cell death may be responsible for neurodegeneration and the aging-related deterioration of the brain. The loss of CIN-affected neurons probably underlies the contradiction between reports addressing ontogenetic changes of karyotypes within the aged brain. In future studies, the combination of single-cell visualization and whole-genome techniques with systems biology methods would certainly define the intrinsic role of CIN in the aging of the normal and diseased brain.
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Affiliation(s)
- Ivan Y. Iourov
- Yurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, 117152 Moscow, Russia; (Y.B.Y.); (S.G.V.)
- Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, 125412 Moscow, Russia
- Department of Medical Biological Disciplines, Belgorod State University, 308015 Belgorod, Russia
- Correspondence: ; Tel.: +7-495-109-03-93 (ext. 3500)
| | - Yuri B. Yurov
- Yurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, 117152 Moscow, Russia; (Y.B.Y.); (S.G.V.)
- Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, 125412 Moscow, Russia
| | - Svetlana G. Vorsanova
- Yurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, 117152 Moscow, Russia; (Y.B.Y.); (S.G.V.)
- Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, 125412 Moscow, Russia
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The Cytogenomic "Theory of Everything": Chromohelkosis May Underlie Chromosomal Instability and Mosaicism in Disease and Aging. Int J Mol Sci 2020; 21:ijms21218328. [PMID: 33171981 PMCID: PMC7664247 DOI: 10.3390/ijms21218328] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 01/28/2023] Open
Abstract
Mechanisms for somatic chromosomal mosaicism (SCM) and chromosomal instability (CIN) are not completely understood. During molecular karyotyping and bioinformatic analyses of children with neurodevelopmental disorders and congenital malformations (n = 612), we observed colocalization of regular chromosomal imbalances or copy number variations (CNV) with mosaic ones (n = 47 or 7.7%). Analyzing molecular karyotyping data and pathways affected by CNV burdens, we proposed a mechanism for SCM/CIN, which had been designated as “chromohelkosis” (from the Greek words chromosome ulceration/open wound). Briefly, structural chromosomal imbalances are likely to cause local instability (“wreckage”) at the breakpoints, which results either in partial/whole chromosome loss (e.g., aneuploidy) or elongation of duplicated regions. Accordingly, a function for classical/alpha satellite DNA (protection from the wreckage towards the centromere) has been hypothesized. Since SCM and CIN are ubiquitously involved in development, homeostasis and disease (e.g., prenatal development, cancer, brain diseases, aging), we have metaphorically (ironically) designate the system explaining chromohelkosis contribution to SCM/CIN as the cytogenomic “theory of everything”, similar to the homonymous theory in physics inasmuch as it might explain numerous phenomena in chromosome biology. Recognizing possible empirical and theoretical weaknesses of this “theory”, we nevertheless believe that studies of chromohelkosis-like processes are required to understand structural variability and flexibility of the genome.
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