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Ressler AK, Snellings DA, Girard R, Gallione CJ, Lightle R, Allen AS, Awad IA, Marchuk DA. Single-nucleus DNA sequencing reveals hidden somatic loss-of-heterozygosity in Cerebral Cavernous Malformations. Nat Commun 2023; 14:7009. [PMID: 37919320 PMCID: PMC10622526 DOI: 10.1038/s41467-023-42908-w] [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: 04/21/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023] Open
Abstract
Cerebral Cavernous Malformations (CCMs) are vascular malformations of the central nervous system which can lead to moderate to severe neurological phenotypes in patients. A majority of CCM lesions are driven by a cancer-like three-hit mutational mechanism, including a somatic, activating mutation in the oncogene PIK3CA, as well as biallelic loss-of-function mutations in a CCM gene. However, standard sequencing approaches often fail to yield a full complement of pathogenic mutations in many CCMs. We suggest this reality reflects the limited sensitivity to identify low-frequency variants and the presence of mutations undetectable with bulk short-read sequencing. Here we report a single-nucleus DNA-sequencing approach that leverages the underlying biology of CCMs to identify lesions with somatic loss-of-heterozygosity, a class of such hidden mutations. We identify an alternative genetic mechanism for CCM pathogenesis and establish a method that can be repurposed to investigate the genetic underpinning of other disorders with multiple somatic mutations.
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Affiliation(s)
- Andrew K Ressler
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA.
| | - Daniel A Snellings
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Romuald Girard
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, IL, USA
| | - Carol J Gallione
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Rhonda Lightle
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, IL, USA
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, 27710, USA
| | - Issam A Awad
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, IL, USA
| | - Douglas A Marchuk
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA.
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Labrijn-Marks I, Somers-Bolman GM, In 't Groen SLM, Hoogeveen-Westerveld M, Kroos MA, Ala-Mello S, Amaral O, Miranda CS, Mavridou I, Michelakakis H, Naess K, Verheijen FW, Hoefsloot LH, Dijkhuizen T, Benjamins M, van den Hout HJM, van der Ploeg AT, Pijnappel WWMP, Saris JJ, Halley DJ. Segmental and total uniparental isodisomy (UPiD) as a disease mechanism in autosomal recessive lysosomal disorders: evidence from SNP arrays. Eur J Hum Genet 2019; 27:919-927. [PMID: 30737479 PMCID: PMC6777471 DOI: 10.1038/s41431-019-0348-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/29/2018] [Accepted: 01/08/2019] [Indexed: 12/13/2022] Open
Abstract
Analyses in our diagnostic DNA laboratory include genes involved in autosomal recessive (AR) lysosomal storage disorders such as glycogenosis type II (Pompe disease) and mucopolysaccharidosis type I (MPSI, Hurler disease). We encountered 4 cases with apparent homozygosity for a disease-causing sequence variant that could be traced to one parent only. In addition, in a young child with cardiomyopathy, in the absence of other symptoms, a diagnosis of Pompe disease was considered. Remarkably, he presented with different enzymatic and genotypic features between leukocytes and skin fibroblasts. All cases were examined with microsatellite markers and SNP genotyping arrays. We identified one case of total uniparental disomy (UPD) of chromosome 17 leading to Pompe disease and three cases of segmental uniparental isodisomy (UPiD) causing Hurler-(4p) or Pompe disease (17q). One Pompe patient with unusual combinations of features was shown to have a mosaic segmental UPiD of chromosome 17q. The chromosome 17 UPD cases amount to 11% of our diagnostic cohort of homozygous Pompe patients (plus one case of pseudoheterozygosity) where segregation analysis was possible. We conclude that inclusion of parental DNA is mandatory for reliable DNA diagnostics. Mild or unusual phenotypes of AR diseases should alert physicians to the possibility of mosaic segmental UPiD. SNP genotyping arrays are used in diagnostic workup of patients with developmental delay. Our results show that even small Regions of Homozygosity that include telomeric areas are worth reporting, regardless of the imprinting status of the chromosome, as they might indicate segmental UPiD.
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Affiliation(s)
- Ineke Labrijn-Marks
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Galhana M Somers-Bolman
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stijn L M In 't Groen
- Molecular Stem Cell Biology, Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Pediatrics, Division of Metabolic Diseases and Genetics, Erasmus University Medical Center-Sophia, Rotterdam, The Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marianne Hoogeveen-Westerveld
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.,Molecular Stem Cell Biology, Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marian A Kroos
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.,Molecular Stem Cell Biology, Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sirpa Ala-Mello
- Department of Clinical Genetics, Helsinki University Hospital, Helsinki, Finland
| | - Olga Amaral
- Department of Human Genetics, Unit of Research and Development, National Institute of Health Dr Ricardo Jorge, Porto, Portugal
| | | | - Irene Mavridou
- Department of Enzymology and Cellular Function, Institute of Child Health, Athens, Greece
| | - Helen Michelakakis
- Department of Enzymology and Cellular Function, Institute of Child Health, Athens, Greece
| | - Karin Naess
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Frans W Verheijen
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lies H Hoefsloot
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Trijnie Dijkhuizen
- Department of Genetics, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Marloes Benjamins
- Department of Genetics, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Hannerieke J M van den Hout
- Department of Pediatrics, Division of Metabolic Diseases and Genetics, Erasmus University Medical Center-Sophia, Rotterdam, The Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ans T van der Ploeg
- Department of Pediatrics, Division of Metabolic Diseases and Genetics, Erasmus University Medical Center-Sophia, Rotterdam, The Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - W W M Pim Pijnappel
- Molecular Stem Cell Biology, Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Pediatrics, Division of Metabolic Diseases and Genetics, Erasmus University Medical Center-Sophia, Rotterdam, The Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jasper J Saris
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Dicky J Halley
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.
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