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Liu H, Guan L, Su X, Zhao L, Shu Q, Zhang J. A broken network of susceptibility genes in the monocytes of Crohn's disease patients. Life Sci Alliance 2024; 7:e202302394. [PMID: 38925865 PMCID: PMC11208737 DOI: 10.26508/lsa.202302394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Genome-wide association studies have identified over 200 genetic loci associated with inflammatory bowel disease; however, the mechanism of such a large amount of susceptibility genes remains uncertain. In this study, we integrated bioinformatics analysis and two independent single-cell transcriptome datasets to investigate the expression network of 232 susceptibility genes in Crohn's disease (CD) patients and healthy controls. The study revealed that most of the susceptibility genes are specifically and strictly expressed in the monocytes of the human intestinal tract. The susceptibility genes established a network within the monocytes of health control. The robustness of a gene network may prevent disease onset that is influenced by the genetic and environmental alteration in the expression of susceptibility genes. In contrast, we showed a sparse network in pediatric/adult CD patients, suggesting the broken network contributed to the CD etiology. The network status of susceptibility genes at the single-cell level of monocytes provided novel insight into the etiology.
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Affiliation(s)
- Hankui Liu
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Genomics, Shenzhen, China
| | - Liping Guan
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Genomics, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Su
- BGI Genomics, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lijian Zhao
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Genomics, Shenzhen, China
- Hebei Medical University, Shijiazhuang, China
| | - Qing Shu
- Department of Gastroenterology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Jianguo Zhang
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Research, Shenzhen, China
- Hebei Medical University, Shijiazhuang, China
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2
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Yamada M, Mizuno S, Inaba M, Uehara T, Inagaki H, Suzuki H, Miya F, Takenouchi T, Kurahashi H, Kosaki K. Truncating variants of the sterol recognition region of SHH cause hypertelorism phenotype rather than hypotelorism-holoprosencephaly. Am J Med Genet A 2024; 194:e63614. [PMID: 38562108 DOI: 10.1002/ajmg.a.63614] [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: 01/19/2024] [Revised: 03/04/2024] [Accepted: 03/16/2024] [Indexed: 04/04/2024]
Abstract
Sonic hedgehog signaling molecule (SHH) is a key molecule in the cilia-mediated signaling pathway and a critical morphogen in embryogenesis. The association between loss-of-function variants of SHH and holoprosencephaly is well established. In mice experiments, reduced or increased signaling of SHH have been shown to be associated with narrowing or excessive expansion of the facial midline, respectively. Herein, we report two unrelated patients with de novo truncating variants of SHH presenting with hypertelorism rather than hypotelorism. The first patient was a 13-year-old girl. Her facial features included hypertelorism, strabismus, telecanthus, malocclusion, frontal bossing, and wide widow's peak. She had borderline developmental delay and agenesis of the corpus callosum. She had a nonsense variant of SHH: Chr7(GRCh38):g.155802987C > T, NM_000193.4:c.1302G > A, p.(Trp434*). The second patient was a 25-year-old girl. Her facial features included hypertelorism and wide widow's peak. She had developmental delay and agenesis of the corpus callosum. She had a frameshift variant of SHH: Chr7(GRCh38):g.155803072_155803074delCGGinsT, NM_000193.4:c.1215_1217delCCGinsA, p.(Asp405Glufs*92). The hypertelorism phenotype contrasts sharply with the prototypical hypotelorism-holoprosencephaly phenotype associated with loss-of-function of SHH. We concluded that a subset of truncating variants of SHH could be associated with hypertelorism rather than hypotelorism.
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Affiliation(s)
- Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Seiji Mizuno
- Department of Pediatrics, Central Hospital, Aichi Developmental Disability Center, Kasugai, Japan
| | - Mie Inaba
- Department of Pediatrics, Central Hospital, Aichi Developmental Disability Center, Kasugai, Japan
| | - Tomoko Uehara
- Department of Pediatrics, Central Hospital, Aichi Developmental Disability Center, Kasugai, Japan
| | - Hidehito Inagaki
- Division of Molecular Genetics, Center for Medical Science, Fujita Health University, Toyoake, Japan
| | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Fuyuki Miya
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Center for Medical Science, Fujita Health University, Toyoake, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
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3
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Li H, Rajani V, Sengar AS, Salter MW. Src dependency of the regulation of LTP by alternative splicing of GRIN1 exon 5. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230236. [PMID: 38853562 DOI: 10.1098/rstb.2023.0236] [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: 10/31/2023] [Accepted: 02/11/2024] [Indexed: 06/11/2024] Open
Abstract
Alternative splicing of Grin1 exon 5 regulates induction of long-term potentiation (LTP) at Schaffer collateral-CA1 synapses: LTP in mice lacking the GluN1 exon 5-encoded N1 cassette (GluN1a mice) is significantly increased compared with that in mice compulsorily expressing this exon (GluN1b mice). The mechanism underlying this difference is unknown. Here, we report that blocking the non-receptor tyrosine kinase Src prevents induction of LTP in GluN1a mice but not in GluN1b. We find that activating Src enhances pharmacologically isolated synaptic N-methyl-d-aspartate receptor (NMDAR) currents in GluN1a mice but not in GluN1b. Moreover, we observe that Src activation increases the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor component of Schaffer collateral-evoked excitatory post-synaptic potentials in GluN1a mice, but this increase is prevented by blocking NMDARs. We conclude that at these synapses, NMDARs in GluN1a mice are subject to upregulation by Src that mediates induction of LTP, whereas NMDARs in GluN1b mice are not regulated by Src, leading to Src-resistance of LTP. Thus, we have uncovered that a key regulatory mechanism for synaptic potentiation is gated by differential splicing of exon 5 of Grin1. This article is part of a discussion meeting issue 'Long-term potentiation: 50 years on'.
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Affiliation(s)
- Hongbin Li
- Program in Neurosciences & Mental Health, The Hospital for Sick Children , Toronto, ON M5G 1X8, Canada
| | - Vishaal Rajani
- Program in Neurosciences & Mental Health, The Hospital for Sick Children , Toronto, ON M5G 1X8, Canada
| | - Ameet S Sengar
- Program in Neurosciences & Mental Health, The Hospital for Sick Children , Toronto, ON M5G 1X8, Canada
| | - Michael W Salter
- Program in Neurosciences & Mental Health, The Hospital for Sick Children , Toronto, ON M5G 1X8, Canada
- Department of Physiology, University of Toronto , Toronto, ON M5S 1A8, Canada
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4
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Zeng T, Spence JP, Mostafavi H, Pritchard JK. Bayesian estimation of gene constraint from an evolutionary model with gene features. Nat Genet 2024:10.1038/s41588-024-01820-9. [PMID: 38977852 DOI: 10.1038/s41588-024-01820-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 05/29/2024] [Indexed: 07/10/2024]
Abstract
Measures of selective constraint on genes have been used for many applications, including clinical interpretation of rare coding variants, disease gene discovery and studies of genome evolution. However, widely used metrics are severely underpowered at detecting constraints for the shortest ~25% of genes, potentially causing important pathogenic mutations to be overlooked. Here we developed a framework combining a population genetics model with machine learning on gene features to enable accurate inference of an interpretable constraint metric, shet. Our estimates outperform existing metrics for prioritizing genes important for cell essentiality, human disease and other phenotypes, especially for short genes. Our estimates of selective constraint should have wide utility for characterizing genes relevant to human disease. Finally, our inference framework, GeneBayes, provides a flexible platform that can improve the estimation of many gene-level properties, such as rare variant burden or gene expression differences.
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Affiliation(s)
- Tony Zeng
- Department of Genetics, Stanford University, Stanford, CA, USA.
| | | | - Hakhamanesh Mostafavi
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Population Health, New York University, New York, NY, USA
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Biology, Stanford University, Stanford, CA, USA.
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Bhattacharya A, Parlanti P, Cavallo L, Farrow E, Spivey T, Renieri A, Mari F, Manzini MC. A novel framework for functional annotation of variants of uncertain significance in ID/ASD risk gene CC2D1A. Hum Mol Genet 2024; 33:1229-1240. [PMID: 38652285 DOI: 10.1093/hmg/ddae070] [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: 11/30/2023] [Revised: 03/07/2024] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are genetically heterogeneous with hundreds of identified risk genes, most affecting only a few patients. Novel missense variants in these genes are being discovered as clinical exome sequencing is now routinely integrated into diagnosis, yet most of them are annotated as variants of uncertain significance (VUS). VUSs are a major roadblock in using patient genetics to inform clinical action. We developed a framework to characterize VUSs in Coiled-coil and C2 domain containing 1A (CC2D1A), a gene causing autosomal recessive ID with comorbid ASD in 40% of cases. We analyzed seven VUSs (p.Pro319Leu, p.Ser327Leu, p.Gly441Val, p.Val449Met, p.Thr580Ile, p.Arg886His and p.Glu910Lys) from four cases of individuals with ID and ASD. Variants were cloned and overexpressed in HEK293 individually and in their respective heterozygous combination. CC2D1A is a signaling scaffold that positively regulates PKA-CREB signaling by repressing phosphodiesterase 4D (PDE4D) to prevent cAMP degradation. After testing multiple parameters including direct interaction between PDE4D and CC2D1A, cAMP levels and CREB activation, we found that the most sensitive readout was CREB transcriptional activity using a luciferase assay. Compared to WT CC2D1A, five VUSs (p.Pro319Leu, p.Gly441Val, p.Val449Met, p.Thr580Ile, and p.Arg886His) led to significantly blunted response to forskolin induced CREB activation. This luciferase assay approach can be scaled up to annotate ~150 CC2D1A VUSs that are currently listed in ClinVar. Since CREB activation is a common denominator for multiple ASD/ID genes, our paradigm can also be adapted for their VUSs.
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Affiliation(s)
- Aniket Bhattacharya
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Paola Parlanti
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Luca Cavallo
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Edward Farrow
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, 2121 I St NW, Washington, DC 20052, United States
| | - Tyler Spivey
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, 2121 I St NW, Washington, DC 20052, United States
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Viale Bracci 2, 53100 Siena, Italy
| | - Francesca Mari
- Medical Genetics, University of Siena, Viale Bracci 2, 53100 Siena, Italy
| | - M Chiara Manzini
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
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Currey L, Mitchell B, Al-Khalily M, McElnea SJ, Kozulin P, Harkins D, Pelenyi A, Fenlon L, Suarez R, Kurniawan ND, Burne TH, Harris L, Thor S, Piper M. Polycomb repressive complex 2 is critical for mouse cortical glutamatergic neuron development. Cereb Cortex 2024; 34:bhae268. [PMID: 38960704 PMCID: PMC11221884 DOI: 10.1093/cercor/bhae268] [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: 11/21/2023] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 07/05/2024] Open
Abstract
The Polycomb Repressive Complex 2 (PRC2) regulates corticogenesis, yet the consequences of mutations to this epigenetic modifier in the mature brain are poorly defined. Importantly, PRC2 core genes are haploinsufficient and causative of several human neurodevelopmental disorders. To address the role of PRC2 in mature cortical structure and function, we conditionally deleted the PRC2 gene Eed from the developing mouse dorsal telencephalon. Adult homozygotes displayed smaller forebrain structures. Single-nucleus transcriptomics revealed that glutamatergic neurons were particularly affected, exhibiting dysregulated gene expression profiles, accompanied by aberrations in neuronal morphology and connectivity. Remarkably, homozygous mice performed well on challenging cognitive tasks. In contrast, while heterozygous mice did not exhibit clear anatomical or behavioral differences, they displayed dysregulation of neuronal genes and altered neuronal morphology that was strikingly different from homozygous phenotypes. Collectively, these data reveal how alterations to PRC2 function shape the mature brain and reveal a dose-specific role for PRC2 in determining glutamatergic neuron identity.
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Affiliation(s)
- Laura Currey
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Benjamin Mitchell
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Majd Al-Khalily
- Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD 4072, Australia
| | - Sarah-Jayne McElnea
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peter Kozulin
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Danyon Harkins
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alexandra Pelenyi
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Laura Fenlon
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Rodrigo Suarez
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Nyoman D Kurniawan
- Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD 4072, Australia
| | - Thomas H Burne
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD 4076, Australia
| | - Lachlan Harris
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Cancer Neuroscience Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Stefan Thor
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
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7
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Dols-Icardo O, Carbayo Á, Jericó I, Blasco-Martínez O, Álvarez-Sánchez E, López Pérez MA, Bernal S, Rodríguez-Santiago B, Cusco I, Turon-Sans J, Cabezas-Torres M, Caballero-Ávila M, Vesperinas A, Llansó L, Pagola-Lorz I, Torné L, Valle-Tamayo N, Muñoz L, Rubio-Guerra S, Illán-Gala I, Cortés-Vicente E, Gelpi E, Rojas-García R. Identification of a pathogenic mutation in ARPP21 in patients with amyotrophic lateral sclerosis. J Neurol Neurosurg Psychiatry 2024:jnnp-2024-333834. [PMID: 38960585 DOI: 10.1136/jnnp-2024-333834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/17/2024] [Indexed: 07/05/2024]
Abstract
BACKGROUND AND OBJECTIVE Between 5% and 10% of amyotrophic lateral sclerosis (ALS) cases have a family history of the disease, 30% of which do not have an identifiable underlying genetic cause after a comprehensive study of the known ALS-related genes. Based on a significantly increased incidence of ALS in a small geographical region from Spain, the aim of this work was to identify novel ALS-related genes in ALS cases with negative genetic testing. METHODS We detected an increased incidence of both sporadic and, especially, familial ALS cases in a small region from Spain compared with available demographic and epidemiological data. We performed whole genome sequencing in a group of 12 patients with ALS (5 of them familial) from this unique area. We expanded the study to include affected family members and additional cases from a wider surrounding region. RESULTS We identified a shared missense mutation (c.1586C>T; p.Pro529Leu) in the cyclic AMP regulated phosphoprotein 21 (ARPP21) gene that encodes an RNA-binding protein, in a total of 10 patients with ALS from 7 unrelated families. No mutations were found in other ALS-causing genes. CONCLUSIONS While previous studies have dismissed a causal role of ARPP21 in ALS, our results strongly support ARPP21 as a novel ALS-causing gene.
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Affiliation(s)
- Oriol Dols-Icardo
- Sant Pau Memory Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Álvaro Carbayo
- Motor Neuron Disease Clinic, Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Department of Medicine, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Ivonne Jericó
- Neuromuscular and Motor Neuron Diseases Research Group, Department of Neurology, Hospital Universitario de Navarra, Pamplona, Spain
- Health Research Institute of Navarra (IdisNa), Pamplona, Spain
| | | | - Esther Álvarez-Sánchez
- Sant Pau Memory Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | | | - Sara Bernal
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Genetics Department, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Benjamín Rodríguez-Santiago
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Genetics Department, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Genome Instability and DNA Repair Group, Department of Genetics and Microbiology, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Ivon Cusco
- Genetics Department, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Janina Turon-Sans
- Motor Neuron Disease Clinic, Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Department of Medicine, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Manuel Cabezas-Torres
- Motor Neuron Disease Clinic, Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Marta Caballero-Ávila
- Motor Neuron Disease Clinic, Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Department of Medicine, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Ana Vesperinas
- Motor Neuron Disease Clinic, Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Department of Medicine, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Laura Llansó
- Motor Neuron Disease Clinic, Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Department of Medicine, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Inmaculada Pagola-Lorz
- Neuromuscular and Motor Neuron Diseases Research Group, Department of Neurology, Hospital Universitario de Navarra, Pamplona, Spain
- Health Research Institute of Navarra (IdisNa), Pamplona, Spain
| | - Laura Torné
- Neuromuscular and Motor Neuron Diseases Research Group, Department of Neurology, Hospital Universitario de Navarra, Pamplona, Spain
- Health Research Institute of Navarra (IdisNa), Pamplona, Spain
| | - Natalia Valle-Tamayo
- Sant Pau Memory Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Laia Muñoz
- Sant Pau Memory Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Sara Rubio-Guerra
- Sant Pau Memory Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Ignacio Illán-Gala
- Sant Pau Memory Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Elena Cortés-Vicente
- Motor Neuron Disease Clinic, Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Department of Medicine, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Ellen Gelpi
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Ricard Rojas-García
- Motor Neuron Disease Clinic, Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Department of Medicine, Universitat Autonoma de Barcelona, Barcelona, Spain
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8
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Scatolini M, Grisanti S, Tomaiuolo P, Grosso E, Basile V, Cosentini D, Puglisi S, Laganà M, Perotti P, Saba L, Rossini E, Palermo F, Sigala S, Volante M, Berruti A, Terzolo M. Germline NGS targeted analysis in adult patients with sporadic adrenocortical carcinoma. Eur J Cancer 2024; 205:114088. [PMID: 38714106 DOI: 10.1016/j.ejca.2024.114088] [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: 12/13/2023] [Revised: 04/11/2024] [Accepted: 04/21/2024] [Indexed: 05/09/2024]
Abstract
BACKGROUND Adrenocortical carcinoma (ACC) is a rare cancer that arises sporadically or due to hereditary syndromes. Data on germline variants (GVs) in sporadic ACC are limited. Our aim was to characterize GVs of genes potentially related to adrenal diseases in 150 adult patients with sporadic ACC. METHODS This was a retrospective analysis of stage I-IV ACC patients with sporadic ACC from two reference centers for ACC in Italy. Patients were included in the analysis if they had confirmed diagnosis of ACC, a frozen peripheral blood sample and complete clinical and follow-up data. Next generation sequencing technology was used to analyze the prevalence of GVs in a custom panel of 17 genes belonging to either cancer-predisposition genes or adrenocortical-differentiation genes categories. RESULTS We identified 18 GVs based on their frequency, enrichment and predicted functional characteristics. We found six pathogenic (P) or likely pathogenic (LP) variants in ARMC5, CTNNB1, MSH2, PDE11A and TP53 genes; and twelve variants lacking evidence of pathogenicity. New unique P/LP variants were identified in TP53 (p.G105D) and, for the first time, in ARMC5 (p.P731R). The presence of P/LP GVs was associated with reduced survival outcomes and had a significant and independent impact on both progression-free survival and overall survival. CONCLUSIONS GVs were present in 6.7 % of patients with sporadic ACC, and we identified novel variants of ARMC5 and TP53. These findings may improve understanding of ACC pathogenesis and enable genetic counseling of patients and their families.
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Affiliation(s)
- Maria Scatolini
- Molecular Oncology Laboratory, Fondazione Edo ed Elvo Tempia, 13875 Ponderano, BI, Italy
| | - Salvatore Grisanti
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, ASST Spedali Civili, 25123 Brescia, Italy
| | - Pasquale Tomaiuolo
- Molecular Oncology Laboratory, Fondazione Edo ed Elvo Tempia, 13875 Ponderano, BI, Italy; Internal Medicine, Department of Clinical and Biological Sciences, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy
| | - Enrico Grosso
- Molecular Oncology Laboratory, Fondazione Edo ed Elvo Tempia, 13875 Ponderano, BI, Italy
| | - Vittoria Basile
- Internal Medicine, Department of Clinical and Biological Sciences, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy
| | - Deborah Cosentini
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, ASST Spedali Civili, 25123 Brescia, Italy
| | - Soraya Puglisi
- Internal Medicine, Department of Clinical and Biological Sciences, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy.
| | - Marta Laganà
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, ASST Spedali Civili, 25123 Brescia, Italy
| | - Paola Perotti
- Internal Medicine, Department of Clinical and Biological Sciences, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy
| | - Laura Saba
- Internal Medicine, Department of Clinical and Biological Sciences, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy
| | - Elisa Rossini
- Department of Molecular & Translational Medicine, Section of Pharmacology, University of Brescia, 25123 Brescia, Italy
| | - Flavia Palermo
- Molecular Oncology Laboratory, Fondazione Edo ed Elvo Tempia, 13875 Ponderano, BI, Italy
| | - Sandra Sigala
- Department of Molecular & Translational Medicine, Section of Pharmacology, University of Brescia, 25123 Brescia, Italy
| | - Marco Volante
- Pathology Unit, Oncology department, University of Turin, San Luigi Gonzaga University Hospital, Regione Gonzole 10, 10043 Orbassano, Turin, Italy
| | - Alfredo Berruti
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, ASST Spedali Civili, 25123 Brescia, Italy
| | - Massimo Terzolo
- Internal Medicine, Department of Clinical and Biological Sciences, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy
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9
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Ma M, Ganapathi M, Zheng Y, Tan KL, Kanca O, Bove KE, Quintanilla N, Sag SO, Temel SG, LeDuc CA, McPartland AJ, Pereira EM, Shen Y, Hagen J, Thomas CP, Nguyen Galván NT, Pan X, Lu S, Rosenfeld JA, Calame DG, Wangler MF, Lupski JR, Pehlivan D, Hertel PM, Chung WK, Bellen HJ. Homozygous missense variants in YKT6 result in loss of function and are associated with developmental delay, with or without severe infantile liver disease and risk for hepatocellular carcinoma. Genet Med 2024; 26:101125. [PMID: 38522068 DOI: 10.1016/j.gim.2024.101125] [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: 09/21/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024] Open
Abstract
PURPOSE YKT6 plays important roles in multiple intracellular vesicle trafficking events but has not been associated with Mendelian diseases. METHODS We report 3 unrelated individuals with rare homozygous missense variants in YKT6 who exhibited neurological disease with or without a progressive infantile liver disease. We modeled the variants in Drosophila. We generated wild-type and variant genomic rescue constructs of the fly ortholog dYkt6 and compared their ability in rescuing the loss-of-function phenotypes in mutant flies. We also generated a dYkt6KozakGAL4 allele to assess the expression pattern of dYkt6. RESULTS Two individuals are homozygous for YKT6 [NM_006555.3:c.554A>G p.(Tyr185Cys)] and exhibited normal prenatal course followed by failure to thrive, developmental delay, and progressive liver disease. Haplotype analysis identified a shared homozygous region flanking the variant, suggesting a common ancestry. The third individual is homozygous for YKT6 [NM_006555.3:c.191A>G p.(Tyr64Cys)] and exhibited neurodevelopmental disorders and optic atrophy. Fly dYkt6 is essential and is expressed in the fat body (analogous to liver) and central nervous system. Wild-type genomic rescue constructs can rescue the lethality and autophagic flux defects, whereas the variants are less efficient in rescuing the phenotypes. CONCLUSION The YKT6 variants are partial loss-of-function alleles, and the p.(Tyr185Cys) is more severe than p.(Tyr64Cys).
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Affiliation(s)
- Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Mythily Ganapathi
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Yiming Zheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Kai-Li Tan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Kevin E Bove
- Department of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Norma Quintanilla
- Department of Pathology and Immunology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX
| | - Sebnem O Sag
- Department of Medical Genetics, Faculty of Medicine, Uludag University, Bursa, Turkey
| | - Sehime G Temel
- Department of Medical Genetics, Faculty of Medicine, Uludag University, Bursa, Turkey
| | | | | | | | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY
| | - Jacob Hagen
- Department of Systems Biology, Columbia University Medical Center, New York, NY
| | - Christie P Thomas
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
| | | | - Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Baylor Genetics Laboratories, Houston, TX
| | - Daniel G Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX; Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX
| | - Paula M Hertel
- Texas Children's Hospital, Houston, TX; Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX.
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10
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Lodewijk GA, de Geus M, Guimarães RLFP, Jacobs FMJ. Emergence of the ZNF675 Gene During Primate Evolution-Influenced Human Neurodevelopment Through Changing HES1 Autoregulation. J Comp Neurol 2024; 532:e25648. [PMID: 38958676 DOI: 10.1002/cne.25648] [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: 12/31/2023] [Revised: 04/27/2024] [Accepted: 05/30/2024] [Indexed: 07/04/2024]
Abstract
In this study, we investigated recurrent copy number variations (CNVs) in the 19p12 locus, which are associated with neurodevelopmental disorders. The two genes in this locus, ZNF675 and ZNF681, arose via gene duplication in primates, and their presence in several pathological CNVs in the human population suggests that either or both of these genes are required for normal human brain development. ZNF675 and ZNF681 are members of the Krüppel-associated box zinc finger (KZNF) protein family, a class of transcriptional repressors important for epigenetic silencing of specific genomic regions. About 170 primate-specific KZNFs are present in the human genome. Although KZNFs are primarily associated with repressing retrotransposon-derived DNA, evidence is emerging that they can be co-opted for other gene regulatory processes. We show that genetic deletion of ZNF675 causes developmental defects in cortical organoids, and our data suggest that part of the observed neurodevelopmental phenotype is mediated by a gene regulatory role of ZNF675 on the promoter of the neurodevelopmental gene Hes family BHLH transcription factor 1 (HES1). We also find evidence for the recently evolved regulation of genes involved in neurological disorders, microcephalin 1 and sestrin 3. We show that ZNF675 interferes with HES1 auto-inhibition, a process essential for the maintenance of neural progenitors. As a striking example of how some KZNFs have integrated into preexisting gene expression networks, these findings suggest the emergence of ZNF675 has caused a change in the balance of HES1 autoregulation. The association of ZNF675 CNV with human developmental disorders and ZNF675-mediated regulation of neurodevelopmental genes suggests that it evolved into an important factor for human brain development.
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Affiliation(s)
- Gerrald A Lodewijk
- Swammerdam Institute for Life Sciences, Evolutionary Neurogenomics, University of Amsterdam, Amsterdam, The Netherlands
| | - Matthijs de Geus
- Swammerdam Institute for Life Sciences, Evolutionary Neurogenomics, University of Amsterdam, Amsterdam, The Netherlands
| | - Rita L F P Guimarães
- Swammerdam Institute for Life Sciences, Evolutionary Neurogenomics, University of Amsterdam, Amsterdam, The Netherlands
| | - Frank M J Jacobs
- Swammerdam Institute for Life Sciences, Evolutionary Neurogenomics, University of Amsterdam, Amsterdam, The Netherlands
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11
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Phua YL, D'Annibale OM, Karunanidhi A, Mohsen AW, Kirmse B, Dobrowolski SF, Vockley J. A multiomics approach reveals evidence for phenylbutyrate as a potential treatment for combined D,L-2- hydroxyglutaric aciduria. Mol Genet Metab 2024; 142:108495. [PMID: 38772223 DOI: 10.1016/j.ymgme.2024.108495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/30/2024] [Accepted: 05/13/2024] [Indexed: 05/23/2024]
Abstract
PURPOSE To identify therapies for combined D, L-2-hydroxyglutaric aciduria (C-2HGA), a rare genetic disorder caused by recessive variants in the SLC25A1 gene. METHODS Patients C-2HGA were identified and diagnosed by whole exome sequencing and biochemical genetic testing. Patient derived fibroblasts were then treated with phenylbutyrate and the functional effects assessed by metabolomics and RNA-sequencing. RESULTS In this study, we demonstrated that C-2HGA patient derived fibroblasts exhibited impaired cellular bioenergetics. Moreover, Fibroblasts form one patient exhibited worsened cellular bioenergetics when supplemented with citrate. We hypothesized that treating patient cells with phenylbutyrate (PB), an FDA approved pharmaceutical drug that conjugates glutamine for renal excretion, would reduce mitochondrial 2-ketoglutarate, thereby leading to improved cellular bioenergetics. Metabolomic and RNA-seq analyses of PB-treated fibroblasts demonstrated a significant decrease in intracellular 2-ketoglutarate, 2-hydroxyglutarate, and in levels of mRNA coding for citrate synthase and isocitrate dehydrogenase. Consistent with the known action of PB, an increased level of phenylacetylglutamine in patient cells was consistent with the drug acting as 2-ketoglutarate sink. CONCLUSION Our pre-clinical studies suggest that citrate supplementation has the possibility exacerbating energy metabolism in this condition. However, improvement in cellular bioenergetics suggests phenylbutyrate might have interventional utility for this rare disease.
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MESH Headings
- Humans
- Phenylbutyrates/pharmacology
- Phenylbutyrates/therapeutic use
- Fibroblasts/metabolism
- Fibroblasts/drug effects
- Glutarates/metabolism
- Ketoglutaric Acids/metabolism
- Energy Metabolism/drug effects
- Energy Metabolism/genetics
- Mitochondria/drug effects
- Mitochondria/metabolism
- Mitochondria/genetics
- Metabolomics
- Exome Sequencing
- Citrate (si)-Synthase/metabolism
- Citrate (si)-Synthase/genetics
- Brain Diseases, Metabolic, Inborn/drug therapy
- Brain Diseases, Metabolic, Inborn/genetics
- Brain Diseases, Metabolic, Inborn/metabolism
- Isocitrate Dehydrogenase/genetics
- Isocitrate Dehydrogenase/metabolism
- Brain Diseases, Metabolic/drug therapy
- Brain Diseases, Metabolic/genetics
- Brain Diseases, Metabolic/metabolism
- Brain Diseases, Metabolic/pathology
- Multiomics
- Mitochondrial Proteins
- Organic Anion Transporters
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Affiliation(s)
- Yu Leng Phua
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Pathology, Clinical Biochemical Genetics Laboratory, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olivia M D'Annibale
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Anuradha Karunanidhi
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Al-Walid Mohsen
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Brian Kirmse
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Steven F Dobrowolski
- Department of Pathology, Clinical Biochemical Genetics Laboratory, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Jerry Vockley
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.
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12
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Tanudisastro HA, Deveson IW, Dashnow H, MacArthur DG. Sequencing and characterizing short tandem repeats in the human genome. Nat Rev Genet 2024; 25:460-475. [PMID: 38366034 DOI: 10.1038/s41576-024-00692-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2023] [Indexed: 02/18/2024]
Abstract
Short tandem repeats (STRs) are highly polymorphic sequences throughout the human genome that are composed of repeated copies of a 1-6-bp motif. Over 1 million variable STR loci are known, some of which regulate gene expression and influence complex traits, such as height. Moreover, variants in at least 60 STR loci cause genetic disorders, including Huntington disease and fragile X syndrome. Accurately identifying and genotyping STR variants is challenging, in particular mapping short reads to repetitive regions and inferring expanded repeat lengths. Recent advances in sequencing technology and computational tools for STR genotyping from sequencing data promise to help overcome this challenge and solve genetically unresolved cases and the 'missing heritability' of polygenic traits. Here, we compare STR genotyping methods, analytical tools and their applications to understand the effect of STR variation on health and disease. We identify emergent opportunities to refine genotyping and quality-control approaches as well as to integrate STRs into variant-calling workflows and large cohort analyses.
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Affiliation(s)
- Hope A Tanudisastro
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Ira W Deveson
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Harriet Dashnow
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia.
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13
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Ma K, Huang S, Ng KK, Lake NJ, Joseph S, Xu J, Lek A, Ge L, Woodman KG, Koczwara KE, Cohen J, Ho V, O'Connor CL, Brindley MA, Campbell KP, Lek M. Deep Mutational Scanning in Disease-related Genes with Saturation Mutagenesis-Reinforced Functional Assays (SMuRF). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.12.548370. [PMID: 37873263 PMCID: PMC10592615 DOI: 10.1101/2023.07.12.548370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Interpretation of disease-causing genetic variants remains a challenge in human genetics. Current costs and complexity of deep mutational scanning methods hamper crowd-sourcing approaches toward genome-wide resolution of variants in disease-related genes. Our framework, Saturation Mutagenesis-Reinforced Functional assays (SMuRF), addresses these issues by offering simple and cost-effective saturation mutagenesis, as well as streamlining functional assays to enhance the interpretation of unresolved variants. Applying SMuRF to neuromuscular disease genes FKRP and LARGE1 , we generated functional scores for all possible coding single nucleotide variants, which aid in resolving clinically reported variants of uncertain significance. SMuRF also demonstrates utility in predicting disease severity, resolving critical structural regions, and providing training datasets for the development of computational predictors. Our approach opens new directions for enabling variant-to-function insights for disease genes in a manner that is broadly useful for crowd-sourcing implementation across standard research laboratories.
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14
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Yuan X, Zhang S, Shang H, Tang Y. A novel mutation in SORD gene associated with distal hereditary motor neuropathies. BMC Med Genomics 2024; 17:169. [PMID: 38915017 PMCID: PMC11194961 DOI: 10.1186/s12920-024-01940-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 06/18/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Distal hereditary motor neuropathy (dHMN) is a heterogeneous group of hereditary diseases caused by the gradual degeneration of the lower motor neuron. More than 30 genes associated with dHMN have been reported, while 70-80% of those with the condition are still unable to receive a genetic diagnosis. METHODS A 26-year-old man experiencing gradual weakness in his lower limbs was referred to our hospital, and data on clinical features, laboratory tests, and electrophysiological tests were collected. To identify the disease-causing mutation, we conducted whole exome sequencing (WES) and then validated it through Sanger sequencing for the proband and his parents. Silico analysis was performed to predict the pathogenesis of the identified mutations. A literature review of all reported mutations of the related gene for the disease was performed. RESULTS The patient presented with dHMN phenotype harboring a novel homozygous variant c.361G > C (p.Ala121Pro) in SORD, inherited from his parents, respectively. A121 is a highly conserved site and the mutation was categorized as "likely pathogenic" according to the criteria and guidelines of the American College of Medical Genetics and Genomics (ACMG). A total of 13 published articles including 101 patients reported 18 SORD variants. Almost all described cases have the homozygous deletion variant c.757delG (p.A253Qfs*27) or compound heterozygous state of a combination of c.757delG (p.A253Qfs*27) with another variant. The variant c.361G > C (p.Ala121Pro) detected in our patient was the second homozygous variant in SORD-associated hereditary neuropathy. CONCLUSION One novel homozygous variant c.361G > C (p.Ala121Pro) in SORD was identified in a Chinese patient with dHMN phenotype, which expands the mutation spectrum of SORD-associated hereditary neuropathy and underscores the significance of screening for SORD variants in patients with undiagnosed hereditary neuropathy patients.
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Affiliation(s)
- Xiaoqin Yuan
- Department of Neurology, School of Medicine, Mianyang Central Hospital, University of Electronic Science and Technology of China, Mianyang, Sichuan, 621000, China
| | - Shanshan Zhang
- Department of Neurology, School of Medicine, Mianyang Central Hospital, University of Electronic Science and Technology of China, Mianyang, Sichuan, 621000, China
| | - Huifang Shang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Yufeng Tang
- Department of Neurology, School of Medicine, Mianyang Central Hospital, University of Electronic Science and Technology of China, Mianyang, Sichuan, 621000, China.
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15
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Yangzes S, Verma A, Kaur A, Spalkit S, Kakkar N, Gupta A. Multimodal Imaging in Mucolipidosis Type IV: Siblings With Novel Genetic Variant. Cornea 2024:00003226-990000000-00587. [PMID: 38913974 DOI: 10.1097/ico.0000000000003612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/18/2024] [Indexed: 06/26/2024]
Abstract
PURPOSE Utilization of multimodal imaging techniques to diagnose cases of mucolipidosis type IV (ML-IV) and report a new genetic variant. METHODS This study is a case report. RESULTS Case 1 involves a 4-year-old boy with corneal haziness and global developmental delay who showed an increased reflectivity of the corneal epithelium on anterior segment optical coherence tomography (AS-OCT). In addition, neurologic evaluation was suggestive of ML-IV. Further genetics evaluation confirmed ML-IV. Histology of the button revealed a thickened epithelial basement membrane. Case 2, the younger sibling, showed a milder corneal haze with similar changes on AS-OCT prompting us to further evaluate for ML-IV by genetics (positive MCOLN1 gene mutation). Both instances highlighted varied ML-IV presentations, but a persistent feature was hyperreflective epithelium. CONCLUSIONS Our study emphasizes AS-OCT's role in screening ML-IV and advocates the role of genetic counseling of affected parents. We present 2 South-Asian siblings with ML-IV with a new genetic variant, emphasizing the utility of detailed ophthalmic and neurologic assessments using multimodal imaging.
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Affiliation(s)
- Sonam Yangzes
- Advanced Eye Centre, Department of Ophthalmology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Anjali Verma
- Advanced Eye Centre, Department of Ophthalmology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Anupriya Kaur
- Advanced Pediatric Centre, Department of Pediatrics, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Stanzin Spalkit
- Department of Radiodiagnosis, All India Institute of Medical Sciences, New Delhi, India; and
| | - Nandita Kakkar
- Department of Histopathology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Amit Gupta
- Advanced Eye Centre, Department of Ophthalmology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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16
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Wu R, Khamrui S, Dodatko T, Leandro J, Sabovic A, Violante S, Cross JR, Marsan E, Kumar K, DeVita RJ, Lazarus MB, Houten SM. Characterization, Structure, and Inhibition of the Human Succinyl-CoA:glutarate-CoA Transferase, a Putative Genetic Modifier of Glutaric Aciduria Type 1. ACS Chem Biol 2024. [PMID: 38915184 DOI: 10.1021/acschembio.4c00204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Glutaric Aciduria Type 1 (GA1) is a serious inborn error of metabolism with no pharmacological treatments. A novel strategy to treat this disease is to divert the toxic biochemical intermediates to less toxic or nontoxic metabolites. Here, we report a putative novel target, succinyl-CoA:glutarate-CoA transferase (SUGCT), which we hypothesize suppresses the GA1 metabolic phenotype through decreasing glutaryl-CoA and the derived 3-hydroxyglutaric acid. SUGCT is a type III CoA transferase that uses succinyl-CoA and glutaric acid as substrates. We report the structure of SUGCT, develop enzyme- and cell-based assays, and identify valsartan and losartan carboxylic acid as inhibitors of the enzyme in a high-throughput screen of FDA-approved compounds. The cocrystal structure of SUGCT with losartan carboxylic acid revealed a novel pocket in the active site and further validated the high-throughput screening approach. These results may form the basis for the future development of new pharmacological intervention to treat GA1.
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Affiliation(s)
- Ruoxi Wu
- Department of Pharmacological Sciences, Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Susmita Khamrui
- Department of Pharmacological Sciences, Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Tetyana Dodatko
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - João Leandro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Amanda Sabovic
- Department of Pharmacological Sciences, Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Sara Violante
- The Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, New York 10021, United States
| | - Justin R Cross
- The Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, New York 10021, United States
| | - Eric Marsan
- Department of Pharmacological Sciences, Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Kunal Kumar
- Department of Pharmacological Sciences, Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Robert J DeVita
- Department of Pharmacological Sciences, Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Michael B Lazarus
- Department of Pharmacological Sciences, Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Sander M Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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17
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Lucaci AG, Brew WE, Lamanna J, Selberg A, Carnevale V, Moore AR, Kosakovsky Pond SL. The evolution of mammalian Rem2: unraveling the impact of purifying selection and coevolution on protein function, and implications for human disorders. FRONTIERS IN BIOINFORMATICS 2024; 4:1381540. [PMID: 38978817 PMCID: PMC11228553 DOI: 10.3389/fbinf.2024.1381540] [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: 02/03/2024] [Accepted: 05/28/2024] [Indexed: 07/10/2024] Open
Abstract
Rad And Gem-Like GTP-Binding Protein 2 (Rem2), a member of the RGK family of Ras-like GTPases, is implicated in Huntington's disease and Long QT Syndrome and is highly expressed in the brain and endocrine cells. We examine the evolutionary history of Rem2 identified in various mammalian species, focusing on the role of purifying selection and coevolution in shaping its sequence and protein structural constraints. Our analysis of Rem2 sequences across 175 mammalian species found evidence for strong purifying selection in 70% of non-invariant codon sites which is characteristic of essential proteins that play critical roles in biological processes and is consistent with Rem2's role in the regulation of neuronal development and function. We inferred epistatic effects in 50 pairs of codon sites in Rem2, some of which are predicted to have deleterious effects on human health. Additionally, we reconstructed the ancestral evolutionary history of mammalian Rem2 using protein structure prediction of extinct and extant sequences which revealed the dynamics of how substitutions that change the gene sequence of Rem2 can impact protein structure in variable regions while maintaining core functional mechanisms. By understanding the selective pressures, protein- and gene - interactions that have shaped the sequence and structure of the Rem2 protein, we gain a stronger understanding of its biological and functional constraints.
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Affiliation(s)
- Alexander G Lucaci
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- Weill Cornell Medicine, The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, United States
| | - William E Brew
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - Jason Lamanna
- Department of Biology, Temple University, Philadelphia, PA, United States
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, United States
| | - Avery Selberg
- Department of Biology, Temple University, Philadelphia, PA, United States
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
| | - Vincenzo Carnevale
- Department of Biology, Temple University, Philadelphia, PA, United States
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, United States
| | - Anna R Moore
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - Sergei L Kosakovsky Pond
- Department of Biology, Temple University, Philadelphia, PA, United States
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
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18
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Kuo ME, Parish M, Jonatzke KE, Antonellis A. Comprehensive assessment of recessive, pathogenic AARS1 alleles in a humanized yeast model reveals loss-of-function and dominant-negative effects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599900. [PMID: 38979321 PMCID: PMC11230197 DOI: 10.1101/2024.06.20.599900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Alanyl-tRNA synthetase 1 ( AARS1 ) encodes the enzyme that ligates tRNA molecules to alanine in the cytoplasm, which is required for protein translation. Variants in AARS1 have been implicated in early-onset, multi-system recessive phenotypes and in later-onset dominant peripheral neuropathy; to date, no single variant has been associated with both dominant and recessive diseases raising questions about shared mechanisms between the two inheritance patterns. AARS1 variants associated with recessive disease are predicted to result in null or hypomorphic alleles and this has been demonstrated, in part, via yeast complementation assays. However, pathogenic alleles have not been assessed in a side-by-side manner to carefully scrutinize the strengths and limitations of this model system. To address this, we employed a humanized yeast model to evaluate the functional consequences of all AARS1 missense variants reported in recessive disease. The majority of variants showed variable loss-of-function effects, ranging from no growth to significantly reduced growth. These data deem yeast a reliable model to test the functional consequences of human AARS1 variants; however, our data indicate that this model is prone to false-negative results and is not informative for genotype-phenotype studies. We next tested missense variants associated with no growth for dominant-negative effects. Interestingly, K81T AARS1 , a variant implicated in recessive disease, demonstrated loss-of-function and dominant-negative effects, indicating that certain AARS1 variants may be capable of causing both dominant and recessive disease phenotypes.
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19
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Reyna-Fabián ME, Fernández-Hernández L, Enríquez-Flores S, Apam-Garduño D, Prado-Larrea C, Seo GH, Khang R, Cortés-González V. Deciphering the etiology of undiagnosed ocular anomalies along with systemic alterations in pediatric patients through whole exome sequencing. Sci Rep 2024; 14:14380. [PMID: 38909058 PMCID: PMC11193775 DOI: 10.1038/s41598-024-65227-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 06/18/2024] [Indexed: 06/24/2024] Open
Abstract
Inherited and developmental eye diseases are quite diverse and numerous, and determining their genetic cause is challenging due to their high allelic and locus heterogeneity. New molecular approaches, such as whole exome sequencing (WES), have proven to be powerful molecular tools for addressing these cases. The present study used WES to identify the genetic etiology in ten unrelated Mexican pediatric patients with complex ocular anomalies and other systemic alterations of unknown etiology. The WES approach allowed us to identify five clinically relevant variants in the GZF1, NFIX, TRRAP, FGFR2 and PAX2 genes associated with Larsen, Malan, developmental delay with or without dysmorphic facies and autism, LADD1 and papillorenal syndromes. Mutations located in GZF1 and NFIX were classified as pathogenic, those in TRRAP and FGFR2 were classified as likely pathogenic variants, and those in PAX2 were classified as variants of unknown significance. Protein modeling of the two missense FGFR2 p.(Arg210Gln) and PAX2 p.(Met3Thr) variants showed that these changes could induce potential structural alterations in important functional regions of the proteins. Notably, four out of the five variants were not previously reported, except for the TRRAP gene. Consequently, WES enabled the identification of the genetic cause in 40% of the cases reported. All the syndromes reported herein are very rare, with phenotypes that may overlap with other genetic entities.
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Affiliation(s)
- Miriam E Reyna-Fabián
- Laboratorio de Biología Molecular, Subdirección de Investigación Médica, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Liliana Fernández-Hernández
- Laboratorio de Biología Molecular, Subdirección de Investigación Médica, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Sergio Enríquez-Flores
- Laboratorio de Biomoléculas y Salud Infantil, Instituto Nacional de Pediatría, Mexico City, México
| | - David Apam-Garduño
- Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, México
- Departamento de Genética, Asociación Para Evitar la Ceguera en México, Vicente García Torres No. 46 Barrio San Lucas, Coyoacán, C.P. 04030, Mexico City, México
| | - Carolina Prado-Larrea
- Departamento de Glaucoma, Asociación Para Evitar la Ceguera en México, Mexico City, México
| | - Go Hun Seo
- Medical Genetics Division, 3Billion, Inc., Seoul, South Korea
| | - Rin Khang
- Medical Genetics Division, 3Billion, Inc., Seoul, South Korea
| | - Vianney Cortés-González
- Departamento de Genética, Asociación Para Evitar la Ceguera en México, Vicente García Torres No. 46 Barrio San Lucas, Coyoacán, C.P. 04030, Mexico City, México.
- Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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20
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Chong JX, Berger SI, Baxter S, Smith E, Xiao C, Calame DG, Hawley MH, Rivera-Munoz EA, DiTroia S, Bamshad MJ, Rehm HL. Considerations for reporting variants in novel candidate genes identified during clinical genomic testing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.579012. [PMID: 38370830 PMCID: PMC10871197 DOI: 10.1101/2024.02.05.579012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Since the first novel gene discovery for a Mendelian condition was made via exome sequencing (ES), the rapid increase in the number of genes known to underlie Mendelian conditions coupled with the adoption of exome (and more recently, genome) sequencing by diagnostic testing labs has changed the landscape of genomic testing for rare disease. Specifically, many individuals suspected to have a Mendelian condition are now routinely offered clinical ES. This commonly results in a precise genetic diagnosis but frequently overlooks the identification of novel candidate genes. Such candidates are also less likely to be identified in the absence of large-scale gene discovery research programs. Accordingly, clinical laboratories have both the opportunity, and some might argue a responsibility, to contribute to novel gene discovery which should in turn increase the diagnostic yield for many conditions. However, clinical diagnostic laboratories must necessarily balance priorities for throughput, turnaround time, cost efficiency, clinician preferences, and regulatory constraints, and often do not have the infrastructure or resources to effectively participate in either clinical translational or basic genome science research efforts. For these and other reasons, many laboratories have historically refrained from broadly sharing potentially pathogenic variants in novel genes via networks like Matchmaker Exchange, much less reporting such results to ordering providers. Efforts to report such results are further complicated by a lack of guidelines for clinical reporting and interpretation of variants in novel candidate genes. Nevertheless, there are myriad benefits for many stakeholders, including patients/families, clinicians, researchers, if clinical laboratories systematically and routinely identify, share, and report novel candidate genes. To facilitate this change in practice, we developed criteria for triaging, sharing, and reporting novel candidate genes that are most likely to be promptly validated as underlying a Mendelian condition and translated to use in clinical settings.
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Affiliation(s)
- Jessica X. Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
| | - Seth I. Berger
- Center for Genetic Medicine Research, Children’s National Research Institute, 111 Michigan Ave, NW, Washington, DC, 20010, USA
| | - Samantha Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02141, USA
| | - Erica Smith
- Department of Clinical Diagnostics, Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | - Changrui Xiao
- Department of Neurology, University of California Irvine, 200 South Manchester Ave. St 206E, Orange, CA, 92868, USA
| | - Daniel G. Calame
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Neurosciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Megan H. Hawley
- Clinical Operations, Invitae, 485F US-1 Suite 110, Iselin, NJ, 08830, USA
| | - E. Andres Rivera-Munoz
- Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza T605, Houston, TX, 77030, USA
| | - Stephanie DiTroia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02141, USA
| | | | - Michael J. Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
- Department of Pediatrics, Division of Genetic Medicine, Seattle Children’s Hospital, Seattle, WA, 98195, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02141, USA
- Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge St, Boston, MA, 02114, USA
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21
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Goto K, Koyanagi Y, Akiyama M, Murakami Y, Fukushima M, Fujiwara K, Iijima H, Yamaguchi M, Endo M, Hashimoto K, Ishizu M, Hirakata T, Mizobuchi K, Takayama M, Ota J, Sajiki AF, Kominami T, Ushida H, Fujita K, Kaneko H, Ueno S, Hayashi T, Terao C, Hotta Y, Murakami A, Kuniyoshi K, Kusaka S, Wada Y, Abe T, Nakazawa T, Ikeda Y, Momozawa Y, Sonoda KH, Nishiguchi KM. Disease-specific variant interpretation highlighted the genetic findings in 2325 Japanese patients with retinitis pigmentosa and allied diseases. J Med Genet 2024; 61:613-620. [PMID: 38499336 DOI: 10.1136/jmg-2023-109750] [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: 11/10/2023] [Accepted: 03/02/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND As gene-specific therapy for inherited retinal dystrophy (IRD) advances, unified variant interpretation across institutes is becoming increasingly important. This study aims to update the genetic findings of 86 retinitis pigmentosa (RP)-related genes in a large number of Japanese patients with RP by applying the standardised variant interpretation guidelines for Japanese patients with IRD (J-IRD-VI guidelines) built upon the American College of Medical Genetics and Genomics and the Association for Molecular Pathology rules, and assess the contribution of these genes in RP-allied diseases. METHODS We assessed 2325 probands with RP (n=2155, including n=1204 sequenced previously with the same sequencing panel) and allied diseases (n=170, newly analysed), including Usher syndrome, Leber congenital amaurosis and cone-rod dystrophy (CRD). Target sequencing using a panel of 86 genes was performed. The variants were interpreted according to the J-IRD-VI guidelines. RESULTS A total of 3564 variants were detected, of which 524 variants were interpreted as pathogenic or likely pathogenic. Among these 524 variants, 280 (53.4%) had been either undetected or interpreted as variants of unknown significance or benign variants in our earlier study of 1204 patients with RP. This led to a genetic diagnostic rate in 38.6% of patients with RP, with EYS accounting for 46.7% of the genetically solved patients, showing a 9% increase in diagnostic rate from our earlier study. The genetic diagnostic rate for patients with CRD was 28.2%, with RP-related genes significantly contributing over other allied diseases. CONCLUSION A large-scale genetic analysis using the J-IRD-VI guidelines highlighted the population-specific genetic findings for Japanese patients with IRD; these findings serve as a foundation for the clinical application of gene-specific therapies.
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Affiliation(s)
- Kensuke Goto
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshito Koyanagi
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masato Akiyama
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Ocular Pathology and Imaging Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yusuke Murakami
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masatoshi Fukushima
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kohta Fujiwara
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hanae Iijima
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Mitsuyo Yamaguchi
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Mikiko Endo
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Kazuki Hashimoto
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masataka Ishizu
- Department of Ophthalmology, University of Miyazaki Faculty of Medicine, Miyazaki, Japan
| | - Toshiaki Hirakata
- Department of Ophthalmology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kei Mizobuchi
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| | - Masakazu Takayama
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Junya Ota
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ai Fujita Sajiki
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taro Kominami
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroaki Ushida
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kosuke Fujita
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroki Kaneko
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shinji Ueno
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Ophthalmology, Hirosaki University Graduate School of Medicine, Hisoraki, Japan
| | - Takaaki Hayashi
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Yoshihiro Hotta
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Akira Murakami
- Department of Ophthalmology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kazuki Kuniyoshi
- Department of Ophthalmology, Kindai University Faculty of Medicine, Osaka-sayama, Japan
| | - Shunji Kusaka
- Department of Ophthalmology, Kindai University Faculty of Medicine, Osaka-sayama, Japan
| | | | - Toshiaki Abe
- Division of Clinical Cell Therapy, Tohoku University Graduate School of Medicine United Centers for Advanced Research and Translational Medicine, Sendai, Japan
| | - Toru Nakazawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yasuhiro Ikeda
- Department of Ophthalmology, University of Miyazaki Faculty of Medicine, Miyazaki, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Koh-Hei Sonoda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koji M Nishiguchi
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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22
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Burghel GJ, Ellingford JM, Wright R, Bradford L, Miller J, Watt C, Edgerley J, Naeem F, Banka S. Systematic reanalysis of copy number losses of uncertain clinical significance. J Med Genet 2024; 61:621-625. [PMID: 38604752 DOI: 10.1136/jmg-2023-109559] [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: 10/12/2023] [Accepted: 03/28/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND Reanalysis of exome/genome data improves diagnostic yield. However, the value of reanalysis of clinical array comparative genomic hybridisation (aCGH) data has never been investigated. Case-by-case reanalysis can be challenging in busy diagnostic laboratories. METHODS AND RESULTS We harmonised historical postnatal clinical aCGH results from ~16 000 patients tested via our diagnostic laboratory over ~7 years with current clinical guidance. This led to identification of 37 009 copy number losses (CNLs) including 33 857 benign, 2173 of uncertain significance and 979 pathogenic. We found benign CNLs to be significantly less likely to encompass haploinsufficient genes compared with the pathogenic or CNLs of uncertain significance in our database. Based on this observation, we developed a reanalysis pipeline using up-to-date disease association data and haploinsufficiency scores and shortlisted 207 CNLs of uncertain significance encompassing at least one autosomal dominant disease-gene associated with haploinsufficiency or loss-of-function mechanism. Clinical scientist reviews led to reclassification of 15 CNLs of uncertain significance as pathogenic or likely pathogenic. This was ~0.7% of the starting cohort of 2173 CNLs of uncertain significance and 7.2% of 207 shortlisted CNLs. The reclassified CNLs included first cases of CNV-mediated disease for some genes where all previously described cases involved only point variants. Interestingly, some CNLs could not be reclassified because the phenotypes of patients with CNLs seemed distinct from the known clinical features resulting from point variants, thus raising questions about accepted underlying disease mechanisms. CONCLUSIONS Reanalysis of clinical aCGH data increases diagnostic yield.
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Affiliation(s)
- George J Burghel
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Jamie M Ellingford
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Ronnie Wright
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Lauren Bradford
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Jake Miller
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Christopher Watt
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Jonathan Edgerley
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Farah Naeem
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
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23
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Smith CEL, Laugel-Haushalter V, Hany U, Best S, Taylor RL, Poulter JA, Wortmann SB, Feichtinger RG, Mayr JA, Al Bahlani S, Nikolopoulos G, Rigby A, Black GC, Watson CM, Mansour S, Inglehearn CF, Mighell AJ, Bloch-Zupan A. Biallelic variants in Plexin B2 ( PLXNB2) cause amelogenesis imperfecta, hearing loss and intellectual disability. J Med Genet 2024; 61:689-698. [PMID: 38458752 DOI: 10.1136/jmg-2023-109728] [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: 11/02/2023] [Accepted: 02/22/2024] [Indexed: 03/10/2024]
Abstract
BACKGROUND Plexins are large transmembrane receptors for the semaphorin family of signalling proteins. Semaphorin-plexin signalling controls cellular interactions that are critical during development as well as in adult life stages. Nine plexin genes have been identified in humans, but despite the apparent importance of plexins in development, only biallelic PLXND1 and PLXNA1 variants have so far been associated with Mendelian genetic disease. METHODS Eight individuals from six families presented with a recessively inherited variable clinical condition, with core features of amelogenesis imperfecta (AI) and sensorineural hearing loss (SNHL), with variable intellectual disability. Probands were investigated by exome or genome sequencing. Common variants and those unlikely to affect function were excluded. Variants consistent with autosomal recessive inheritance were prioritised. Variant segregation analysis was performed by Sanger sequencing. RNA expression analysis was conducted in C57Bl6 mice. RESULTS Rare biallelic pathogenic variants in plexin B2 (PLXNB2), a large transmembrane semaphorin receptor protein, were found to segregate with disease in all six families. The variants identified include missense, nonsense, splicing changes and a multiexon deletion. Plxnb2 expression was detected in differentiating ameloblasts. CONCLUSION We identify rare biallelic pathogenic variants in PLXNB2 as a cause of a new autosomal recessive, phenotypically diverse syndrome with AI and SNHL as core features. Intellectual disability, ocular disease, ear developmental abnormalities and lymphoedema were also present in multiple cases. The variable syndromic human phenotype overlaps with that seen in Plxnb2 knockout mice, and, together with the rarity of human PLXNB2 variants, may explain why pathogenic variants in PLXNB2 have not been reported previously.
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Affiliation(s)
- Claire E L Smith
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Virginie Laugel-Haushalter
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Strasbourg, France
| | - Ummey Hany
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Sunayna Best
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Rachel L Taylor
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
- EMQN CIC, Manchester, UK
| | - James A Poulter
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Saskia B Wortmann
- Department of Paediatrics, University Children's Hospital, Salzburger Landesklinken (SALK) and Paracelsus Medical University, Salzburg, Austria
- Amalia Children's Hospital, Radboudumc, Nijmegen, The Netherlands
| | - Rene G Feichtinger
- Department of Paediatrics, University Children's Hospital, Salzburger Landesklinken (SALK) and Paracelsus Medical University, Salzburg, Austria
| | - Johannes A Mayr
- Department of Paediatrics, University Children's Hospital, Salzburger Landesklinken (SALK) and Paracelsus Medical University, Salzburg, Austria
| | - Suhaila Al Bahlani
- Dental & OMFS Clinic, Al Nahdha Hospital, Government of Oman Ministry of Health, Muscat, Oman
| | | | - Alice Rigby
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
- School of Dentistry, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Graeme C Black
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Christopher M Watson
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St James's University Hospital, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Sahar Mansour
- Lymphovascular Research Unit, Molecular and Clinical Sciences Research Institute, St George's Hospital, University of London, London, UK
- SW Thames Regional Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Chris F Inglehearn
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Alan J Mighell
- School of Dentistry, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Agnès Bloch-Zupan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Strasbourg, France
- Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France
- Centre de référence des maladies rares orales et dentaires O-Rares, Filière Santé Maladies rares TETE COU, European Reference Network CRANIO, Pôle de Médecine et Chirurgie Bucco-dentaires, Hôpital Civil, Hôpitaux Universitaires de Strasbourg (HUS), Strasbourg, France
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24
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Chen M, Dahl A. A robust model for cell type-specific interindividual variation in single-cell RNA sequencing data. Nat Commun 2024; 15:5229. [PMID: 38898015 PMCID: PMC11186839 DOI: 10.1038/s41467-024-49242-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has been widely used to characterize cell types based on their average gene expression profiles. However, most studies do not consider cell type-specific variation across donors. Modelling this cell type-specific inter-individual variation could help elucidate cell type-specific biology and inform genes and cell types underlying complex traits. We therefore develop a new model to detect and quantify cell type-specific variation across individuals called CTMM (Cell Type-specific linear Mixed Model). We use extensive simulations to show that CTMM is powerful and unbiased in realistic settings. We also derive calibrated tests for cell type-specific interindividual variation, which is challenging given the modest sample sizes in scRNA-seq. We apply CTMM to scRNA-seq data from human induced pluripotent stem cells to characterize the transcriptomic variation across donors as cells differentiate into endoderm. We find that almost 100% of transcriptome-wide variability between donors is differentiation stage-specific. CTMM also identifies individual genes with statistically significant stage-specific variability across samples, including 85 genes that do not have significant stage-specific mean expression. Finally, we extend CTMM to partition interindividual covariance between stages, which recapitulates the overall differentiation trajectory. Overall, CTMM is a powerful tool to illuminate cell type-specific biology in scRNA-seq.
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Affiliation(s)
- Minhui Chen
- Section of Genetic Medicine, University of Chicago, Chicago, IL, 60637, USA.
| | - Andy Dahl
- Section of Genetic Medicine, University of Chicago, Chicago, IL, 60637, USA.
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Nagelberg AL, Sihota TS, Chuang YC, Shi R, Chow JLM, English J, MacAulay C, Lam S, Lam WL, Lockwood WW. Integrative genomics identifies SHPRH as a tumor suppressor gene in lung adenocarcinoma that regulates DNA damage response. Br J Cancer 2024:10.1038/s41416-024-02755-y. [PMID: 38890444 DOI: 10.1038/s41416-024-02755-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Identification of driver mutations and development of targeted therapies has considerably improved outcomes for lung cancer patients. However, significant limitations remain with the lack of identified drivers in a large subset of patients. Here, we aimed to assess the genomic landscape of lung adenocarcinomas (LUADs) from individuals without a history of tobacco use to reveal new genetic drivers of lung cancer. METHODS Integrative genomic analyses combining whole-exome sequencing, copy number, and mutational information for 83 LUAD tumors was performed and validated using external datasets to identify genetic variants with a predicted functional consequence and assess association with clinical outcomes. LUAD cell lines with alteration of identified candidates were used to functionally characterize tumor suppressive potential using a conditional expression system both in vitro and in vivo. RESULTS We identified 21 genes with evidence of positive selection, including 12 novel candidates that have yet to be characterized in LUAD. In particular, SNF2 Histone Linker PHD RING Helicase (SHPRH) was identified due to its frequency of biallelic disruption and location within the familial susceptibility locus on chromosome arm 6q. We found that low SHPRH mRNA expression is associated with poor survival outcomes in LUAD patients. Furthermore, we showed that re-expression of SHPRH in LUAD cell lines with inactivating alterations for SHPRH reduces their in vitro colony formation and tumor burden in vivo. Finally, we explored the biological pathways associated SHPRH inactivation and found an association with the tolerance of LUAD cells to DNA damage. CONCLUSIONS These data suggest that SHPRH is a tumor suppressor gene in LUAD, whereby its expression is associated with more favorable patient outcomes, reduced tumor and mutational burden, and may serve as a predictor of response to DNA damage. Thus, further exploration into the role of SHPRH in LUAD development may make it a valuable biomarker for predicting LUAD risk and prognosis.
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Affiliation(s)
- Amy L Nagelberg
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Tianna S Sihota
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Yu-Chi Chuang
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | - Rocky Shi
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | - Justine L M Chow
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - John English
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Calum MacAulay
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Stephen Lam
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Wan L Lam
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | - William W Lockwood
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada.
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada.
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Brichova M, Klimova A, Heissigerova J, Svozilkova P, Vaneckova M, Dolezalova P, Nemcova D, Michalickova M, Jedlickova J, Dudakova L, Liskova P. Blau Syndrome: Challenging Molecular Genetic Diagnostics of Autoinflammatory Disease. Genes (Basel) 2024; 15:799. [PMID: 38927735 PMCID: PMC11203189 DOI: 10.3390/genes15060799] [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: 05/10/2024] [Revised: 06/13/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
The aim of this study was to describe the clinical and molecular genetic findings in seven individuals from three unrelated families with Blau syndrome. A complex ophthalmic and general health examination including diagnostic imaging was performed. The NOD2 mutational hot spot located in exon 4 was Sanger sequenced in all three probands. Two individuals also underwent autoinflammatory disorder gene panel screening, and in one subject, exome sequencing was performed. Blau syndrome presenting as uveitis, skin rush or arthritis was diagnosed in four cases from three families. In two individuals from one family, only camptodactyly was noted, while another member had camptodactyly in combination with non-active uveitis and angioid streaks. One proband developed two attacks of meningoencephalitis attributed to presumed neurosarcoidosis, which is a rare finding in Blau syndrome. The probands from families 1 and 2 carried pathogenic variants in NOD2 (NM_022162.3): c.1001G>A p.(Arg334Gln) and c.1000C>T p.(Arg334Trp), respectively. In family 3, two variants of unknown significance in a heterozygous state were found: c.1412G>T p.(Arg471Leu) in NOD2 and c.928C>T p.(Arg310*) in NLRC4 (NM_001199139.1). In conclusion, Blau syndrome is a phenotypically highly variable, and there is a need to raise awareness about all clinical manifestations, including neurosarcoidosis. Variants of unknown significance pose a significant challenge regarding their contribution to etiopathogenesis of autoinflammatory diseases.
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Affiliation(s)
- Michaela Brichova
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, U Nemocnice 2, 128 08 Prague, Czech Republic; (M.B.); (J.H.); (P.S.); (M.M.)
| | - Aneta Klimova
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, U Nemocnice 2, 128 08 Prague, Czech Republic; (M.B.); (J.H.); (P.S.); (M.M.)
| | - Jarmila Heissigerova
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, U Nemocnice 2, 128 08 Prague, Czech Republic; (M.B.); (J.H.); (P.S.); (M.M.)
| | - Petra Svozilkova
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, U Nemocnice 2, 128 08 Prague, Czech Republic; (M.B.); (J.H.); (P.S.); (M.M.)
| | - Manuela Vaneckova
- Department of Radiology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Katerinska 30, 128 21 Prague, Czech Republic;
| | - Pavla Dolezalova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 2, 128 08 Prague, Czech Republic; (P.D.); (D.N.); (J.J.); (L.D.)
| | - Dana Nemcova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 2, 128 08 Prague, Czech Republic; (P.D.); (D.N.); (J.J.); (L.D.)
| | - Marcela Michalickova
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, U Nemocnice 2, 128 08 Prague, Czech Republic; (M.B.); (J.H.); (P.S.); (M.M.)
| | - Jana Jedlickova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 2, 128 08 Prague, Czech Republic; (P.D.); (D.N.); (J.J.); (L.D.)
| | - Lubica Dudakova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 2, 128 08 Prague, Czech Republic; (P.D.); (D.N.); (J.J.); (L.D.)
| | - Petra Liskova
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, U Nemocnice 2, 128 08 Prague, Czech Republic; (M.B.); (J.H.); (P.S.); (M.M.)
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 2, 128 08 Prague, Czech Republic; (P.D.); (D.N.); (J.J.); (L.D.)
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Strober BJ, Zhang MJ, Amariuta T, Rossen J, Price AL. Fine-mapping causal tissues and genes at disease-associated loci. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.11.01.23297909. [PMID: 37961337 PMCID: PMC10635248 DOI: 10.1101/2023.11.01.23297909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Heritable diseases often manifest in a highly tissue-specific manner, with different disease loci mediated by genes in distinct tissues or cell types. We propose Tissue-Gene Fine-Mapping (TGFM), a fine-mapping method that infers the posterior probability (PIP) for each gene-tissue pair to mediate a disease locus by analyzing GWAS summary statistics (and in-sample LD) and leveraging eQTL data from diverse tissues to build cis-predicted expression models; TGFM also assigns PIPs to causal variants that are not mediated by gene expression in assayed genes and tissues. TGFM accounts for both co-regulation across genes and tissues and LD between SNPs (generalizing existing fine-mapping methods), and incorporates genome-wide estimates of each tissue's contribution to disease as tissue-level priors. TGFM was well-calibrated and moderately well-powered in simulations; unlike previous methods, TGFM was able to attain correct calibration by modeling uncertainty in cis-predicted expression models. We applied TGFM to 45 UK Biobank diseases/traits (average N = 316K) using eQTL data from 38 GTEx tissues. TGFM identified an average of 147 PIP > 0.5 causal genetic elements per disease/trait, of which 11% were gene-tissue pairs. Implicated gene-tissue pairs were concentrated in known disease-critical tissues, and causal genes were strongly enriched in disease-relevant gene sets. Causal gene-tissue pairs identified by TGFM recapitulated known biology (e.g., TPO-thyroid for Hypothyroidism), but also included biologically plausible novel findings (e.g., SLC20A2-artery aorta for Diastolic blood pressure). Further application of TGFM to single-cell eQTL data from 9 cell types in peripheral blood mononuclear cells (PBMC), analyzed jointly with GTEx tissues, identified 30 additional causal gene-PBMC cell type pairs at PIP > 0.5-primarily for autoimmune disease and blood cell traits, including the biologically plausible example of CD52 in classical monocyte cells for Monocyte count. In conclusion, TGFM is a robust and powerful method for fine-mapping causal tissues and genes at disease-associated loci.
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Affiliation(s)
- Benjamin J. Strober
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Martin Jinye Zhang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Tiffany Amariuta
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jordan Rossen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alkes L. Price
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Dulamea AO, Lupescu IC. Cerebral cavernous malformations - An overview on genetics, clinical aspects and therapeutic strategies. J Neurol Sci 2024; 461:123044. [PMID: 38749279 DOI: 10.1016/j.jns.2024.123044] [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: 10/16/2023] [Revised: 04/28/2024] [Accepted: 05/08/2024] [Indexed: 06/13/2024]
Abstract
Cerebral cavernous malformations (CCMs) are abnormally packed blood vessels lined with endothelial cells, that do not exhibit intervening tight junctions, lack muscular and elastic layers and are usually surrounded by hemosiderin and gliosis. CCMs may be sporadic or familial autosomal dominant (FCCMs) caused by loss of function mutations in CCM1 (KRIT1), CCM2 (MGC4607), and CCM3 (PDCD10) genes. In the FCCMs, patients have multiple CCMs, different family members are affected, and developmental venous anomalies are absent. CCMs may be asymptomatic or may manifest with focal neurological deficits with or without associated hemorrhage andseizures. Recent studies identify a digenic "triple-hit" mechanism involving the aquisition of three distinct genetic mutations that culminate in phosphatidylinositol-3-kinase (PIK3CA) gain of function, as the basis for rapidly growing and clinically symptomatic CCMs. The pathophysiology of CCMs involves signaling aberrations in the neurovascular unit, including proliferative dysangiogenesis, blood-brain barrier hyperpermeability, inflammation and immune mediated processes, anticoagulant vascular domain, and gut microbiome-driven mechanisms. Clinical trials are investigating potential therapies, magnetic resonance imaging and plasma biomarkers for hemorrhage and CCMs-related epilepsy, as well as different techniques of neuronavigation and neurosonology to guide surgery in order to minimize post-operatory morbidity and mortality. This review addresses the recent data about the natural history, genetics, neuroimaging and therapeutic approaches for CCMs.
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Affiliation(s)
- Adriana Octaviana Dulamea
- Carol Davila University of Medicine and Pharmacy, 37 Dionisie Lupu Street, 020021 Bucharest, Romania; Fundeni Clinical Institute, Department of Neurology, 258 Fundeni Street, 022328 Bucharest, Romania.
| | - Ioan Cristian Lupescu
- Carol Davila University of Medicine and Pharmacy, 37 Dionisie Lupu Street, 020021 Bucharest, Romania; Fundeni Clinical Institute, Department of Neurology, 258 Fundeni Street, 022328 Bucharest, Romania
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Ilic N, Maric N, Maver A, Armengol L, Kravljanac R, Cirkovic J, Krstic J, Radivojevic D, Cirkovic S, Ostojic S, Krasic S, Paripovic A, Vukomanovic V, Peterlin B, Maric G, Sarajlija A. Reverse Phenotyping after Whole-Exome Sequencing in Children with Developmental Delay/Intellectual Disability-An Exception or a Necessity? Genes (Basel) 2024; 15:789. [PMID: 38927725 PMCID: PMC11203244 DOI: 10.3390/genes15060789] [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: 05/02/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
This study delves into the diagnostic yield of whole-exome sequencing (WES) in pediatric patients presenting with developmental delay/intellectual disability (DD/ID), while also exploring the utility of Reverse Phenotyping (RP) in refining diagnoses. A cohort of 100 pediatric patients underwent WES, yielding a diagnosis in 66% of cases. Notably, RP played a significant role in cases with negative prior genetic testing, underscoring its significance in complex diagnostic scenarios. The study revealed a spectrum of genetic conditions contributing to DD/ID, illustrating the heterogeneity of etiological factors. Despite challenges, WES demonstrated effectiveness, particularly in cases with metabolic abnormalities. Reverse phenotyping was indicated in half of the patients with positive WES findings. Neural network models exhibited moderate-to-exceptional predictive abilities for aiding in patient selection for WES and RP. These findings emphasize the importance of employing comprehensive genetic approaches and RP in unraveling the genetic underpinnings of DD/ID, thereby facilitating personalized management and genetic counseling for affected individuals and families. This research contributes insights into the genetic landscape of DD/ID, enhancing our understanding and guiding clinical practice in this particular field of clinical genetics.
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Affiliation(s)
- Nikola Ilic
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.C.); (J.K.)
| | - Nina Maric
- Clinic for Children Diseases, University Clinical Center of the Republic of Srpska, Banja Luka 78000, Bosnia and Herzegovina;
| | - Ales Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.M.); (B.P.)
| | - Lluis Armengol
- CIBER en Epidemiología y Salud Pública (CIBERESP), Genes and Disease Program, Center for Genomic Regulation (CRG-UPF), 08003 Barcelona, Spain;
| | - Ruzica Kravljanac
- Department of Neurology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (R.K.); (S.O.)
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
| | - Jana Cirkovic
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.C.); (J.K.)
| | - Jovana Krstic
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.C.); (J.K.)
| | - Danijela Radivojevic
- Laboratory of Medical Genetics, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (D.R.); (S.C.)
| | - Sanja Cirkovic
- Laboratory of Medical Genetics, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (D.R.); (S.C.)
| | - Slavica Ostojic
- Department of Neurology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (R.K.); (S.O.)
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
| | - Stasa Krasic
- Department of Cardiology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia;
| | - Aleksandra Paripovic
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
- Department of Nephrology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia
| | - Vladislav Vukomanovic
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
- Department of Cardiology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia;
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.M.); (B.P.)
| | - Gorica Maric
- Institute of Epidemiology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia;
| | - Adrijan Sarajlija
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.C.); (J.K.)
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
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Qin G, Dai J, Chien S, Martins TJ, Loera B, Nguyen QH, Oakes ML, Tercan B, Aguilar B, Hagen L, McCune J, Gelinas R, Monnat RJ, Shmulevich I, Becker PS. Mutation Patterns Predict Drug Sensitivity in Acute Myeloid Leukemia. Clin Cancer Res 2024; 30:2659-2671. [PMID: 38619278 PMCID: PMC11176916 DOI: 10.1158/1078-0432.ccr-23-1674] [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: 06/07/2023] [Revised: 08/15/2023] [Accepted: 12/08/2023] [Indexed: 04/16/2024]
Abstract
PURPOSE The inherent genetic heterogeneity of acute myeloid leukemia (AML) has challenged the development of precise and effective therapies. The objective of this study was to elucidate the genomic basis of drug resistance or sensitivity, identify signatures for drug response prediction, and provide resources to the research community. EXPERIMENTAL DESIGN We performed targeted sequencing, high-throughput drug screening, and single-cell genomic profiling on leukemia cell samples derived from patients with AML. Statistical approaches and machine learning models were applied to identify signatures for drug response prediction. We also integrated large public datasets to understand the co-occurring mutation patterns and further investigated the mutation profiles in the single cells. The features revealed in the co-occurring or mutual exclusivity pattern were further subjected to machine learning models. RESULTS We detected genetic signatures associated with sensitivity or resistance to specific agents, and identified five co-occurring mutation groups. The application of single-cell genomic sequencing unveiled the co-occurrence of variants at the individual cell level, highlighting the presence of distinct subclones within patients with AML. Using the mutation pattern for drug response prediction demonstrates high accuracy in predicting sensitivity to some drug classes, such as MEK inhibitors for RAS-mutated leukemia. CONCLUSIONS Our study highlights the importance of considering the gene mutation patterns for the prediction of drug response in AML. It provides a framework for categorizing patients with AML by mutations that enable drug sensitivity prediction.
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Affiliation(s)
| | - Jin Dai
- Division of Hematology, University of Washington, Seattle, Washington
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Sylvia Chien
- Division of Hematology, University of Washington, Seattle, Washington
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Timothy J. Martins
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Brenda Loera
- City of Hope National Medical Center, Duarte, California
| | - Quy H. Nguyen
- University of California, Irvine, Irvine, California
| | | | - Bahar Tercan
- Institute for Systems Biology, Seattle, Washington
| | | | - Lauren Hagen
- Institute for Systems Biology, Seattle, Washington
| | | | | | - Raymond J. Monnat
- Lab Medicine|Pathology and Genome Sciences, University of Washington, Seattle, Washington
| | | | - Pamela S. Becker
- Division of Hematology, University of Washington, Seattle, Washington
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
- City of Hope National Medical Center, Duarte, California
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Ralli S, Vira T, Robles-Espinoza CD, Adams DJ, Brooks-Wilson AR. Variant ranking pipeline for complex familial disorders. Sci Rep 2024; 14:13599. [PMID: 38866901 PMCID: PMC11169219 DOI: 10.1038/s41598-024-64169-3] [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: 08/03/2023] [Accepted: 06/05/2024] [Indexed: 06/14/2024] Open
Abstract
Identifying genetic susceptibility factors for complex disorders remains a challenging task. To analyze collections of small and large pedigrees where genetic heterogeneity is likely, but biological commonalities are plausible, we have developed a weights-based pipeline to prioritize variants and genes. The Weights-based vAriant Ranking in Pedigrees (WARP) pipeline prioritizes variants using 5 weights: disease incidence rate, number of cases in a family, genome fraction shared amongst cases in a family, allele frequency and variant deleteriousness. Weights, except for the population allele frequency weight, are normalized between 0 and 1. Weights are combined multiplicatively to produce family-specific-variant weights that are then averaged across all families in which the variant is observed to generate a multifamily weight. Sorting multifamily weights in descending order creates a ranked list of variants and genes for further investigation. WARP was validated using familial melanoma sequence data from the European Genome-phenome Archive. The pipeline identified variation in known germline melanoma genes POT1, MITF and BAP1 in 4 out of 13 families (31%). Analysis of the other 9 families identified several interesting genes, some of which might have a role in melanoma. WARP provides an approach to identify disease predisposing genes in studies with small and large pedigrees.
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Affiliation(s)
- Sneha Ralli
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Tariq Vira
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | | | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Angela R Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada.
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
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Joris S, Giron P, Olsen C, Seneca S, Gheldof A, Staessens S, Shahi RB, De Brakeleer S, Teugels E, De Grève J, Hes FJ. Identification of RAD17 as a candidate cancer predisposition gene in families with histories of pancreatic and breast cancers. BMC Cancer 2024; 24:723. [PMID: 38872153 PMCID: PMC11170902 DOI: 10.1186/s12885-024-12442-z] [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: 06/20/2023] [Accepted: 05/28/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Among the 10% of pancreatic cancers that occur in a familial context, around a third carry a pathogenic variant in a cancer predisposition gene. Genetic studies of pancreatic cancer predisposition are limited by high mortality rates amongst index patients and other affected family members. The genetic risk for pancreatic cancer is often shared with breast cancer susceptibility genes, most notably BRCA2, PALB2, ATM and BRCA1. Therefore, we hypothesized that additional shared genetic etiologies might be uncovered by studying families presenting with both breast and pancreatic cancer. METHODS Focusing on a multigene panel of 276 DNA Damage Repair (DDR) genes, we performed next-generation sequencing in a cohort of 41 families with at least three breast cancer cases and one pancreatic cancer. When the index patient with pancreatic cancer was deceased, close relatives (first or second-degree) affected with breast cancer were tested (39 families). RESULTS We identified 27 variants of uncertain significance in DDR genes. A splice site variant (c.1605 + 2T > A) in the RAD17 gene stood out, as a likely loss of function variant. RAD17 is a checkpoint protein that recruits the MRN (MRE11-RAD50-NBS1) complex to initiate DNA signaling, leading to DNA double-strand break repair. CONCLUSION Within families with breast and pancreatic cancer, we identified RAD17 as a novel candidate predisposition gene. Further genetic studies are warranted to better understand the potential pathogenic effect of RAD17 variants and in other DDR genes.
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Affiliation(s)
- Sofie Joris
- Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, Brussels, 1090, Belgium.
- The Oncology Research Center, the Laboratory for Medical & Molecular Oncology (LMMO), Faculty of Medicine, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
| | - Philippe Giron
- Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, Brussels, 1090, Belgium
| | - Catharina Olsen
- Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, Brussels, 1090, Belgium
| | - Sara Seneca
- Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, Brussels, 1090, Belgium
| | - Alexander Gheldof
- Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, Brussels, 1090, Belgium
| | - Shula Staessens
- The Oncology Research Center, the Laboratory for Medical & Molecular Oncology (LMMO), Faculty of Medicine, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Rajendra Bahadur Shahi
- The Oncology Research Center, the Laboratory for Medical & Molecular Oncology (LMMO), Faculty of Medicine, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Sylvia De Brakeleer
- The Oncology Research Center, the Laboratory for Medical & Molecular Oncology (LMMO), Faculty of Medicine, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Erik Teugels
- The Oncology Research Center, the Laboratory for Medical & Molecular Oncology (LMMO), Faculty of Medicine, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Jacques De Grève
- Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, Brussels, 1090, Belgium
- The Oncology Research Center, the Laboratory for Medical & Molecular Oncology (LMMO), Faculty of Medicine, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Frederik J Hes
- Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, Brussels, 1090, Belgium
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Liu HK, Hao HL, You H, Feng F, Qi XH, Huang XY, Hou B, Tian CG, Wang H, Yang HM, Wang J, Wu R, Fang H, Zhou JN, Zhang JG, Zhang ZX. A Cysteinyl-tRNA Synthetase Mutation Causes Novel Autosomal-Dominant Inheritance of a Parkinsonism/Spinocerebellar-Ataxia Complex. Neurosci Bull 2024:10.1007/s12264-024-01231-0. [PMID: 38869703 DOI: 10.1007/s12264-024-01231-0] [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: 08/19/2023] [Accepted: 12/22/2023] [Indexed: 06/14/2024] Open
Abstract
This study aimed to identify possible pathogenic genes in a 90-member family with a rare combination of multiple neurodegenerative disease phenotypes, which has not been depicted by the known neurodegenerative disease. We performed physical and neurological examinations with International Rating Scales to assess signs of ataxia, Parkinsonism, and cognitive function, as well as brain magnetic resonance imaging scans with seven sequences. We searched for co-segregations of abnormal repeat-expansion loci, pathogenic variants in known spinocerebellar ataxia-related genes, and novel rare mutations via whole-genome sequencing and linkage analysis. A rare co-segregating missense mutation in the CARS gene was validated by Sanger sequencing and the aminoacylation activity of mutant CARS was measured by spectrophotometric assay. This pedigree presented novel late-onset core characteristics including cerebellar ataxia, Parkinsonism, and pyramidal signs in all nine affected members. Brain magnetic resonance imaging showed cerebellar/pons atrophy, pontine-midline linear hyperintensity, decreased rCBF in the bilateral basal ganglia and cerebellar dentate nucleus, and hypo-intensities of the cerebellar dentate nuclei, basal ganglia, mesencephalic red nuclei, and substantia nigra, all of which suggested neurodegeneration. Whole-genome sequencing identified a novel pathogenic heterozygous mutation (E795V) in the CARS gene, meanwhile, exhibited none of the known repeat-expansions or point mutations in pathogenic genes. Remarkably, this CARS mutation causes a 20% decrease in aminoacylation activity to charge tRNACys with L-cysteine in protein synthesis compared with that of the wild type. All family members carrying a heterozygous mutation CARS (E795V) had the same clinical manifestations and neuropathological changes of Parkinsonism and spinocerebellar-ataxia. These findings identify novel pathogenesis of Parkinsonism-spinocerebellar ataxia and provide insights into its genetic architecture.
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Affiliation(s)
- Han-Kui Liu
- BGI Genomics and BGI Research, Shenzhen, 518083, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Clin Lab, BGI Genomics, Shijiazhuang, 050011, China
| | - Hong-Lin Hao
- Department of Neurology, Clinical Epidemiology Unit, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Hui You
- Department of Neurology, Clinical Epidemiology Unit, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Feng Feng
- Department of Neurology, Clinical Epidemiology Unit, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xiu-Hong Qi
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | | | - Bo Hou
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | | | - Han Wang
- Department of Neurology, Clinical Epidemiology Unit, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | | | - Jian Wang
- BGI Genomics and BGI Research, Shenzhen, 518083, China
| | - Rui Wu
- Department of Pathology, Beijing Key Laboratory of Biomarker Research and Transformation for Neurodegenerative Diseases, Peking University Third Hospital, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Hui Fang
- Anhui Provincial Children's Hospital, Children's Hospital of Fudan University, Hefei, 230051, China
| | - Jiang-Ning Zhou
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Institute of Brain Science, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Jian-Guo Zhang
- BGI Genomics and BGI Research, Shenzhen, 518083, China.
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Clin Lab, BGI Genomics, Shijiazhuang, 050011, China.
| | - Zhen-Xin Zhang
- Department of Neurology, Clinical Epidemiology Unit, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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Gudmundsson S, Singer-Berk M, Stenton SL, Goodrich JK, Wilson MW, Einson J, Watts NA, Lappalainen T, Rehm HL, MacArthur DG, O’Donnell-Luria A. Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.593113. [PMID: 38915639 PMCID: PMC11195293 DOI: 10.1101/2024.06.12.593113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Incomplete penetrance, or absence of disease phenotype in an individual with a disease-associated variant, is a major challenge in variant interpretation. Studying individuals with apparent incomplete penetrance can shed light on underlying drivers of altered phenotype penetrance. Here, we investigate clinically relevant variants from ClinVar in 807,162 individuals from the Genome Aggregation Database (gnomAD), demonstrating improved representation in gnomAD version 4. We then conduct a comprehensive case-by-case assessment of 734 predicted loss of function variants (pLoF) in 77 genes associated with severe, early-onset, highly penetrant haploinsufficient disease. We identified explanations for the presumed lack of disease manifestation in 701 of the variants (95%). Individuals with unexplained lack of disease manifestation in this set of disorders rarely occur, underscoring the need and power of deep case-by-case assessment presented here to minimize false assignments of disease risk, particularly in unaffected individuals with higher rates of secondary properties that result in rescue.
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Affiliation(s)
- Sanna Gudmundsson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sarah L. Stenton
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Julia K. Goodrich
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael W. Wilson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nicholas A Watts
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Tuuli Lappalainen
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
- New York Genome Center, New York, NY, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Daniel G. MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Anne O’Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine & Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
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Hahn E, Mighton C, Fisher Y, Wong A, Di Gioacchino V, Watkins N, Mayers J, Bombard Y, Charames GS, Lerner-Ellis J. Variant classification changes over time in the clinical molecular diagnostic laboratory setting. J Med Genet 2024:jmg-2023-109772. [PMID: 38806232 DOI: 10.1136/jmg-2023-109772] [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: 11/20/2023] [Accepted: 05/12/2024] [Indexed: 05/30/2024]
Abstract
BACKGROUND Variant classification in the setting of germline genetic testing is necessary for patients and their families to receive proper care. Variants are classified as pathogenic (P), likely pathogenic (LP), uncertain significance (VUS), likely benign (LB) and benign (B) using the standards and guidelines recommended by the American College of Medical Genetics and the Association for Molecular Pathology, with modifications for specific genes. As the literature continues to rapidly expand, and evidence continues to accumulate, prior classifications can be updated accordingly. In this study, we aim to characterise variant reclassifications in Ontario. METHODS DNA samples from patients seen at hereditary cancer clinics in Ontario from January 2012 to April 2022 were submitted for testing. Patients met provincial eligibility criteria for testing for hereditary cancer syndromes or polycystic kidney disease. Reclassification events were determined to be within their broader category of significance (B to LB or vice versa, or P to LP or vice versa) or outside of their broader category as significance (ie, significant reclassifications from B/LB or VUS or P/LP, from P/LP to VUS or B/LB, or from VUS to any other category). RESULTS Of the 8075 unique variants included in this study, 23.7% (1912) of variants were reassessed, and 7.2% (578) of variants were reclassified. Of these, 351 (60.7%) variants were reclassified outside of their broader category of significance. Overall, the final classification was significantly different for 336 (58.1%) variants. Importantly, most reclassified variants were downgraded to a more benign classification (n=245; 72.9%). Of note, most reclassified VUS was downgraded to B/LB (n=233; 84.7%). CONCLUSIONS The likelihood for reclassification of variants on reassessment is high. Most reclassified variants were downgraded to a more benign classification. Our findings highlight the importance of periodic variant reassessment to ensure timely and appropriate care for patients and their families.
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Affiliation(s)
- Elan Hahn
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Chloe Mighton
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Genomics Health Services Research Program, St Michael's Hospital Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Yael Fisher
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Andrew Wong
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Vanessa Di Gioacchino
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas Watkins
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Justin Mayers
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Yvonne Bombard
- Genomics Health Services Research Program, St Michael's Hospital Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - George S Charames
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
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Sun Y, Men W, Kennerknecht I, Fang W, Zheng HF, Zhang W, Rao Y. Human genetics of face recognition: discovery of MCTP2 mutations in humans with face blindness (congenital prosopagnosia). Genetics 2024; 227:iyae047. [PMID: 38547502 DOI: 10.1093/genetics/iyae047] [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: 12/24/2023] [Accepted: 03/19/2024] [Indexed: 06/06/2024] Open
Abstract
Face recognition is important for both visual and social cognition. While prosopagnosia or face blindness has been known for seven decades and face-specific neurons for half a century, the molecular genetic mechanism is not clear. Here we report results after 17 years of research with classic genetics and modern genomics. From a large family with 18 congenital prosopagnosia (CP) members with obvious difficulties in face recognition in daily life, we uncovered a fully cosegregating private mutation in the MCTP2 gene which encodes a calcium binding transmembrane protein expressed in the brain. After screening through cohorts of 6589, we found more CPs and their families, allowing detection of more CP associated mutations in MCTP2. Face recognition differences were detected between 14 carriers with the frameshift mutation S80fs in MCTP2 and 19 noncarrying volunteers. Six families including one with 10 members showed the S80fs-CP correlation. Functional magnetic resonance imaging found association of impaired recognition of individual faces by MCTP2 mutant CPs with reduced repetition suppression to repeated facial identities in the right fusiform face area. Our results have revealed genetic predisposition of MCTP2 mutations in CP, 76 years after the initial report of prosopagnosia and 47 years after the report of the first CP. This is the first time a gene required for a higher form of visual social cognition was found in humans.
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Affiliation(s)
- Yun Sun
- Chinese Institutes for Medical Research, Capital Medical University, Beijing 100069, China
- Chinese Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen 518107, China
| | - Weiwei Men
- Center for MRI Research, Academy for Advanced Interdisciplinary Studies, Beijing Key Lab for Medical Physics and Engineering, Institute of Heavy Ion Physics, School of Physics, Peking University, Beijing 100871, China
| | - Ingo Kennerknecht
- Institute of Human Genetics, Westfälische Wilhelms-Universität, Münster 48149, Germany
| | - Wan Fang
- Chinese Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hou-Feng Zheng
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Wenxia Zhang
- Chinese Institutes for Medical Research, Capital Medical University, Beijing 100069, China
- Chinese Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yi Rao
- Chinese Institutes for Medical Research, Capital Medical University, Beijing 100069, China
- Chinese Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen 518107, China
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de Wagenaar NP, van den Bersselaar LM, Odijk HJHM, Stefens SJM, Reinhardt DP, Roos-Hesselink JW, Kanaar R, Verhagen JMA, Brüggenwirth HT, van de Laar IMBH, van der Pluijm I, Essers J. Functional analysis of cell lines derived from SMAD3-related Loeys-Dietz syndrome patients provides insights into genotype-phenotype relation. Hum Mol Genet 2024; 33:1090-1104. [PMID: 38538566 PMCID: PMC11153339 DOI: 10.1093/hmg/ddae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/23/2024] [Accepted: 03/06/2024] [Indexed: 06/07/2024] Open
Abstract
RATIONALE Pathogenic (P)/likely pathogenic (LP) SMAD3 variants cause Loeys-Dietz syndrome type 3 (LDS3), which is characterized by arterial aneurysms, dissections and tortuosity throughout the vascular system combined with osteoarthritis. OBJECTIVES Investigate the impact of P/LP SMAD3 variants with functional tests on patient-derived fibroblasts and vascular smooth muscle cells (VSMCs), to optimize interpretation of SMAD3 variants. METHODS A retrospective analysis on clinical data from individuals with a P/LP SMAD3 variant and functional analyses on SMAD3 patient-derived VSMCs and SMAD3 patient-derived fibroblasts, differentiated into myofibroblasts. RESULTS Individuals with dominant negative (DN) SMAD3 variant in the MH2 domain exhibited more major events (66.7% vs. 44.0%, P = 0.054), occurring at a younger age compared to those with haploinsufficient (HI) variants. The age at first major event was 35.0 years [IQR 29.0-47.0] in individuals with DN variants in MH2, compared to 46.0 years [IQR 40.0-54.0] in those with HI variants (P = 0.065). Fibroblasts carrying DN SMAD3 variants displayed reduced differentiation potential, contrasting with increased differentiation potential in HI SMAD3 variant fibroblasts. HI SMAD3 variant VSMCs showed elevated SMA expression and altered expression of alternative MYH11 isoforms. DN SMAD3 variant myofibroblasts demonstrated reduced extracellular matrix formation compared to control cell lines. CONCLUSION Distinguishing between P/LP HI and DN SMAD3 variants can be achieved by assessing differentiation potential, and SMA and MYH11 expression. The differences between DN and HI SMAD3 variant fibroblasts and VSMCs potentially contribute to the differences in disease manifestation. Notably, myofibroblast differentiation seems a suitable alternative in vitro test system compared to VSMCs.
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Affiliation(s)
- Nathalie P de Wagenaar
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Department of Cardiology and European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Lisa M van den Bersselaar
- Department of Clinical Genetics and European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Hanny J H M Odijk
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Sanne J M Stefens
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Dieter P Reinhardt
- Faculty of Medicine and Health Sciences, McGill University, 3640 University Street, Montreal, QC H3A 0C7, Canada
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, 3640 University Street, Montreal, QC H3A 0C7, Canada
| | - Jolien W Roos-Hesselink
- Department of Cardiology and European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Judith M A Verhagen
- Department of Clinical Genetics and European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Hennie T Brüggenwirth
- Department of Clinical Genetics and European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Ingrid M B H van de Laar
- Department of Clinical Genetics and European Reference Network for Rare Multisystemic Vascular Disease (VASCERN), HTAD Rare Disease Working Group, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Ingrid van der Pluijm
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Department of Vascular Surgery, Cardiovascular Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Jeroen Essers
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Department of Vascular Surgery, Cardiovascular Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Department of Radiotherapy, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
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Steux C, Szpiech ZA. The Maintenance of Deleterious Variation in Wild Chinese Rhesus Macaques. Genome Biol Evol 2024; 16:evae115. [PMID: 38795368 PMCID: PMC11157460 DOI: 10.1093/gbe/evae115] [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: 10/06/2023] [Revised: 04/25/2024] [Accepted: 05/22/2024] [Indexed: 05/27/2024] Open
Abstract
Understanding how deleterious variation is shaped and maintained in natural populations is important in conservation and evolutionary biology, as decreased fitness caused by these deleterious mutations can potentially lead to an increase in extinction risk. It is known that demographic processes can influence these patterns. For example, population bottlenecks and inbreeding increase the probability of inheriting identical-by-descent haplotypes from a recent common ancestor, creating long tracts of homozygous genotypes called runs of homozygosity (ROH), which have been associated with an accumulation of mildly deleterious homozygotes. Counterintuitively, positive selection can also maintain deleterious variants in a population through genetic hitchhiking. Here, we analyze the whole genomes of 79 wild Chinese rhesus macaques across five subspecies and characterize patterns of deleterious variation with respect to ROH and signals of recent positive selection. We show that the fraction of homozygotes occurring in long ROH is significantly higher for deleterious homozygotes than tolerated ones, whereas this trend is not observed for short and medium ROH. This confirms that inbreeding, by generating these long tracts of homozygosity, is the main driver of the high burden of homozygous deleterious alleles in wild macaque populations. Furthermore, we show evidence that homozygous LOF variants are being purged. Next, we identify seven deleterious variants at high frequency in regions putatively under selection near genes involved with olfaction and other processes. Our results shed light on how evolutionary processes can shape the distribution of deleterious variation in wild nonhuman primates.
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Affiliation(s)
- Camille Steux
- Department of Biology, Pennsylvania State University, University Park, USA
- Centre de Recherche sur la Biodiversité et l’Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3—Paul Sabatier (UT3), Toulouse, France
| | - Zachary A Szpiech
- Department of Biology, Pennsylvania State University, University Park, USA
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, USA
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Tritto V, Bettinaglio P, Mangano E, Cesaretti C, Marasca F, Castronovo C, Bordoni R, Battaglia C, Saletti V, Ranzani V, Bodega B, Eoli M, Natacci F, Riva P. Genetic/epigenetic effects in NF1 microdeletion syndrome: beyond the haploinsufficiency, looking at the contribution of not deleted genes. Hum Genet 2024; 143:775-795. [PMID: 38874808 PMCID: PMC11186880 DOI: 10.1007/s00439-024-02683-0] [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: 03/15/2024] [Accepted: 06/03/2024] [Indexed: 06/15/2024]
Abstract
NF1 microdeletion syndrome, accounting for 5-11% of NF1 patients, is caused by a deletion in the NF1 region and it is generally characterized by a severe phenotype. Although 70% of NF1 microdeletion patients presents the same 1.4 Mb type-I deletion, some patients may show additional clinical features. Therefore, the contribution of several pathogenic mechanisms, besides haploinsufficiency of some genes within the deletion interval, is expected and needs to be defined. We investigated an altered expression of deletion flanking genes by qPCR in patients with type-1 NF1 deletion, compared to healthy donors, possibly contributing to the clinical traits of NF1 microdeletion syndrome. In addition, the 1.4-Mb deletion leads to changes in the 3D chromatin structure in the 17q11.2 region. Specifically, this deletion alters DNA-DNA interactions in the regions flanking the breakpoints, as demonstrated by our 4C-seq analysis. This alteration likely causes position effect on the expression of deletion flanking genes.Interestingly, 4C-seq analysis revealed that in microdeletion patients, an interaction was established between the RHOT1 promoter and the SLC6A4 gene, which showed increased expression. We performed NGS on putative modifier genes, and identified two "likely pathogenic" rare variants in RAS pathway, possibly contributing to incidental phenotypic features.This study provides new insights into understanding the pathogenesis of NF1 microdeletion syndrome and suggests a novel pathomechanism that contributes to the expression phenotype in addition to haploinsufficiency of genes located within the deletion.This is a pivotal approach that can be applied to unravel microdeletion syndromes, improving precision medicine, prognosis and patients' follow-up.
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Affiliation(s)
- Viviana Tritto
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Segrate, Milan, Italy
| | - Paola Bettinaglio
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Segrate, Milan, Italy
| | - Eleonora Mangano
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Segrate (Milan), Italy
| | - Claudia Cesaretti
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy
| | - Federica Marasca
- Genome Biology Unit, Istituto Nazionale di Genetica Molecolare (INGM) "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Chiara Castronovo
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Segrate (Milan), Italy
| | - Roberta Bordoni
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Segrate (Milan), Italy
| | - Cristina Battaglia
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Segrate, Milan, Italy
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Segrate (Milan), Italy
| | - Veronica Saletti
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Valeria Ranzani
- Genome Biology Unit, Istituto Nazionale di Genetica Molecolare (INGM) "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Beatrice Bodega
- Genome Biology Unit, Istituto Nazionale di Genetica Molecolare (INGM) "Romeo ed Enrica Invernizzi", Milan, Italy
- Department of Biosciences (DBS), University of Milan, Milan, Italy
| | - Marica Eoli
- Molecular Neuroncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Federica Natacci
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy.
| | - Paola Riva
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Segrate, Milan, Italy.
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40
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Lee NY, Hum M, Wong M, Ong PY, Lee SC, Lee ASG. Alleviating misclassified germline variants in underrepresented populations: A strategy using popmax. Genet Med 2024; 26:101124. [PMID: 38522067 DOI: 10.1016/j.gim.2024.101124] [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: 09/08/2023] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024] Open
Abstract
PURPOSE Germline variant interpretation often depends on population-matched control cohorts. This is not feasible for population groups that are underrepresented in current population reference databases. METHODS We classify germline variants with population-matched controls for 2 ancestrally diverse cohorts of patients: 132 early-onset or familial colorectal carcinoma patients from Singapore and 100 early-onset colorectal carcinoma patients from the United States. The effects of using a population-mismatched control cohort are simulated by swapping the control cohorts used for each patient cohort, with or without the popmax computational strategy. RESULTS Population-matched classifications revealed a combined 62 pathogenic or likely pathogenic (P/LP) variants in 34 genes across both cohorts. Using a population-mismatched control cohort resulted in misclassification of non-P/LP variants as P/LP, driven by the absence of ancestry-specific rare variants in the control cohort. Popmax was more effective in alleviating misclassifications for the Singapore cohort than the US cohort. CONCLUSION Underrepresented population groups can suffer from higher rates of false-positive P/LP results. Popmax can partially alleviate these misclassifications, but its efficacy still depends on the degree with which the population groups are represented in the control cohort.
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Affiliation(s)
- Ning Yuan Lee
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore
| | - Melissa Hum
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore
| | - Matthew Wong
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore
| | - Pei-Yi Ong
- Department of Hematology-Oncology, National University Cancer Institute, Singapore (NCIS), National University Health System, Singapore
| | - Soo-Chin Lee
- Department of Hematology-Oncology, National University Cancer Institute, Singapore (NCIS), National University Health System, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Cancer Science Institute, Singapore (CSI), National University of Singapore, Singapore
| | - Ann S G Lee
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore; SingHealth Duke-NUS Oncology Academic Clinical Programme (ONCO ACP), Duke-NUS Medical School, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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Barbotin AL, Boursier A, Jourdain AS, Moerman A, Rabat B, Chehimi M, Thuillier C, Ghoumid J, Smol T. Identification of a novel CFAP61 homozygous splicing variant associated with multiple morphological abnormalities of the flagella. J Assist Reprod Genet 2024; 41:1499-1505. [PMID: 38775994 PMCID: PMC11224159 DOI: 10.1007/s10815-024-03139-0] [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: 01/25/2024] [Accepted: 05/07/2024] [Indexed: 07/05/2024] Open
Abstract
In this study, we investigated the role of a newly identified homozygous variant (c.1245 + 6T > C) in the CFAP61 gene in the development of multiple morphologically abnormal flagella (MMAF) in an infertile patient. Using exome sequencing, we identified this variant, which led to exon 12 skipping and the production of a truncated CFAP61 protein. Transmission electron microscopy analysis of the patient's spermatozoa revealed various flagellar abnormalities, including defective nuclear chromatin condensation, axoneme disorganization, and mitochondria embedded in residual cytoplasmic droplets. Despite a fertilization rate of 83.3% through ICSI, there was no successful pregnancy due to poor embryo quality.Our findings suggest a link between the identified CFAP61 variant and MMAF, indicating potential disruption in radial spokes' assembly or function crucial for normal ciliary motility. Furthermore, nearly half of the observed sperm heads displayed chromatin condensation defects, possibly contributing to the low blastulation rate. This case underscores the significance of genetic counseling and testing, particularly for couples dealing with infertility and MMAF. Early identification of such genetic variants can guide appropriate interventions and improve reproductive outcomes.
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Affiliation(s)
- Anne-Laure Barbotin
- UMRS1172 Development and Plasticity of the Neuroendocrine Brain, University of Lille, Lille, France
- Institut de Biologie de la Reproduction-Spermiologie-CECOS, CHU Lille, Lille, France
| | - Angèle Boursier
- UMRS1172 Development and Plasticity of the Neuroendocrine Brain, University of Lille, Lille, France
- Institut de Biologie de la Reproduction-Spermiologie-CECOS, CHU Lille, Lille, France
| | - Anne-Sophie Jourdain
- ULR7364 -RADEME - Maladies Rares du Développement Embryonnaire, University of Lille, Lille, France
- Institut de Génétique Médicale, CHU Lille, Avenue Oscar Lambret, F-59000, Lille, France
| | | | - Baptiste Rabat
- ULR7364 -RADEME - Maladies Rares du Développement Embryonnaire, University of Lille, Lille, France
| | - Mariam Chehimi
- Institut de Biologie de la Reproduction-Spermiologie-CECOS, CHU Lille, Lille, France
| | - Caroline Thuillier
- Institut de Génétique Médicale, CHU Lille, Avenue Oscar Lambret, F-59000, Lille, France
| | - Jamal Ghoumid
- ULR7364 -RADEME - Maladies Rares du Développement Embryonnaire, University of Lille, Lille, France
- Clinique de Génétique Guy Fontaine, CHU Lille, Lille, France
| | - Thomas Smol
- ULR7364 -RADEME - Maladies Rares du Développement Embryonnaire, University of Lille, Lille, France.
- Institut de Génétique Médicale, CHU Lille, Avenue Oscar Lambret, F-59000, Lille, France.
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Bernstein N, Spencer Chapman M, Nyamondo K, Chen Z, Williams N, Mitchell E, Campbell PJ, Cohen RL, Nangalia J. Analysis of somatic mutations in whole blood from 200,618 individuals identifies pervasive positive selection and novel drivers of clonal hematopoiesis. Nat Genet 2024; 56:1147-1155. [PMID: 38744975 PMCID: PMC11176083 DOI: 10.1038/s41588-024-01755-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 04/17/2024] [Indexed: 05/16/2024]
Abstract
Human aging is marked by the emergence of a tapestry of clonal expansions in dividing tissues, particularly evident in blood as clonal hematopoiesis (CH). CH, linked to cancer risk and aging-related phenotypes, often stems from somatic mutations in a set of established genes. However, the majority of clones lack known drivers. Here we infer gene-level positive selection in whole blood exomes from 200,618 individuals in UK Biobank. We identify 17 additional genes, ZBTB33, ZNF318, ZNF234, SPRED2, SH2B3, SRCAP, SIK3, SRSF1, CHEK2, CCDC115, CCL22, BAX, YLPM1, MYD88, MTA2, MAGEC3 and IGLL5, under positive selection at a population level, and validate this selection pattern in 10,837 whole genomes from single-cell-derived hematopoietic colonies. Clones with mutations in these genes grow in frequency and size with age, comparable to classical CH drivers. They correlate with heightened risk of infection, death and hematological malignancy, highlighting the significance of these additional genes in the aging process.
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Affiliation(s)
| | - Michael Spencer Chapman
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Kudzai Nyamondo
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Zhenghao Chen
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | | | - Emily Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | | | | | - Jyoti Nangalia
- Wellcome Sanger Institute, Hinxton, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
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Demirdas S, van den Bersselaar LM, Lechner R, Bos J, Alsters SI, Baars MJ, Baas AF, Baysal Ö, van der Crabben SN, Dulfer E, Giesbertz NA, Helderman-van den Enden AT, Hilhorst-Hofstee Y, Kempers MJ, Komdeur FL, Loeys B, Majoor-Krakauer D, Ockeloen CW, Overwater E, van Tintelen PJ, Voorendt M, de Waard V, Maugeri A, Brüggenwirth HT, van de Laar IM, Houweling AC. Vascular Ehlers-Danlos Syndrome: A Comprehensive Natural History Study in a Dutch National Cohort of 142 Patients. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2024; 17:e003978. [PMID: 38623759 PMCID: PMC11188628 DOI: 10.1161/circgen.122.003978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/11/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND Vascular Ehlers-Danlos syndrome (vEDS) is a rare connective tissue disorder with a high risk for arterial, bowel, and uterine rupture, caused by heterozygous pathogenic variants in COL3A1. The aim of this cohort study is to provide further insights into the natural history of vEDS and describe genotype-phenotype correlations in a Dutch multicenter cohort to optimize patient care and increase awareness of the disease. METHODS Individuals with vEDS throughout the Netherlands were included. The phenotype was charted by retrospective analysis of molecular and clinical data, combined with a one-time physical examination. RESULTS A total of 142 individuals (50% female) participated the study, including 46 index patients (32%). The overall median age at genetic diagnosis was 41.0 years. More than half of the index patients (54.3%) and relatives (53.1%) had a physical appearance highly suggestive of vEDS. In these individuals, major events were not more frequent (P=0.90), but occurred at a younger age (P=0.01). A major event occurred more often and at a younger age in men compared with women (P<0.001 and P=0.004, respectively). Aortic aneurysms (P=0.003) and pneumothoraces (P=0.029) were more frequent in men. Aortic dissection was more frequent in individuals with a COL3A1 variant in the first quarter of the collagen helical domain (P=0.03). CONCLUSIONS Male sex, type and location of the COL3A1 variant, and physical appearance highly suggestive of vEDS are risk factors for the occurrence and early age of onset of major events. This national multicenter cohort study of Dutch individuals with vEDS provides a valuable basis for improving guidelines for the diagnosing, follow-up, and treatment of individuals with vEDS.
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Affiliation(s)
- Serwet Demirdas
- Department of Clinical Genetics, Cardiovascular Institute, Erasmus Medical Center, University Medical Center, Rotterdam, the Netherlands (S.D., L.M.v.d.B., R.L., D.M.-K., H.T.B., I.M.B.H.v.d.L.)
- European Reference Network ReCONNET, Ehlers Danlos Syndrome Working Group, Rotterdam, the Netherlands (S.D.)
| | - Lisa M. van den Bersselaar
- Department of Clinical Genetics, Cardiovascular Institute, Erasmus Medical Center, University Medical Center, Rotterdam, the Netherlands (S.D., L.M.v.d.B., R.L., D.M.-K., H.T.B., I.M.B.H.v.d.L.)
| | - Rosan Lechner
- Department of Clinical Genetics, Cardiovascular Institute, Erasmus Medical Center, University Medical Center, Rotterdam, the Netherlands (S.D., L.M.v.d.B., R.L., D.M.-K., H.T.B., I.M.B.H.v.d.L.)
| | - Jessica Bos
- Department of Human Genetics, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, the Netherlands (J.B., S.I.M.A., M.J.H.B., S.N.v.d.C., F.L.K., E.O., A.M., A.C.H.)
- Department of Human Genetics, Amsterdam University Medical Center, University of Amsterdam, the Netherlands (J.B., S.I.M.A., M.J.H.B., S.N.v.d.C., F.L.K., E.O., A.C.H.)
| | - Suzanne I.M. Alsters
- Department of Human Genetics, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, the Netherlands (J.B., S.I.M.A., M.J.H.B., S.N.v.d.C., F.L.K., E.O., A.M., A.C.H.)
- Department of Human Genetics, Amsterdam University Medical Center, University of Amsterdam, the Netherlands (J.B., S.I.M.A., M.J.H.B., S.N.v.d.C., F.L.K., E.O., A.C.H.)
| | - Marieke J.H. Baars
- Department of Human Genetics, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, the Netherlands (J.B., S.I.M.A., M.J.H.B., S.N.v.d.C., F.L.K., E.O., A.M., A.C.H.)
- Department of Human Genetics, Amsterdam University Medical Center, University of Amsterdam, the Netherlands (J.B., S.I.M.A., M.J.H.B., S.N.v.d.C., F.L.K., E.O., A.C.H.)
| | - Annette F. Baas
- Department of Genetics, University Medical Center Utrecht, the Netherlands (A.F.B., N.A.A.G., P.J.v.T.)
| | - Özlem Baysal
- Department of Human Genetics, Radboud University Nijmegen Medical Center, the Netherlands (O.B., M.J.E.K., B.L., C.W.O., M.V.)
| | - Saskia N. van der Crabben
- Department of Human Genetics, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, the Netherlands (J.B., S.I.M.A., M.J.H.B., S.N.v.d.C., F.L.K., E.O., A.M., A.C.H.)
- Department of Human Genetics, Amsterdam University Medical Center, University of Amsterdam, the Netherlands (J.B., S.I.M.A., M.J.H.B., S.N.v.d.C., F.L.K., E.O., A.C.H.)
| | - Eelco Dulfer
- Department of Genetics, University Medical Center Groningen, the Netherlands (E.D., E.O.)
| | - Noor A.A. Giesbertz
- Department of Genetics, University Medical Center Utrecht, the Netherlands (A.F.B., N.A.A.G., P.J.v.T.)
| | | | - Yvonne Hilhorst-Hofstee
- Department of Clinical Genetics, Leiden University Medical Center, the Netherlands (Y.H.-H.)
| | - Marlies J.E. Kempers
- Department of Human Genetics, Radboud University Nijmegen Medical Center, the Netherlands (O.B., M.J.E.K., B.L., C.W.O., M.V.)
| | - Fenne L. Komdeur
- Department of Human Genetics, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, the Netherlands (J.B., S.I.M.A., M.J.H.B., S.N.v.d.C., F.L.K., E.O., A.M., A.C.H.)
- Department of Human Genetics, Amsterdam University Medical Center, University of Amsterdam, the Netherlands (J.B., S.I.M.A., M.J.H.B., S.N.v.d.C., F.L.K., E.O., A.C.H.)
| | - Bart Loeys
- Department of Human Genetics, Radboud University Nijmegen Medical Center, the Netherlands (O.B., M.J.E.K., B.L., C.W.O., M.V.)
| | - Daniëlle Majoor-Krakauer
- Department of Clinical Genetics, Cardiovascular Institute, Erasmus Medical Center, University Medical Center, Rotterdam, the Netherlands (S.D., L.M.v.d.B., R.L., D.M.-K., H.T.B., I.M.B.H.v.d.L.)
| | - Charlotte W. Ockeloen
- Department of Human Genetics, Radboud University Nijmegen Medical Center, the Netherlands (O.B., M.J.E.K., B.L., C.W.O., M.V.)
| | - Eline Overwater
- Department of Human Genetics, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, the Netherlands (J.B., S.I.M.A., M.J.H.B., S.N.v.d.C., F.L.K., E.O., A.M., A.C.H.)
- Department of Human Genetics, Amsterdam University Medical Center, University of Amsterdam, the Netherlands (J.B., S.I.M.A., M.J.H.B., S.N.v.d.C., F.L.K., E.O., A.C.H.)
- Department of Genetics, University Medical Center Groningen, the Netherlands (E.D., E.O.)
| | - Peter J. van Tintelen
- Department of Genetics, University Medical Center Utrecht, the Netherlands (A.F.B., N.A.A.G., P.J.v.T.)
| | - Marsha Voorendt
- Department of Human Genetics, Radboud University Nijmegen Medical Center, the Netherlands (O.B., M.J.E.K., B.L., C.W.O., M.V.)
| | - Vivian de Waard
- Department of Medical Biochemistry, Amsterdam University Medical Center, Amsterdam Cardiovascular Sciences, the Netherlands (V.d.W.)
| | - Alessandra Maugeri
- Department of Human Genetics, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, the Netherlands (J.B., S.I.M.A., M.J.H.B., S.N.v.d.C., F.L.K., E.O., A.M., A.C.H.)
| | - Hennie T. Brüggenwirth
- Department of Clinical Genetics, Cardiovascular Institute, Erasmus Medical Center, University Medical Center, Rotterdam, the Netherlands (S.D., L.M.v.d.B., R.L., D.M.-K., H.T.B., I.M.B.H.v.d.L.)
| | - Ingrid M.B.H. van de Laar
- Department of Clinical Genetics, Cardiovascular Institute, Erasmus Medical Center, University Medical Center, Rotterdam, the Netherlands (S.D., L.M.v.d.B., R.L., D.M.-K., H.T.B., I.M.B.H.v.d.L.)
- European Reference Network for Rare Multisystemic Vascular Disease, Medium Sized Arteries Working Group, Rotterdam, the Netherlands (I.M.B.H.v.d.L.)
| | - Arjan C. Houweling
- Department of Human Genetics, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, the Netherlands (J.B., S.I.M.A., M.J.H.B., S.N.v.d.C., F.L.K., E.O., A.M., A.C.H.)
- Department of Human Genetics, Amsterdam University Medical Center, University of Amsterdam, the Netherlands (J.B., S.I.M.A., M.J.H.B., S.N.v.d.C., F.L.K., E.O., A.C.H.)
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Wang T, Wang X, Teng Y, Wu L, Zhu F, Ma D, Wang H, Liu X. APLAID complicated with arrhythmogenic dilated cardiomyopathy caused by a novel PLCG2 variant. Immunol Res 2024; 72:512-519. [PMID: 38243104 DOI: 10.1007/s12026-024-09455-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 01/10/2024] [Indexed: 01/21/2024]
Affiliation(s)
- Tianjiao Wang
- Department of Pediatrics, The Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, 314000, China
| | - Xinyu Wang
- Department of Pediatrics, Jiaxing University Master Degree Cultivation Base Zhejiang Chinese Medical University, Jiaxing, Zhejiang, 314000, China
- Department of Pediatrics, The Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, 314000, China
| | - Yiqun Teng
- Department of Pediatrics, The Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, 314000, China
| | - Lifang Wu
- Department of Pediatrics, Pinghu Maternal and Child Health Center, Jiaxing, Zhejiang, 314200, China
| | - Feng Zhu
- Department of Pediatrics, The Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, 314000, China
| | - Danjie Ma
- Department of Ultrasound, The Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, 314000, China
| | - Hua Wang
- Department of Pediatrics, The Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, 314000, China.
| | - Xiaolin Liu
- Department of General Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, 314000, China.
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Zhang Z, Wang T, Xu M, Zhang Z, Wang H, Xue J, Wang W. Deciphering the pancreatic cancer microbiome in Mainland China: Impact of Exiguobacterium/Bacillus ratio on tumor progression and prognostic significance. Pharmacol Res 2024; 204:107197. [PMID: 38692467 DOI: 10.1016/j.phrs.2024.107197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
The existing body of research underscores the critical impact of intratumoral microbiomes on the progression of pancreatic ductal adenocarcinoma (PDAC), particularly in reshaping the tumor microenvironment and influencing gemcitabine resistance. However, peritumoral tissues' microbiome, distinct from PDAC tumors, remain understudied, and Western-centric analyses overlooking potential variations in dietary-influenced microbiomes. Our study addresses this gap by 16 S rRNA sequencing of PDAC tumors and matched peritumoral tissues from Chinese Mainland patients. Our research has uncovered that the microbiome composition within tumors and paired peritumoral tissues exhibits a high degree of similarity, albeit with certain discrepancies. Notably, Exiguobacterium is found to be more abundant within the tumor tissues. Further investigations have revealed that a lower Exiguobacterium/Bacillus ratio in both the tumor and peritumoral tissues of PDAC patients is indicative of a more favorable prognosis. Further exploration utilizing an orthotopic tumor model demonstrates that the probiotic Bacillus Coagulans impedes PDAC progression, accompanied by an increased infiltration of inflammatory neutrophils in tumors. Additionally, in the subgroup with a low Exiguobacterium/Bacillus ratio, whole-exome sequencing reveals elevated missense mutations in ABL2 and MSH2. The elevated expression of ABL2 and MSH2 has been correlated with poorer prognostic outcomes in PDAC patients. Together, these insights shed light on risk factors influencing PDAC progression and unveil potential therapeutic targets, alongside probiotic intervention strategies.
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Affiliation(s)
- Zhengyan Zhang
- State Key Laboratory of Systems Medicine for Cancer, Stem Cell Research Center, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ting Wang
- Department of Pathology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming Xu
- Department of Gastroenterology, Shanghai Hongkou District Jiangwan Hospital, China
| | - Zhihan Zhang
- Department of Pathology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huaizhi Wang
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, Chongqing University, Chongqing, China.
| | - Jing Xue
- State Key Laboratory of Systems Medicine for Cancer, Stem Cell Research Center, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Wei Wang
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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García-Aznar JM, Alonso Alvarez S, Bernal Del Castillo T. Pivotal role of BCL11B in the immune, hematopoietic and nervous systems: a review of the BCL11B-associated phenotypes from the genetic perspective. Genes Immun 2024; 25:232-241. [PMID: 38472338 PMCID: PMC11178493 DOI: 10.1038/s41435-024-00263-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
The transcription factor BCL11B plays an essential role in the development of central nervous system and T cell differentiation by regulating the expression of numerous genes involved in several pathways. Monoallelic defects in the BCL11B gene leading to loss-of-function are associated with a wide spectrum of phenotypes, including neurological disorders with or without immunological features and susceptibility to hematological malignancies. From the genetic point of view, the landscape of BCL11B mutations reported so far does not fully explain the genotype-phenotype correlation. In this review, we sought to compile the phenotypic and genotypic variables associated with previously reported mutations in this gene in order to provide a better understanding of the consequences of deleterious variants. We also highlight the importance of a careful evaluation of the mutation type, its location and the pattern of inheritance of the variants in order to assign the most accurate pathogenicity and actionability of the genetic findings.
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Affiliation(s)
- José María García-Aznar
- Healthincode, A Coruña, Spain.
- Universitary Institute of Oncology of Principado de Asturias (IUOPA), Oviedo, Spain.
- Health Research Institute of Principado de Asturias, Oviedo, Spain.
| | - Sara Alonso Alvarez
- Universitary Institute of Oncology of Principado de Asturias (IUOPA), Oviedo, Spain
- Health Research Institute of Principado de Asturias, Oviedo, Spain
- Hematology Department, Hospital Universitario Clínico de Asturias, Oviedo, Spain
| | - Teresa Bernal Del Castillo
- Universitary Institute of Oncology of Principado de Asturias (IUOPA), Oviedo, Spain
- Health Research Institute of Principado de Asturias, Oviedo, Spain
- Hematology Department, Hospital Universitario Clínico de Asturias, Oviedo, Spain
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Laurent R, Gineau L, Utge J, Lafosse S, Phoeung CL, Hegay T, Olaso R, Boland A, Deleuze JF, Toupance B, Heyer E, Leutenegger AL, Chaix R. Measuring the Efficiency of Purging by non-random Mating in Human Populations. Mol Biol Evol 2024; 41:msae094. [PMID: 38839045 PMCID: PMC11184347 DOI: 10.1093/molbev/msae094] [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: 10/30/2023] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024] Open
Abstract
Human populations harbor a high concentration of deleterious genetic variants. Here, we tested the hypothesis that non-random mating practices affect the distribution of these variants, through exposure in the homozygous state, leading to their purging from the population gene pool. To do so, we produced whole-genome sequencing data for two pairs of Asian populations exhibiting different alliance rules and rates of inbreeding, but with similar effective population sizes. The results show that populations with higher rates of inbred matings do not purge deleterious variants more efficiently. Purging therefore has a low efficiency in human populations, and different mating practices lead to a similar mutational load.
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Affiliation(s)
- Romain Laurent
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | - Laure Gineau
- IRD, MERIT, Université Paris Cité, 75006 Paris, France
| | - José Utge
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | - Sophie Lafosse
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | | | - Tatyana Hegay
- Laboratory of Genome-cell technology, Institute of Immunology and Human genomics, Academy of Sciences, Tashkent, Uzbekistan
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Université Paris-Saclay, 91057, Evry, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Université Paris-Saclay, 91057, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Université Paris-Saclay, 91057, Evry, France
| | - Bruno Toupance
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
- Eco-Anthropologie, Université Paris Cité, 75006 Paris, France
| | - Evelyne Heyer
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | | | - Raphaëlle Chaix
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
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Ebstein F, Latypova X, Sharon Hung KY, Prado MA, Lee BH, Möller S, Wendlandt M, Zieba BA, Florenceau L, Vignard V, Poirier L, Toutain B, Moroni I, Dubucs C, Chassaing N, Horvath J, Prokisch H, Küry S, Bézieau S, Paulo JA, Finley D, Krüger E, Ghezzi D, Isidor B. Biallelic USP14 variants cause a syndromic neurodevelopmental disorder. Genet Med 2024; 26:101120. [PMID: 38469793 DOI: 10.1016/j.gim.2024.101120] [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: 08/08/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/13/2024] Open
Abstract
PURPOSE Imbalances in protein homeostasis affect human brain development, with the ubiquitin-proteasome system (UPS) and autophagy playing crucial roles in neurodevelopmental disorders (NDD). This study explores the impact of biallelic USP14 variants on neurodevelopment, focusing on its role as a key hub connecting UPS and autophagy. METHODS Here, we identified biallelic USP14 variants in 4 individuals from 3 unrelated families: 1 fetus, a newborn with a syndromic NDD and 2 siblings affected by a progressive neurological disease. Specifically, the 2 siblings from the latter family carried 2 compound heterozygous variants c.8T>C p.(Leu3Pro) and c.988C>T p.(Arg330∗), whereas the fetus had a homozygous frameshift c.899_902del p.(Lys300Serfs∗24) variant, and the newborn patient harbored a homozygous frameshift c.233_236del p.(Leu78Glnfs∗11) variant. Functional studies were conducted using sodium dodecyl-sulfate polyacrylamide gel electrophoresis, western blotting, and mass spectrometry analyses in both patient-derived and CRISPR-Cas9-generated cells. RESULTS Our investigations indicated that the USP14 variants correlated with reduced N-terminal methionine excision, along with profound alterations in proteasome, autophagy, and mitophagy activities. CONCLUSION Biallelic USP14 variants in NDD patients perturbed protein degradation pathways, potentially contributing to disorder etiology. Altered UPS, autophagy, and mitophagy activities underscore the intricate interplay, elucidating their significance in maintaining proper protein homeostasis during brain development.
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Affiliation(s)
- Frédéric Ebstein
- University Medicine Greifswald, Institute of Medical Biochemistry and Molecular Biology, Greifswald, Germany; Nantes Université, CNRS, INSERM, L'Institut du Thorax, Nantes, France.
| | - Xenia Latypova
- Nantes Université, Service de Génétique Médicale, CHU Nantes, Nantes Cedex 1, France
| | | | - Miguel A Prado
- Dept of Cell Biology, Harvard Medical School, Boston, MA; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Byung-Hoon Lee
- Dept of Cell Biology, Harvard Medical School, Boston, MA; Dept of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Sophie Möller
- University Medicine Greifswald, Institute of Medical Biochemistry and Molecular Biology, Greifswald, Germany
| | - Martin Wendlandt
- University Medicine Greifswald, Institute of Medical Biochemistry and Molecular Biology, Greifswald, Germany
| | - Barbara A Zieba
- University Medicine Greifswald, Institute of Medical Biochemistry and Molecular Biology, Greifswald, Germany
| | | | - Virginie Vignard
- Nantes Université, CNRS, INSERM, L'Institut du Thorax, Nantes, France; Nantes Université, Service de Génétique Médicale, CHU Nantes, Nantes Cedex 1, France
| | - Léa Poirier
- Nantes Université, CNRS, INSERM, L'Institut du Thorax, Nantes, France
| | - Bérénice Toutain
- Nantes Université, CNRS, INSERM, L'Institut du Thorax, Nantes, France
| | - Isabella Moroni
- Department of Pediatric Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Charlotte Dubucs
- Département anatomie et cytologie pathologiques, CHU Toulouse, Toulouse, France; Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Nicolas Chassaing
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Judit Horvath
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Sébastien Küry
- Nantes Université, CNRS, INSERM, L'Institut du Thorax, Nantes, France; Nantes Université, Service de Génétique Médicale, CHU Nantes, Nantes Cedex 1, France
| | - Stéphane Bézieau
- Nantes Université, CNRS, INSERM, L'Institut du Thorax, Nantes, France; Nantes Université, Service de Génétique Médicale, CHU Nantes, Nantes Cedex 1, France
| | - Joao A Paulo
- Dept of Cell Biology, Harvard Medical School, Boston, MA
| | - Daniel Finley
- Dept of Cell Biology, Harvard Medical School, Boston, MA
| | - Elke Krüger
- University Medicine Greifswald, Institute of Medical Biochemistry and Molecular Biology, Greifswald, Germany
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy; Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Bertrand Isidor
- Nantes Université, CNRS, INSERM, L'Institut du Thorax, Nantes, France; Nantes Université, Service de Génétique Médicale, CHU Nantes, Nantes Cedex 1, France.
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49
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Schwantes-An TH, Whitfield JB, Aithal GP, Atkinson SR, Bataller R, Botwin G, Chalasani NP, Cordell HJ, Daly AK, Darlay R, Day CP, Eyer F, Foroud T, Gawrieh S, Gleeson D, Goldman D, Haber PS, Jacquet JM, Lammert CS, Liang T, Liangpunsakul S, Masson S, Mathurin P, Moirand R, McQuillin A, Moreno C, Morgan MY, Mueller S, Müllhaupt B, Nagy LE, Nahon P, Nalpas B, Naveau S, Perney P, Pirmohamed M, Seitz HK, Soyka M, Stickel F, Thompson A, Thursz MR, Trépo E, Morgan TR, Seth D. A polygenic risk score for alcohol-associated cirrhosis among heavy drinkers with European ancestry. Hepatol Commun 2024; 8:e0431. [PMID: 38727677 PMCID: PMC11093576 DOI: 10.1097/hc9.0000000000000431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/01/2023] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Polygenic Risk Scores (PRS) based on results from genome-wide association studies offer the prospect of risk stratification for many common and complex diseases. We developed a PRS for alcohol-associated cirrhosis by comparing single-nucleotide polymorphisms among patients with alcohol-associated cirrhosis (ALC) versus drinkers who did not have evidence of liver fibrosis/cirrhosis. METHODS Using a data-driven approach, a PRS for ALC was generated using a meta-genome-wide association study of ALC (N=4305) and an independent cohort of heavy drinkers with ALC and without significant liver disease (N=3037). It was validated in 2 additional independent cohorts from the UK Biobank with diagnosed ALC (N=467) and high-risk drinking controls (N=8981) and participants in the Indiana Biobank Liver cohort with alcohol-associated liver disease (N=121) and controls without liver disease (N=3239). RESULTS A 20-single-nucleotide polymorphisms PRS for ALC (PRSALC) was generated that stratified risk for ALC comparing the top and bottom deciles of PRS in the 2 validation cohorts (ORs: 2.83 [95% CI: 1.82 -4.39] in UK Biobank; 4.40 [1.56 -12.44] in Indiana Biobank Liver cohort). Furthermore, PRSALC improved the prediction of ALC risk when added to the models of clinically known predictors of ALC risk. It also stratified the risk for metabolic dysfunction -associated steatotic liver disease -cirrhosis (3.94 [2.23 -6.95]) in the Indiana Biobank Liver cohort -based exploratory analysis. CONCLUSIONS PRSALC incorporates 20 single-nucleotide polymorphisms, predicts increased risk for ALC, and improves risk stratification for ALC compared with the models that only include clinical risk factors. This new score has the potential for early detection of heavy drinking patients who are at high risk for ALC.
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Affiliation(s)
- Tae-Hwi Schwantes-An
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis IN, USA
| | - John B. Whitfield
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Queensland 4029, Australia
| | - Guruprasad P. Aithal
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals and the University of Nottingham, Nottingham NG7 2UH, UK
| | - Stephen R. Atkinson
- Department of Metabolism, Digestion & Reproduction, Imperial College London, UK
| | - Ramon Bataller
- Center for Liver Diseases, University of Pittsburgh Medical Center, 3471 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Greg Botwin
- Department of Veterans Affairs, VA Long Beach Healthcare System, 5901 East Seventh Street, Long Beach, CA 90822, USA
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California CA 90048, USA
| | - Naga P. Chalasani
- Department of Medicine, Indiana University, Indianapolis, IN 46202-5175, USA
| | - Heather J. Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Ann K. Daly
- Faculty of Medical Sciences, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Rebecca Darlay
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Christopher P. Day
- Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Florian Eyer
- Division of Clinical Toxicology, Department of Internal Medicine 2, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675 Munich, Germany
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis IN, USA
| | - Samer Gawrieh
- Department of Medicine, Indiana University, Indianapolis, IN 46202-5175, USA
| | - Dermot Gleeson
- Liver Unit, Sheffield Teaching Hospitals, AO Floor Robert Hadfield Building, Northern General Hospital, Sheffield S5 7AU, UK
| | - David Goldman
- Office of the Clinical Director and Laboratory of Neurogenetics, NIAAA, Bethesda, MD 20952, USA
| | - Paul S. Haber
- Edith Collins Centre (Translational Research in Alcohol Drugs and Toxicology), Sydney Local Health District, Missenden Road, Camperdown, NSW 2050, Australia
- Faculty of Medicine and Health, the University of Sydney, Sydney, NSW 2006, Australia
| | | | - Craig S. Lammert
- Department of Medicine, Indiana University, Indianapolis, IN 46202-5175, USA
| | - Tiebing Liang
- Department of Medicine, Indiana University, Indianapolis, IN 46202-5175, USA
| | - Suthat Liangpunsakul
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University and Roudebush Veterans Administration Medical Center, Indianapolis, USA
| | - Steven Masson
- Faculty of Medical Sciences, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Philippe Mathurin
- CHRU de Lille, Hôpital Claude Huriez, Rue M. Polonovski CS 70001, 59 037 Lille Cedex, France
| | - Romain Moirand
- Univ Rennes, INRA, INSERM, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
| | - Andrew McQuillin
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London WC1E 6DE, UK
| | - Christophe Moreno
- CUB Hôpital Erasme, Université Libre de Bruxelles, clinique d’Hépatologie, Brussels, Belgium; Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium
| | - Marsha Y. Morgan
- UCL Institute for Liver & Digestive Health, Division of Medicine, Royal Free Campus, University College London, London NW3 2PF, UK
| | - Sebastian Mueller
- Department of Internal Medicine, Salem Medical Center and Center for Alcohol Research, University of Heidelberg, Zeppelinstraße 11-33, 69121 Heidelberg, Germany
| | - Beat Müllhaupt
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Rämistrasse 100, CH-8901 Zurich, Switzerland
| | - Laura E. Nagy
- Lerner Research Institute, 9500 Euclid Avenue, Cleveland, Ohio, OH 44195, USA
| | - Pierre Nahon
- Service d'Hépatologie, APHP Hôpital Avicenne et Université Paris 13, Bobigny, France
- University Paris 13, Bobigny, France
- Inserm U1162 Génomique fonctionnelle des tumeurs solides, Paris, France
| | - Bertrand Nalpas
- Service Addictologie, CHRU Caremeau, 30029 Nîmes, France
- DISC, Inserm, 75013 Paris, France
| | - Sylvie Naveau
- Hôpital Antoine-Béclère, 157 Rue de la Porte de Trivaux, 92140 Clamart, France
| | - Pascal Perney
- Hôpital Universitaire Caremeau, Place du Pr. Robert Debre, 30029 Nîmes, France
| | - Munir Pirmohamed
- MRC Centre for Drug Safety Science, Liverpool Centre for Alcohol Research, University of Liverpool, The Royal Liverpool and Broadgreen University Hospitals NHS Trust, and Liverpool Health Partners, Liverpool, L69 3GL, UK
| | - Helmut K. Seitz
- Department of Internal Medicine, Salem Medical Center and Center for Alcohol Research, University of Heidelberg, Zeppelinstraße 11-33, 69121 Heidelberg, Germany
| | - Michael Soyka
- Psychiatric Hospital University of Munich, Nussbaumsstr.7, 80336 Munich, Germany
| | - Felix Stickel
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Rämistrasse 100, CH-8901 Zurich, Switzerland
| | - Andrew Thompson
- MRC Centre for Drug Safety Science, Liverpool Centre for Alcohol Research, University of Liverpool, The Royal Liverpool and Broadgreen University Hospitals NHS Trust, and Liverpool Health Partners, Liverpool, L69 3GL, UK
- Health Analytics, Lane Clark & Peacock LLP, London, UK
| | - Mark R. Thursz
- Department of Metabolism, Digestion & Reproduction, Imperial College London, UK
| | - Eric Trépo
- CUB Hôpital Erasme, Université Libre de Bruxelles, clinique d’Hépatologie, Brussels, Belgium; Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium
| | - Timothy R. Morgan
- Department of Medicine, University of California, Irvine, USA
- Department of Veterans Affairs, VA Long Beach Healthcare System, 5901 East Seventh Street, Long Beach, CA 90822, USA
| | - Devanshi Seth
- Edith Collins Centre (Translational Research in Alcohol Drugs and Toxicology), Sydney Local Health District, Missenden Road, Camperdown, NSW 2050, Australia
- Faculty of Medicine and Health, the University of Sydney, Sydney, NSW 2006, Australia
- Centenary Institute of Cancer Medicine and Cell Biology, the University of Sydney, Sydney, NSW 2006, Australia
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50
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D'Apolito M, Santacroce R, Vazquez DO, Cordisco G, Fantini CA, D'Andrea G, Leccese A, Colia AL, Martinez P, Zanichelli A, Josviack D, Margaglione M. DAB2IP associates with hereditary angioedema: Insights into the role of VEGF signaling in HAE pathophysiology. J Allergy Clin Immunol 2024:S0091-6749(24)00558-X. [PMID: 38823490 DOI: 10.1016/j.jaci.2024.05.017] [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: 01/21/2024] [Revised: 05/09/2024] [Accepted: 05/24/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND In the recent years, there was an important improvement in the understanding of the pathogenesis of hereditary angioedema (HAE). Notwithstanding, in a large portion of patients with unknown mutation (HAE-UNK) the genetic cause remains to be identified. OBJECTIVES To identify new genetic targets associated with HAE, a large Argentine family with HAE-UNK spanning 3 generations was studied. METHODS Whole exome sequencing was performed on affected family members to identify potential genetic variants associated with HAE-UNK. In silico analyses and experimental studies were applied to assess the role of the identified gene variant. RESULTS A missense variant (p.D239N) in DAB2IP was identified. The variant occurred in the C2-domain, the region interacting with vascular endothelial growth factor receptor 2 (VEGFR2). It was found to be rare, and predicted to have a detrimental effect on the functionality of DAB2IP. Protein structure modeling predicted changes in the mutant p.D239N protein structure, impacting protein stability. The p.D239N variant affected the subcellular localization of VEGFR2. Cells transfected with the DAB2IP-239N transcript exhibited an intracellular distribution, and VEGFR2 remained associated with the cell membrane. The altered localization pattern indicated reduced colocalization of the mutant protein with VEGFR2, suggesting a diminished ability of VEGFR2 binding. CONCLUSIONS The study identified a novel missense variant (p.D239N) in DAB2IP in a family with HAE-UNK and highlighted the role of dysregulated VEGF-mediated signaling in altered endothelial permeability. DAB2IP loss-of-function pathogenic variants lead to the impairment of the endothelial VEGF/VEGFR2 ligand system and represent a new pathophysiologic cause of HAE-UNK.
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Affiliation(s)
- Maria D'Apolito
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Rosa Santacroce
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | | | - Giorgia Cordisco
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | | | - Giovanna D'Andrea
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Angelica Leccese
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Anna Laura Colia
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Pablo Martinez
- Universidad Nacional del Sur, Argentina Hospital Penna de Bahia Blanca, Bahia Blanca, Argentina
| | - Andrea Zanichelli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy; Operative Unit of Medicine, Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Donato, San Donato Milanese, Milan, Italy
| | - Darío Josviack
- Instituto de Medicina Respiratoria, Rafaela, Santa Fe, Argentina
| | - Maurizio Margaglione
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy.
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