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Culbertson EM, Levin TC. Eukaryotic CD-NTase, STING, and viperin proteins evolved via domain shuffling, horizontal transfer, and ancient inheritance from prokaryotes. PLoS Biol 2023; 21:e3002436. [PMID: 38064485 PMCID: PMC10732462 DOI: 10.1371/journal.pbio.3002436] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/20/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Abstract
Animals use a variety of cell-autonomous innate immune proteins to detect viral infections and prevent replication. Recent studies have discovered that a subset of mammalian antiviral proteins have homology to antiphage defense proteins in bacteria, implying that there are aspects of innate immunity that are shared across the Tree of Life. While the majority of these studies have focused on characterizing the diversity and biochemical functions of the bacterial proteins, the evolutionary relationships between animal and bacterial proteins are less clear. This ambiguity is partly due to the long evolutionary distances separating animal and bacterial proteins, which obscures their relationships. Here, we tackle this problem for 3 innate immune families (CD-NTases [including cGAS], STINGs, and viperins) by deeply sampling protein diversity across eukaryotes. We find that viperins and OAS family CD-NTases are ancient immune proteins, likely inherited since the earliest eukaryotes first arose. In contrast, we find other immune proteins that were acquired via at least 4 independent events of horizontal gene transfer (HGT) from bacteria. Two of these events allowed algae to acquire new bacterial viperins, while 2 more HGT events gave rise to distinct superfamilies of eukaryotic CD-NTases: the cGLR superfamily (containing cGAS) that has since diversified via a series of animal-specific duplications and a previously undefined eSMODS superfamily, which more closely resembles bacterial CD-NTases. Finally, we found that cGAS and STING proteins have substantially different histories, with STING protein domains undergoing convergent domain shuffling in bacteria and eukaryotes. Overall, our findings paint a picture of eukaryotic innate immunity as highly dynamic, where eukaryotes build upon their ancient antiviral repertoires through the reuse of protein domains and by repeatedly sampling a rich reservoir of bacterial antiphage genes.
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Affiliation(s)
- Edward M. Culbertson
- University of Pittsburgh, Department of Biological Sciences, Pittsburgh, Pennsylvania, United States of America
| | - Tera C. Levin
- University of Pittsburgh, Department of Biological Sciences, Pittsburgh, Pennsylvania, United States of America
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Culbertson EM, Levin TC. Eukaryotic antiviral immune proteins arose via convergence, horizontal transfer, and ancient inheritance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546753. [PMID: 37425898 PMCID: PMC10327000 DOI: 10.1101/2023.06.27.546753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Animals use a variety of cell-autonomous innate immune proteins to detect viral infections and prevent replication. Recent studies have discovered that a subset of mammalian antiviral proteins have homology to anti-phage defense proteins in bacteria, implying that there are aspects of innate immunity that are shared across the Tree of Life. While the majority of these studies have focused on characterizing the diversity and biochemical functions of the bacterial proteins, the evolutionary relationships between animal and bacterial proteins are less clear. This ambiguity is partly due to the long evolutionary distances separating animal and bacterial proteins, which obscures their relationships. Here, we tackle this problem for three innate immune families (CD-NTases [including cGAS], STINGs, and Viperins) by deeply sampling protein diversity across eukaryotes. We find that Viperins and OAS family CD-NTases are truly ancient immune proteins, likely inherited since the last eukaryotic common ancestor and possibly longer. In contrast, we find other immune proteins that arose via at least four independent events of horizontal gene transfer (HGT) from bacteria. Two of these events allowed algae to acquire new bacterial viperins, while two more HGT events gave rise to distinct superfamilies of eukaryotic CD-NTases: the Mab21 superfamily (containing cGAS) which has diversified via a series of animal-specific duplications, and a previously undefined eSMODS superfamily, which more closely resembles bacterial CD-NTases. Finally, we found that cGAS and STING proteins have substantially different histories, with STINGs arising via convergent domain shuffling in bacteria and eukaryotes. Overall, our findings paint a picture of eukaryotic innate immunity as highly dynamic, where eukaryotes build upon their ancient antiviral repertoires through the reuse of protein domains and by repeatedly sampling a rich reservoir of bacterial anti-phage genes.
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Affiliation(s)
| | - Tera C. Levin
- University of Pittsburgh, Department of Biological Sciences
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3
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Adeberg S, Knoll M, Koelsche C, Bernhardt D, Schrimpf D, Sahm F, König L, Harrabi SB, Hörner-Rieber J, Verma V, Bewerunge-Hudler M, Unterberg A, Sturm D, Jungk C, Herold-Mende C, Wick W, von Deimling A, Debus J, Rieken S, Abdollahi A. DNA-methylome-assisted classification of patients with poor prognostic subventricular zone associated IDH-wildtype glioblastoma. Acta Neuropathol 2022; 144:129-142. [PMID: 35660939 PMCID: PMC9217840 DOI: 10.1007/s00401-022-02443-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/04/2022] [Accepted: 05/21/2022] [Indexed: 11/25/2022]
Abstract
Glioblastoma (GBM) derived from the “stem cell” rich subventricular zone (SVZ) may constitute a therapy-refractory subgroup of tumors associated with poor prognosis. Risk stratification for these cases is necessary but is curtailed by error prone imaging-based evaluation. Therefore, we aimed to establish a robust DNA methylome-based classification of SVZ GBM and subsequently decipher underlying molecular characteristics. MRI assessment of SVZ association was performed in a retrospective training set of IDH-wildtype GBM patients (n = 54) uniformly treated with postoperative chemoradiotherapy. DNA isolated from FFPE samples was subject to methylome and copy number variation (CNV) analysis using Illumina Platform and cnAnalysis450k package. Deep next-generation sequencing (NGS) of a panel of 130 GBM-related genes was conducted (Agilent SureSelect/Illumina). Methylome, transcriptome, CNV, MRI, and mutational profiles of SVZ GBM were further evaluated in a confirmatory cohort of 132 patients (TCGA/TCIA). A 15 CpG SVZ methylation signature (SVZM) was discovered based on clustering and random forest analysis. One third of CpG in the SVZM were associated with MAB21L2/LRBA. There was a 14.8% (n = 8) discordance between SVZM vs. MRI classification. Re-analysis of these patients favored SVZM classification with a hazard ratio (HR) for OS of 2.48 [95% CI 1.35–4.58], p = 0.004 vs. 1.83 [1.0–3.35], p = 0.049 for MRI classification. In the validation cohort, consensus MRI based assignment was achieved in 62% of patients with an intraclass correlation (ICC) of 0.51 and non-significant HR for OS (2.03 [0.81–5.09], p = 0.133). In contrast, SVZM identified two prognostically distinct subgroups (HR 3.08 [1.24–7.66], p = 0.016). CNV alterations revealed loss of chromosome 10 in SVZM– and gains on chromosome 19 in SVZM– tumors. SVZM– tumors were also enriched for differentially mutated genes (p < 0.001). In summary, SVZM classification provides a novel means for stratifying GBM patients with poor prognosis and deciphering molecular mechanisms governing aggressive tumor phenotypes.
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Affiliation(s)
- Sebastian Adeberg
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany.
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany.
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
| | - Maximilian Knoll
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Translational Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
| | - Christian Koelsche
- Department of Neuropathology, University Hospital of Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Denise Bernhardt
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Department of Radiation Oncology, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, University Hospital of Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, University Hospital of Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Laila König
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Semi Ben Harrabi
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Juliane Hörner-Rieber
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Vivek Verma
- Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center Houston, Houston, TX, USA
| | - Melanie Bewerunge-Hudler
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Andreas Unterberg
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Department of Neurosurgery, University Hospital of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
| | - Dominik Sturm
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Angelika Lautenschläger Children's Hospital, University Medical Center for Children and Adolescents, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Christine Jungk
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Department of Neurosurgery, University Hospital of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
| | - Christel Herold-Mende
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
| | - Wolfgang Wick
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Department of Neurooncology, University Hospital Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
| | - Andreas von Deimling
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Department of Neuropathology, University Hospital of Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Juergen Debus
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Stefan Rieken
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Amir Abdollahi
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Translational Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
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Boulin T, Itani O, El Mouridi S, Leclercq-Blondel A, Gendrel M, Macnamara E, Soldatos A, Murphy JL, Gorman MP, Lindsey A, Shimada S, Turner D, Silverman GA, Baldridge D, Malicdan MC, Schedl T, Pak SC. Functional analysis of a de novo variant in the neurodevelopment and generalized epilepsy disease gene NBEA. Mol Genet Metab 2021; 134:195-202. [PMID: 34412939 PMCID: PMC10626981 DOI: 10.1016/j.ymgme.2021.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/21/2021] [Accepted: 07/30/2021] [Indexed: 01/09/2023]
Abstract
Neurobeachin (NBEA) was initially identified as a candidate gene for autism. Recently, variants in NBEA have been associated with neurodevelopmental delay and childhood epilepsy. Here, we report on a novel NBEA missense variant (c.5899G > A, p.Gly1967Arg) in the Domain of Unknown Function 1088 (DUF1088) identified in a child enrolled in the Undiagnosed Diseases Network (UDN), who presented with neurodevelopmental delay and seizures. Modeling of this variant in the Caenorhabditis elegans NBEA ortholog, sel-2, indicated that the variant was damaging to in vivo function as evidenced by altered cell fate determination and trafficking of potassium channels in neurons. The variant effect was indistinguishable from that of the reference null mutation suggesting that the variant is a strong hypomorph or a complete loss-of-function. Our experimental data provide strong support for the molecular diagnosis and pathogenicity of the NBEA p.Gly1967Arg variant and the importance of the DUF1088 for NBEA function.
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Affiliation(s)
- Thomas Boulin
- Institut NeuroMyoGène, Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217, Lyon 69008, France
| | - Omar Itani
- C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA; Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Sonia El Mouridi
- Institut NeuroMyoGène, Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217, Lyon 69008, France
| | - Alice Leclercq-Blondel
- Institut NeuroMyoGène, Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217, Lyon 69008, France
| | - Marie Gendrel
- Institut NeuroMyoGène, Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217, Lyon 69008, France; Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université Paris Sciences et Lettres Research University, Paris 75005, France
| | - Ellen Macnamara
- Undiagnosed Diseases Program Translational Laboratory, NHGRI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ariane Soldatos
- Undiagnosed Diseases Program Translational Laboratory, NHGRI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer L Murphy
- Undiagnosed Diseases Program Translational Laboratory, NHGRI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark P Gorman
- Department of Neurology, Neuroimmunology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anika Lindsey
- C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA; Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Shino Shimada
- Undiagnosed Diseases Program Translational Laboratory, NHGRI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Darian Turner
- C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA; Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Gary A Silverman
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Dustin Baldridge
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - May C Malicdan
- Undiagnosed Diseases Program Translational Laboratory, NHGRI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tim Schedl
- C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA; Department of Genetics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Stephen C Pak
- C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA; Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA.
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Gath N, Gross JM. Zebrafish mab21l2 mutants possess severe defects in optic cup morphogenesis, lens and cornea development. Dev Dyn 2019; 248:514-529. [PMID: 31037784 DOI: 10.1002/dvdy.44] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/09/2019] [Accepted: 04/16/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Mutations in MAB21L2 result in severe ocular defects including microphthalmia, anophthalmia, coloboma, microcornea, and cataracts. The molecular and cellular underpinnings of these defects are unknown, as is the normal cellular function of MAB21L2. Zebrafish mab21l2 au10 mutants possess ocular defects resembling those in humans with MAB21L2 mutations, providing an excellent model to characterize mab21l2 functions during eye development. RESULTS mab21l2 -/- mutants possessed a host of ocular defects including microphthalmia and colobomas as well as small, disorganized lenses and cornea dysgenesis. Decreased proliferation, increased cell death, and defects in marker gene expression were detected in the lens. Cell death in the optic stalk was elevated in mab21l2 -/- mutants and the basement membrane between the edges of the choroid fissure failed to break down. Neuronal differentiation in the retina was normal, however. mab21l2 -/- mutant corneas were disorganized, possessed an increased number of cells, some of which proliferated ectopically, and failed to differentiate the corneal stroma. CONCLUSIONS mab21l2 function is required for morphogenesis and cell survival in the lens and optic cup, and basement membrane breakdown in the choroid fissure. mab21l2 function also regulates proliferation in the lens and cornea; in its absence, the lens is small and mispatterned, and corneal morphogenesis and patterning are also disrupted.
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Affiliation(s)
- Natalie Gath
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas.,Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jeffrey M Gross
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas.,Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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Tsang SW, Guo Y, Chan LH, Huang Y, Chow KL. Generation and characterization of pathogenic Mab21l2(R51C) mouse model. Genesis 2018; 56:e23261. [PMID: 30375740 DOI: 10.1002/dvg.23261] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/18/2018] [Accepted: 10/26/2018] [Indexed: 12/12/2022]
Abstract
MAB21L2(R51C) is one of the five documented MAB21L2 mutations in human patients with bilateral eye malformations identified via whole exome sequencing. In addition to the eye abnormality, patients with MAB21L2 R51C/+ mutation also have skeletal dysplasia and intellectual disability. To evaluate the pathology of this mutant allele systematically in understanding the functional role of MAB21L2 in human development, we introduce the R51C mutation into the mouse genome by CRISPR/Cas9 system to generate a mouse model for detailed characterization. The Mab21l2 R51C/+ mice have eyeless phenotype and skeletal abnormalities. Micro-computed tomography (micro-CT) analysis showed the Mab21l2 R51C/+ mice have no eye balls but with two abnormal tissues underneath the brain. Histological analysis revealed that the early eye development in the mutant embryos is interrupted. In addition, Mab21l2 R51C/+ mice also have joint fusion phenotype; the humerus is fused with radius, whereas femur is fused with tibia. Limbs in the mutant animals are distinctly shorter than the wild type; and deltoid tuberosities in humeri are absent in these Mab21l2 R51C/+ mice. In summary, we showed that our Mab21l2 R51C/+ mutant mice have recapitulated the pathological features in eye and bone of human patients. Further analyses of the mutant phenotype with molecular markers will provide insight on how MAB21L2 guides the optic differentiation and skeletogenesis, revealing specific underlying pathogenic mechanism of the MAB21L2(R51C) mutation.
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Affiliation(s)
- Shun-Wa Tsang
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Yanjiang Guo
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Long-Hei Chan
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Yingyu Huang
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - King L Chow
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong.,Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
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7
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Sribudiani Y, Chauhan RK, Alves MM, Petrova L, Brosens E, Harrison C, Wabbersen T, de Graaf BM, Rügenbrink T, Burzynski G, Brouwer RWW, van IJcken WFJ, Maas SM, de Klein A, Osinga J, Eggen BJL, Burns AJ, Brooks AS, Shepherd IT, Hofstra RMW. Identification of Variants in RET and IHH Pathway Members in a Large Family With History of Hirschsprung Disease. Gastroenterology 2018; 155:118-129.e6. [PMID: 29601828 DOI: 10.1053/j.gastro.2018.03.034] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 02/22/2018] [Accepted: 03/19/2018] [Indexed: 01/10/2023]
Abstract
BACKGROUND & AIMS Hirschsprung disease (HSCR) is an inherited congenital disorder characterized by absence of enteric ganglia in the distal part of the gut. Variants in ret proto-oncogene (RET) have been associated with up to 50% of familial and 35% of sporadic cases. We searched for variants that affect disease risk in a large, multigenerational family with history of HSCR in a linkage region previously associated with the disease (4q31.3-q32.3) and exome wide. METHODS We performed exome sequencing analyses of a family in the Netherlands with 5 members diagnosed with HSCR and 2 members diagnosed with functional constipation. We initially focused on variants in genes located in 4q31.3-q32.3; however, we also performed an exome-wide analysis in which known HSCR or HSCR-associated gene variants predicted to be deleterious were prioritized for further analysis. Candidate genes were expressed in HEK293, COS-7, and Neuro-2a cells and analyzed by luciferase and immunoblot assays. Morpholinos were designed to target exons of candidate genes and injected into 1-cell stage zebrafish embryos. Embryos were allowed to develop and stained for enteric neurons. RESULTS Within the linkage region, we identified 1 putative splice variant in the lipopolysaccharide responsive beige-like anchor protein gene (LRBA). Functional assays could not confirm its predicted effect on messenger RNA splicing or on expression of the mab-21 like 2 gene (MAB21L2), which is embedded in LRBA. Zebrafish that developed following injection of the lrba morpholino had a shortened body axis and subtle gut morphological defects, but no significant reduction in number of enteric neurons compared with controls. Outside the linkage region, members of 1 branch of the family carried a previously unidentified RET variant or an in-frame deletion in the glial cell line derived neurotrophic factor gene (GDNF), which encodes a ligand of RET. This deletion was located 6 base pairs before the last codon. We also found variants in the Indian hedgehog gene (IHH) and its mediator, the transcription factor GLI family zinc finger 3 (GLI3). When expressed in cells, the RET-P399L variant disrupted protein glycosylation and had altered phosphorylation following activation by GDNF. The deletion in GDNF prevented secretion of its gene product, reducing RET activation, and the IHH-Q51K variant reduced expression of the transcription factor GLI1. Injection of morpholinos that target ihh reduced the number of enteric neurons to 13% ± 1.4% of control zebrafish. CONCLUSIONS In a study of a large family with history of HSCR, we identified variants in LRBA, RET, the gene encoding the RET ligand (GDNF), IHH, and a gene encoding a mediator of IHH signaling (GLI3). These variants altered functions of the gene products when expressed in cells and knockout of ihh reduced the number of enteric neurons in the zebrafish gut.
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Affiliation(s)
- Yunia Sribudiani
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Biomedical Sciences, Division of Biochemistry and Molecular Biology, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Rajendra K Chauhan
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Maria M Alves
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lucy Petrova
- Department of Biology, Emory University, Atlanta, Georgia
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Colin Harrison
- Department of Biology, Emory University, Atlanta, Georgia
| | - Tara Wabbersen
- Department of Biology, Emory University, Atlanta, Georgia
| | - Bianca M de Graaf
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Tim Rügenbrink
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Rutger W W Brouwer
- Erasmus Center for Biomics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Saskia M Maas
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jan Osinga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Bart J L Eggen
- Department of Neuroscience, Section Medical Physiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alan J Burns
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands; Neural Development and Gastroenterology Units, UCL Institute of Child Health, London, UK
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Robert M W Hofstra
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands; Neural Development and Gastroenterology Units, UCL Institute of Child Health, London, UK.
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8
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Kurtenbach S, Gießl A, Strömberg S, Kremers J, Atorf J, Rasche S, Neuhaus EM, Hervé D, Brandstätter JH, Asan E, Hatt H, Kilimann MW. The BEACH Protein LRBA Promotes the Localization of the Heterotrimeric G-protein G olf to Olfactory Cilia. Sci Rep 2017; 7:8409. [PMID: 28814779 PMCID: PMC5559528 DOI: 10.1038/s41598-017-08543-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/10/2017] [Indexed: 02/07/2023] Open
Abstract
BEACH domain proteins are involved in membrane protein traffic and human diseases, but their molecular mechanisms are not understood. The BEACH protein LRBA has been implicated in immune response and cell proliferation, and human LRBA mutations cause severe immune deficiency. Here, we report a first functional and molecular phenotype outside the immune system of LRBA-knockout mice: compromised olfaction, manifesting in reduced electro-olfactogram response amplitude, impaired food-finding efficiency, and smaller olfactory bulbs. LRBA is prominently expressed in olfactory and vomeronasal chemosensory neurons of wild-type mice. Olfactory impairment in the LRBA-KO is explained by markedly reduced concentrations (20–40% of wild-type levels) of all three subunits αolf, β1 and γ13 of the olfactory heterotrimeric G-protein, Golf, in the sensory cilia of olfactory neurons. In contrast, cilia morphology and the concentrations of many other proteins of olfactory cilia are not or only slightly affected. LRBA is also highly expressed in photoreceptor cells, another cell type with a specialized sensory cilium and heterotrimeric G-protein-based signalling; however, visual function appeared unimpaired by the LRBA-KO. To our knowledge, this is the first observation that a BEACH protein is required for the efficient subcellular localization of a lipid-anchored protein, and of a ciliary protein.
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Affiliation(s)
- Stefan Kurtenbach
- Department of Cell Physiology, Ruhr University Bochum, D-44780, Bochum, Germany
| | - Andreas Gießl
- Department of Biology, Animal Physiology, University of Erlangen-Nürnberg, D-91058, Erlangen, Germany
| | - Siv Strömberg
- Department of Neuroscience, Uppsala University, S-75124, Uppsala, Sweden
| | - Jan Kremers
- Department of Ophthalmology, University Hospital Erlangen, D-91054, Erlangen, Germany.,Department of Anatomy II, Friedrich-Alexander University Erlangen-Nürnberg, D-91054, Erlangen, Germany
| | - Jenny Atorf
- Department of Ophthalmology, University Hospital Erlangen, D-91054, Erlangen, Germany
| | - Sebastian Rasche
- Department of Cell Physiology, Ruhr University Bochum, D-44780, Bochum, Germany
| | - Eva M Neuhaus
- Department of Pharmacology and Toxikology, University Hospital Jena, D-07747, Jena, Germany
| | - Denis Hervé
- Inserm UMR-S839, Institut du Fer a Moulin, Universite Pierre et Marie Curie, F-75005, Paris, France
| | | | - Esther Asan
- Institute of Anatomy and Cell Biology, University of Würzburg, D-97070, Würzburg, Germany
| | - Hanns Hatt
- Department of Cell Physiology, Ruhr University Bochum, D-44780, Bochum, Germany
| | - Manfred W Kilimann
- Department of Neuroscience, Uppsala University, S-75124, Uppsala, Sweden. .,Department of Molecular Neurobiology, Max Planck Institute for Experimental Medicine, D-37075, Göttingen, Germany.
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9
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Jacobsen KK, Nievergelt CM, Zayats T, Greenwood TA, Anttila V, Akiskal HS, Haavik J, Fasmer OB, Kelsoe JR, Johansson S, Oedegaard KJ. Genome wide association study identifies variants in NBEA associated with migraine in bipolar disorder. J Affect Disord 2015; 172:453-61. [PMID: 25451450 PMCID: PMC4394021 DOI: 10.1016/j.jad.2014.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 10/02/2014] [Accepted: 10/03/2014] [Indexed: 01/19/2023]
Abstract
BACKGROUND Migraine is a common comorbidity among individuals with bipolar disorder, but the underlying mechanisms for this co-occurrence are poorly understood. The aim of this study was to investigate the genetic background of bipolar patients with and without migraine. METHODS We performed a genome-wide association analysis contrasting 460 bipolar migraneurs with 914 bipolar patients without migraine from the Bipolar Genome Study (BiGS). RESULTS We identified one genome-wide significant association between migraine in bipolar disorder patients and rs1160720, an intronic single nucleotide polymorphism (SNP) in the NBEA gene (P=2.97 × 10(-8), OR: 1.82, 95% CI: 1.47-2.25), although this was not replicated in a smaller sample of 289 migraine cases. LIMITATIONS Our study is based on self-reported migraine. CONCLUSIONS NBEA encodes neurobeachin, a scaffolding protein primarily expressed in the brain and involved in trafficking of vesicles containing neurotransmitter receptors. This locus has not previously been implicated in migraine per se. We found no evidence of association in data from the GWAS migraine meta-analysis consortium (n=118,710 participants) suggesting that the association might be specific to migraine co-morbid with bipolar disorder.
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Affiliation(s)
- Kaya K. Jacobsen
- Department of Biomedicine, University of Bergen, Norway,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway,K. G. Jebsen Center for Research on Neuropsychiatric Disorders, University of Bergen, Norway
| | | | - Tetyana Zayats
- Department of Biomedicine, University of Bergen, Norway,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway,K. G. Jebsen Center for Research on Neuropsychiatric Disorders, University of Bergen, Norway
| | | | - Verneri Anttila
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,lnstitute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | | | - Hagop S. Akiskal
- Department of Psychiatry, University of California San Diego, USA,Department of Psychiatry, VA Hospital, San Diego, USA
| | | | - Jan Haavik
- Department of Biomedicine, University of Bergen, Norway,K. G. Jebsen Center for Research on Neuropsychiatric Disorders, University of Bergen, Norway,Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Ole Bernt Fasmer
- K. G. Jebsen Center for Research on Neuropsychiatric Disorders, University of Bergen, Norway,Division of Psychiatry, Haukeland University Hospital, Bergen, Norway,Department of Clinical Medicine, Section for Psychiatry, Faculty of Medicine and Dentistry, University of Bergen, Norway
| | - John R. Kelsoe
- Department of Psychiatry, University of California San Diego, USA,Department of Psychiatry, VA Hospital, San Diego, USA
| | - Stefan Johansson
- Department of Biomedicine, University of Bergen, Norway,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway,K. G. Jebsen Center for Research on Neuropsychiatric Disorders, University of Bergen, Norway,Department of Clinical Science, University of Bergen, Norway
| | - Ketil J. Oedegaard
- K. G. Jebsen Center for Research on Neuropsychiatric Disorders, University of Bergen, Norway,Division of Psychiatry, Haukeland University Hospital, Bergen, Norway,Department of Clinical Medicine, Section for Psychiatry, Faculty of Medicine and Dentistry, University of Bergen, Norway
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10
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Baggio F, Bozzato A, Benna C, Leonardi E, Romoli O, Cognolato M, Tosatto SCE, Costa R, Sandrelli F. 2mit, an intronic gene of Drosophila melanogaster timeless2, is involved in behavioral plasticity. PLoS One 2013; 8:e76351. [PMID: 24098788 PMCID: PMC3786989 DOI: 10.1371/journal.pone.0076351] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 08/27/2013] [Indexed: 12/15/2022] Open
Abstract
Background Intronic genes represent ~6% of the total gene complement in Drosophila melanogaster and ~85% of them encode for proteins. We recently characterized the D. melanogastertimeless2 (tim2) gene, showing its active involvement in chromosomal stability and light synchronization of the adult circadian clock. The protein coding gene named 2mit maps on the 11thtim2 intron in the opposite transcriptional orientation. Methodology/Principal Findings Here we report the molecular and functional characterization of 2mit. The 2mit gene is expressed throughout Drosophila development, localizing mainly in the nervous system during embryogenesis and mostly in the mushroom bodies and ellipsoid body of the central complex in the adult brain. Insilico analyses revealed that 2mit encodes a putative leucine-Rich Repeat transmembrane receptor with intrinsically disordered regions, harboring several fully conserved functional interaction motifs in the cytosolic side. Using insertional mutations, tissue-specific over-expression, and down-regulation approaches, it was found that 2mit is implicated in adult short-term memory, assessed by a courtship conditioning assay. In D. melanogaster, tim2 and 2mit do not seem to be functionally related. Bioinformatic analyses identified 2MIT orthologs in 21 Drosophilidae, 4 Lepidoptera and in Apis mellifera. In addition, the tim2-2mit host-nested gene organization was shown to be present in A. mellifera and maintained among Drosophila species. Within the Drosophilidae 2mit-hosting tim2 intron, insilico approaches detected a neuronal specific transcriptional binding site which might have contributed to preserve the specific host-nested gene association across Drosophila species. Conclusions/Significance Taken together, these results indicate that 2mit, a gene mainly expressed in the nervous system, has a role in the behavioral plasticity of the adult Drosophila. The presence of a putative 2mit regulatory enhancer within the 2mit-hosting tim2 intron could be considered an evolutionary constraint potentially involved in maintaining the tim2-2mit host-nested chromosomal architecture during the evolution of Drosophila species.
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Affiliation(s)
- Francesca Baggio
- Dipartimento di Biologia, Università degli Studi di Padova Padova, Italy
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11
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Cullinane AR, Schäffer AA, Huizing M. The BEACH is hot: a LYST of emerging roles for BEACH-domain containing proteins in human disease. Traffic 2013; 14:749-66. [PMID: 23521701 DOI: 10.1111/tra.12069] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/18/2013] [Accepted: 03/23/2013] [Indexed: 12/19/2022]
Abstract
BEACH (named after 'Beige and Chediak-Higashi') is a conserved ∼280 residue domain, present in nine human BEACH domain containing proteins (BDCPs). Most BDCPs are large, containing a PH-like domain for membrane association preceding their BEACH domain, and containing WD40 and other domains for ligand binding. Recent studies found that mutations in individual BDCPs cause several human diseases. BDCP alterations affect lysosome size (LYST and NSMAF), apoptosis (NSMAF), autophagy (LYST, WDFY3, LRBA), granule size (LYST, NBEAL2, NBEA) or synapse formation (NBEA). However, the roles of each BDCP in these membrane events remain controversial. After reviewing studies on individual BDCPs, we propose a unifying hypothesis that BDCPs act as scaffolding proteins that facilitate membrane events, including both fission and fusion, determined by their binding partners. BDCPs may also bind each other, enabling fusion or fission of vesicles that are not necessarily of the same type. Such mechanisms explain why different BDCPs may have roles in autophagy; each BDCP is specific for the cell type or the cargo, but not necessarily specific for attaching to the autophagosome. Further elucidation of these mechanisms, preferably carrying out the same experiment on multiple BDCPs, and possibly using patients' cells, may identify potential targets for therapy.
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Affiliation(s)
- Andrew R Cullinane
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
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12
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Drosophila rugose is a functional homolog of mammalian Neurobeachin and affects synaptic architecture, brain morphology, and associative learning. J Neurosci 2013; 32:15193-204. [PMID: 23100440 DOI: 10.1523/jneurosci.6424-11.2012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Neurobeachin (Nbea) is implicated in vesicle trafficking in the regulatory secretory pathway, but details on its molecular function are currently unknown. We have used Drosophila melanogaster mutants for rugose (rg), the Drosophila homolog of Nbea, to further elucidate the function of this multidomain protein. Rg is expressed in a granular pattern reminiscent of the Golgi network in neuronal cell bodies and colocalizes with transgenic Nbea, suggesting a function in secretory regulation. In contrast to Nbea(-/-) mice, rg null mutants are viable and fertile and exhibit aberrant associative odor learning, changes in gross brain morphology, and synaptic architecture as determined at the larval neuromuscular junction. At the same time, basal synaptic transmission is essentially unaffected, suggesting that structural and functional aspects are separable. Rg phenotypes can be rescued by a Drosophila rg+ transgene, whereas a mouse Nbea transgene rescues aversive odor learning and synaptic architecture; it fails to rescue brain morphology and appetitive odor learning. This dissociation between the functional redundancy of either the mouse or the fly transgene suggests that their complex composition of numerous functional and highly conserved domains support independent functions. We propose that the detailed compendium of phenotypes exhibited by the Drosophila rg null mutant provided here will serve as a test bed for dissecting the different functional domains of BEACH (for beige and human Chediak-Higashi syndrome) proteins, such as Rugose, mouse Nbea, or Nbea orthologs in other species, such as human.
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13
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Lopez-Herrera G, Tampella G, Pan-Hammarström Q, Herholz P, Trujillo-Vargas C, Phadwal K, Simon A, Moutschen M, Etzioni A, Mory A, Srugo I, Melamed D, Hultenby K, Liu C, Baronio M, Vitali M, Philippet P, Dideberg V, Aghamohammadi A, Rezaei N, Enright V, Du L, Salzer U, Eibel H, Pfeifer D, Veelken H, Stauss H, Lougaris V, Plebani A, Gertz E, Schäffer A, Hammarström L, Grimbacher B. Deleterious mutations in LRBA are associated with a syndrome of immune deficiency and autoimmunity. Am J Hum Genet 2012; 90:986-1001. [PMID: 22608502 PMCID: PMC3370280 DOI: 10.1016/j.ajhg.2012.04.015] [Citation(s) in RCA: 345] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 03/07/2012] [Accepted: 04/11/2012] [Indexed: 12/14/2022] Open
Abstract
Most autosomal genetic causes of childhood-onset hypogammaglobulinemia are currently not well understood. Most affected individuals are simplex cases, but both autosomal-dominant and autosomal-recessive inheritance have been described. We performed genetic linkage analysis in consanguineous families affected by hypogammaglobulinemia. Four consanguineous families with childhood-onset humoral immune deficiency and features of autoimmunity shared genotype evidence for a linkage interval on chromosome 4q. Sequencing of positional candidate genes revealed that in each family, affected individuals had a distinct homozygous mutation in LRBA (lipopolysaccharide responsive beige-like anchor protein). All LRBA mutations segregated with the disease because homozygous individuals showed hypogammaglobulinemia and autoimmunity, whereas heterozygous individuals were healthy. These mutations were absent in healthy controls. Individuals with homozygous LRBA mutations had no LRBA, had disturbed B cell development, defective in vitro B cell activation, plasmablast formation, and immunoglobulin secretion, and had low proliferative responses. We conclude that mutations in LRBA cause an immune deficiency characterized by defects in B cell activation and autophagy and by susceptibility to apoptosis, all of which are associated with a clinical phenotype of hypogammaglobulinemia and autoimmunity.
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Affiliation(s)
- Gabriela Lopez-Herrera
- Department of Immunology, Division of Infection and Immunity, University College London, Royal Free Hospital, London NW3 2QG, UK
- Immunodeficiency Research Unit, National Institute of Pediatrics, Mexico City 04530, Mexico
| | - Giacomo Tampella
- Pediatrics Clinic and Institute of Molecular Medicine A. Novicelli, University of Brescia, Spedali Civili di Brescia, Brescia 25123, Italy
| | - Qiang Pan-Hammarström
- Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, SE-14186 Stockholm, Sweden
| | - Peer Herholz
- Centre of Chronic Immunodeficiency, University Medical Centre, 79108 Freiburg, Germany
| | - Claudia M. Trujillo-Vargas
- Department of Immunology, Division of Infection and Immunity, University College London, Royal Free Hospital, London NW3 2QG, UK
- Group of Primary Immunodeficiencies, University of Antioquia, Medellin 1226, Colombia
| | - Kanchan Phadwal
- Biomedical Research Centre Translational Immunology Lab, National Institute for Health Research, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Anna Katharina Simon
- Biomedical Research Centre Translational Immunology Lab, National Institute for Health Research, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
- Medcial Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Michel Moutschen
- University of Liège Center of Immunology, Laboratory of Immunoendocrinology, Institute of Pathology, Liège-Sart Tilman 4000, Belgium
| | - Amos Etzioni
- Division of Pediatrics and Immunology, Rappaport School of Medicine, Technion, Haifa 31096, Israel
| | - Adi Mory
- Division of Pediatrics and Immunology, Rappaport School of Medicine, Technion, Haifa 31096, Israel
| | - Izhak Srugo
- Division of Pediatrics and Immunology, Rappaport School of Medicine, Technion, Haifa 31096, Israel
| | - Doron Melamed
- Division of Pediatrics and Immunology, Rappaport School of Medicine, Technion, Haifa 31096, Israel
| | - Kjell Hultenby
- Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, SE-14186 Stockholm, Sweden
| | - Chonghai Liu
- Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, SE-14186 Stockholm, Sweden
- Department of Pediatrics, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, China
| | - Manuela Baronio
- Pediatrics Clinic and Institute of Molecular Medicine A. Novicelli, University of Brescia, Spedali Civili di Brescia, Brescia 25123, Italy
| | - Massimiliano Vitali
- Pediatrics Clinic and Institute of Molecular Medicine A. Novicelli, University of Brescia, Spedali Civili di Brescia, Brescia 25123, Italy
| | - Pierre Philippet
- Department of Pediatrics, Centre Hospitalier Chrétien-Esperance, Montegnée 4420, Belgium
| | - Vinciane Dideberg
- University of Liège, Center for Human Genetics, Liège-Sart Tilman B-4000, Belgium
| | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences. Tehran 14194, Iran
| | - Nima Rezaei
- Molecular Immunology Research Center and Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran 14194, Iran
| | - Victoria Enright
- Department of Immunology, Division of Infection and Immunity, University College London, Royal Free Hospital, London NW3 2QG, UK
| | - Likun Du
- Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, SE-14186 Stockholm, Sweden
| | - Ulrich Salzer
- Centre of Chronic Immunodeficiency, University Medical Centre, 79108 Freiburg, Germany
| | - Hermann Eibel
- Centre of Chronic Immunodeficiency, University Medical Centre, 79108 Freiburg, Germany
| | - Dietmar Pfeifer
- Department of Hematology and Oncology, Freiburg University Medical Center, Freiburg 79106, Germany
| | - Hendrik Veelken
- Department of Hematology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Hans Stauss
- Department of Immunology, Division of Infection and Immunity, University College London, Royal Free Hospital, London NW3 2QG, UK
| | - Vassilios Lougaris
- Pediatrics Clinic and Institute of Molecular Medicine A. Novicelli, University of Brescia, Spedali Civili di Brescia, Brescia 25123, Italy
| | - Alessandro Plebani
- Pediatrics Clinic and Institute of Molecular Medicine A. Novicelli, University of Brescia, Spedali Civili di Brescia, Brescia 25123, Italy
| | - E. Michael Gertz
- National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20894, USA
| | - Alejandro A. Schäffer
- National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20894, USA
| | - Lennart Hammarström
- Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, SE-14186 Stockholm, Sweden
| | - Bodo Grimbacher
- Department of Immunology, Division of Infection and Immunity, University College London, Royal Free Hospital, London NW3 2QG, UK
- Centre of Chronic Immunodeficiency, University Medical Centre, 79108 Freiburg, Germany
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14
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Subgroup-specific alternative splicing in medulloblastoma. Acta Neuropathol 2012; 123:485-499. [PMID: 22358458 DOI: 10.1007/s00401-012-0959-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 01/13/2012] [Accepted: 02/11/2012] [Indexed: 12/22/2022]
Abstract
Medulloblastoma comprises four distinct molecular variants: WNT, SHH, Group 3, and Group 4. We analyzed alternative splicing usage in 14 normal cerebellar samples and 103 medulloblastomas of known subgroup. Medulloblastoma samples have a statistically significant increase in alternative splicing as compared to normal fetal cerebella (2.3-times; P < 6.47E-8). Splicing patterns are distinct and specific between molecular subgroups. Unsupervised hierarchical clustering of alternative splicing events accurately assigns medulloblastomas to their correct subgroup. Subgroup-specific splicing and alternative promoter usage was most prevalent in Group 3 (19.4%) and SHH (16.2%) medulloblastomas, while observed less frequently in WNT (3.2%), and Group 4 (9.3%) tumors. Functional annotation of alternatively spliced genes reveals overrepresentation of genes important for neuronal development. Alternative splicing events in medulloblastoma may be regulated in part by the correlative expression of antisense transcripts, suggesting a possible mechanism affecting subgroup-specific alternative splicing. Our results identify additional candidate markers for medulloblastoma subgroup affiliation, further support the existence of distinct subgroups of the disease, and demonstrate an additional level of transcriptional heterogeneity between medulloblastoma subgroups.
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15
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Wang PPS, Ruvinsky I. Family size and turnover rates among several classes of small non-protein-coding RNA genes in Caenorhabditis nematodes. Genome Biol Evol 2012; 4:565-74. [PMID: 22467905 PMCID: PMC3342880 DOI: 10.1093/gbe/evs034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
It is important to understand the forces that shape the size and evolutionary histories of gene families. Here, we investigated the evolution of non–protein-coding RNA genes in the genomes of Caenorhabditis nematodes. We specifically focused on nested arrangements, that is, cases in which an RNA gene is entirely contained in an intron of another gene. Comparing these arrangements between species simplifies the inference of orthology and, therefore, of evolutionary fates of nested genes. Two distinct patterns are evident in the data. Genes encoding small nuclear RNAs (snRNAs) and transfer RNAs form large families, which have persisted since before the common ancestor of Metazoa. Yet, individual genes die relatively rapidly, with few orthologs having survived since the divergence of Caenorhabditis elegans and Caenorhabditis briggsae. In contrast, genes encoding small nucleolar RNAs (snoRNAs) are either single-copy or form small families. Individual snoRNAs turn over at a relatively slow rate—most C. elegans genes have clearly identifiable orthologs in C. briggsae. We also found that in Drosophila, genes from larger snRNA families die at a faster rate than their counterparts from single-gene families. These results suggest that a relationship between family size and the rate of gene turnover may be a general feature of genome evolution.
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Affiliation(s)
- Paul Po-Shen Wang
- Department of Ecology and Evolution, Institute for Genomics and Systems Biology, The University of Chicago, IL, USA
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16
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Niesmann K, Breuer D, Brockhaus J, Born G, Wolff I, Reissner C, Kilimann MW, Rohlmann A, Missler M. Dendritic spine formation and synaptic function require neurobeachin. Nat Commun 2011; 2:557. [PMID: 22109531 PMCID: PMC3482631 DOI: 10.1038/ncomms1565] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 10/26/2011] [Indexed: 01/11/2023] Open
Abstract
A challenge in neuroscience is to understand the mechanisms underlying synapse
formation. Most excitatory synapses in the brain are built on spines, which are
actin-rich protrusions from dendrites. Spines are a major substrate of brain
plasticity, and spine pathologies are observed in various mental illnesses. Here we
investigate the role of neurobeachin (Nbea), a multidomain protein previously linked
to cases of autism, in synaptogenesis. We show that deletion of Nbea leads to
reduced numbers of spinous synapses in cultured neurons from complete knockouts and
in cortical tissue from heterozygous mice, accompanied by altered miniature
postsynaptic currents. In addition, excitatory synapses terminate mostly at
dendritic shafts instead of spine heads in Nbea mutants, and actin becomes less
enriched synaptically. As actin and synaptopodin, a spine-associated protein with
actin-bundling activity, accumulate ectopically near the Golgi apparatus of mutant
neurons, a role emerges for Nbea in trafficking important cargo to pre- and
postsynaptic compartments. Most excitatory synapses in the brain are found on dendritic
spines, but the mechanisms underlying synapse formation are poorly understood. Niesmann
et al. investigate the role of neurobeachin in synaptogenesis, and find that
its deletion leads to fewer spinous synapses and altered postsynaptic
currents.
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Affiliation(s)
- Katharina Niesmann
- Department of Anatomy and Molecular Neurobiology, Westfälische Wilhelms-University, Münster 48149, Germany
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17
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Cederlund ML, Vendrell V, Morrissey ME, Yin J, Gaora PÓ, Smyth VA, Higgins DG, Kennedy BN. mab21l2 transgenics reveal novel expression patterns of mab21l1 and mab21l2, and conserved promoter regulation without sequence conservation. Dev Dyn 2011; 240:745-54. [PMID: 21360786 DOI: 10.1002/dvdy.22573] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2010] [Indexed: 11/10/2022] Open
Abstract
mab21l1 and mab21l2 paralogs have widespread and dynamic expression patterns during vertebrate development. Both genes are expressed in the developing eye, midbrain, neural tube, and branchial arches. Our goal was to identify promoter regions with activity in mab21l2 expression domains. Assays of mab21l2 promoter-EGFP constructs in zebrafish embryos confirm that constructs containing 7.2 or 4.9 kb of mab21l2 promoter region are sufficient to drive expression in known (e.g., tectum, branchial arches) and unexpected domains (e.g., lens and retinal amacrine cells). A comparative analysis identifies complementary and novel expression domains of endogenous mab21l2 (e.g., lens and ventral iridocorneal canal) and mab21l1 (e.g., retinal amacrine and ganglion cells). Interestingly, therefore, despite the absence of conserved non-coding elements, a 4.9-kb mab21l2 promoter is sufficient to recapitulate expression in tissues unique to mab21l1 or mab21l2.
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Affiliation(s)
- Maria L Cederlund
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin, Ireland.
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When needles look like hay: how to find tissue-specific enhancers in model organism genomes. Dev Biol 2010; 350:239-54. [PMID: 21130761 DOI: 10.1016/j.ydbio.2010.11.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 11/11/2010] [Accepted: 11/22/2010] [Indexed: 01/22/2023]
Abstract
A major prerequisite for the investigation of tissue-specific processes is the identification of cis-regulatory elements. No generally applicable technique is available to distinguish them from any other type of genomic non-coding sequence. Therefore, researchers often have to identify these elements by elaborate in vivo screens, testing individual regions until the right one is found. Here, based on many examples from the literature, we summarize how functional enhancers have been isolated from other elements in the genome and how they have been characterized in transgenic animals. Covering computational and experimental studies, we provide an overview of the global properties of cis-regulatory elements, like their specific interactions with promoters and target gene distances. We describe conserved non-coding elements (CNEs) and their internal structure, nucleotide composition, binding site clustering and overlap, with a special focus on developmental enhancers. Conflicting data and unresolved questions on the nature of these elements are highlighted. Our comprehensive overview of the experimental shortcuts that have been found in the different model organism communities and the new field of high-throughput assays should help during the preparation phase of a screen for enhancers. The review is accompanied by a list of general guidelines for such a project.
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