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Reis LM, Seese SE, Costakos D, Semina EV. Congenital anterior segment ocular disorders: Genotype-phenotype correlations and emerging novel mechanisms. Prog Retin Eye Res 2024; 102:101288. [PMID: 39097141 PMCID: PMC11392650 DOI: 10.1016/j.preteyeres.2024.101288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Development of the anterior segment of the eye requires reciprocal sequential interactions between the arising tissues, facilitated by numerous genetic factors. Disruption of any of these processes results in congenital anomalies in the affected tissue(s) leading to anterior segment disorders (ASD) including aniridia, Axenfeld-Rieger anomaly, congenital corneal opacities (Peters anomaly, cornea plana, congenital primary aphakia), and primary congenital glaucoma. Current understanding of the genetic factors involved in ASD remains incomplete, with approximately 50% overall receiving a genetic diagnosis. While some genes are strongly associated with a specific clinical diagnosis, the majority of known factors are linked with highly variable phenotypic presentations, with pathogenic variants in FOXC1, CYP1B1, and PITX2 associated with the broadest spectrum of ASD conditions. This review discusses typical clinical presentations including associated systemic features of various forms of ASD; the latest functional data and genotype-phenotype correlations related to 25 ASD factors including newly identified genes; promising novel candidates; and current and emerging treatments for these complex conditions. Recent developments of interest in the genetics of ASD include identification of phenotypic expansions for several factors, discovery of multiple modes of inheritance for some genes, and novel mechanisms including a growing number of non-coding variants and alleles affecting specific domains/residues and requiring further studies.
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Affiliation(s)
- Linda M Reis
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Sarah E Seese
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Deborah Costakos
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Elena V Semina
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA; Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
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2
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Li J, Wang Q, Yang A, Zhang J. Monoallelic missense variants in MAB21L1 cause a novel autosomal dominant microphthalmia. Ophthalmic Genet 2024:1-7. [PMID: 39016008 DOI: 10.1080/13816810.2024.2378029] [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: 03/23/2024] [Accepted: 07/04/2024] [Indexed: 07/18/2024]
Abstract
PURPOSE The biallelic variant of MAB21L1 has previously been documented in conjunction with the autosomal recessive cerebellar, ocular, craniofacial, and genital syndrome (COFG). The purpose of this study was to investigate the gene-disease association of MAB21L1 and the newly discovered autosomal dominant (AD) microphthalmia. METHODS We report the presence of an exceptionally rare missense variant in a single allele of the Arg51 codon of MAB21L1 among four individuals from a single family diagnosed with microphthalmia, which suggesting an autosomal dominant inheritance pattern. Subsequently, based on comprehensive literature review, we identified another 13 families that have reported cases of autosomal dominant microphthalmos. RESULTS Genotype-phenotype analysis revealed that patients with a single allele missense variant in MAB21L1 exhibited solely eye abnormalities. This starkly diverged from the clinical presentation of COFG, typified by the concurrent occurrence of ocular and extraocular symptoms stemming from the biallelic variant in MAB21L1. Our findings revealed that the heterozygous pathogenic variant in MAB21L1 resulted in the emergence of autosomal dominant microphthalmia. By combining these genetic and experimental evidence, the clinical validity of MAB21L1 and the emerging autosomal dominant microphthalmia can be regarded as moderate. CONCLUSION In summary, there is sufficient convincing evidence to prove that MAB21L1 is a novel pathogenic gene responsible for autosomal dominant microphthalmia, thus offering valuable insights for precise diagnosis and targeted therapeutic interventions in cases of microphthalmia.
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Affiliation(s)
- Jinli Li
- Reproductive Medicine Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qin Wang
- Department of Reproductive Medicine, Affiliated Hospital of Jining Medical University, Jining City, Shandong, China
| | - Aijun Yang
- Department of Reproductive Medicine, Affiliated Hospital of Jining Medical University, Jining City, Shandong, China
| | - Junyu Zhang
- Reproductive Medicine Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
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3
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Wenzl SJ, de Oliveira Mann CC. How enzyme-centered approaches are advancing research on cyclic oligo-nucleotides. FEBS Lett 2024; 598:839-863. [PMID: 38453162 DOI: 10.1002/1873-3468.14838] [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: 12/03/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 03/09/2024]
Abstract
Cyclic nucleotides are the most diversified category of second messengers and are found in all organisms modulating diverse pathways. While cAMP and cGMP have been studied over 50 years, cyclic di-nucleotide signaling in eukaryotes emerged only recently with the anti-viral molecule 2´3´cGAMP. Recent breakthrough discoveries have revealed not only the astonishing chemical diversity of cyclic nucleotides but also surprisingly deep-rooted evolutionary origins of cyclic oligo-nucleotide signaling pathways and structural conservation of the proteins involved in their synthesis and signaling. Here we discuss how enzyme-centered approaches have paved the way for the identification of several cyclic nucleotide signals, focusing on the advantages and challenges associated with deciphering the activation mechanisms of such enzymes.
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Affiliation(s)
- Simon J Wenzl
- Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Carina C de Oliveira Mann
- Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
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4
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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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5
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Banh DV, Roberts CG, Morales-Amador A, Berryhill BA, Chaudhry W, Levin BR, Brady SF, Marraffini LA. Bacterial cGAS senses a viral RNA to initiate immunity. Nature 2023; 623:1001-1008. [PMID: 37968393 PMCID: PMC10686824 DOI: 10.1038/s41586-023-06743-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 10/12/2023] [Indexed: 11/17/2023]
Abstract
Cyclic oligonucleotide-based antiphage signalling systems (CBASS) protect prokaryotes from viral (phage) attack through the production of cyclic oligonucleotides, which activate effector proteins that trigger the death of the infected host1,2. How bacterial cyclases recognize phage infection is not known. Here we show that staphylococcal phages produce a structured RNA transcribed from the terminase subunit genes, termed CBASS-activating bacteriophage RNA (cabRNA), which binds to a positively charged surface of the CdnE03 cyclase and promotes the synthesis of the cyclic dinucleotide cGAMP to activate the CBASS immune response. Phages that escape the CBASS defence harbour mutations that lead to the generation of a longer form of the cabRNA that cannot activate CdnE03. As the mammalian cyclase OAS1 also binds viral double-stranded RNA during the interferon response, our results reveal a conserved mechanism for the activation of innate antiviral defence pathways.
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Affiliation(s)
- Dalton V Banh
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Cameron G Roberts
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Adrian Morales-Amador
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | | | - Waqas Chaudhry
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Bruce R Levin
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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6
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Slavik KM, Kranzusch PJ. CBASS to cGAS-STING: The Origins and Mechanisms of Nucleotide Second Messenger Immune Signaling. Annu Rev Virol 2023; 10:423-453. [PMID: 37380187 DOI: 10.1146/annurev-virology-111821-115636] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Host defense against viral pathogens is an essential function for all living organisms. In cell-intrinsic innate immunity, dedicated sensor proteins recognize molecular signatures of infection and communicate to downstream adaptor or effector proteins to activate immune defense. Remarkably, recent evidence demonstrates that much of the core machinery of innate immunity is shared across eukaryotic and prokaryotic domains of life. Here, we review a pioneering example of evolutionary conservation in innate immunity: the animal cGAS-STING (cyclic GMP-AMP synthase-stimulator of interferon genes) signaling pathway and its ancestor in bacteria, CBASS (cyclic nucleotide-based antiphage signaling system) antiphage defense. We discuss the unique mechanism by which animal cGLRs (cGAS-like receptors) and bacterial CD-NTases (cGAS/dinucleotide-cyclase in Vibrio (DncV)-like nucleotidyltransferases) in these pathways link pathogen detection with immune activation using nucleotide second messenger signals. Comparing the biochemical, structural, and mechanistic details of cGAS-STING, cGLR signaling, and CBASS, we highlight emerging questions in the field and examine evolutionary pressures that may have shaped the origins of nucleotide second messenger signaling in antiviral defense.
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Affiliation(s)
- Kailey M Slavik
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA;
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA;
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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7
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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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8
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Li Y, Slavik KM, Toyoda HC, Morehouse BR, de Oliveira Mann CC, Elek A, Levy S, Wang Z, Mears KS, Liu J, Kashin D, Guo X, Mass T, Sebé-Pedrós A, Schwede F, Kranzusch PJ. cGLRs are a diverse family of pattern recognition receptors in innate immunity. Cell 2023; 186:3261-3276.e20. [PMID: 37379839 PMCID: PMC10527820 DOI: 10.1016/j.cell.2023.05.038] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 04/03/2023] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
Cyclic GMP-AMP synthase (cGAS) is an enzyme in human cells that controls an immune response to cytosolic DNA. Upon binding DNA, cGAS synthesizes a nucleotide signal 2'3'-cGAMP that activates STING-dependent downstream immunity. Here, we discover that cGAS-like receptors (cGLRs) constitute a major family of pattern recognition receptors in innate immunity. Building on recent analysis in Drosophila, we identify >3,000 cGLRs present in nearly all metazoan phyla. A forward biochemical screening of 150 animal cGLRs reveals a conserved mechanism of signaling including response to dsDNA and dsRNA ligands and synthesis of isomers of the nucleotide signals cGAMP, c-UMP-AMP, and c-di-AMP. Combining structural biology and in vivo analysis in coral and oyster animals, we explain how synthesis of distinct nucleotide signals enables cells to control discrete cGLR-STING signaling pathways. Our results reveal cGLRs as a widespread family of pattern recognition receptors and establish molecular rules that govern nucleotide signaling in animal immunity.
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Affiliation(s)
- Yao Li
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Kailey M Slavik
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Hunter C Toyoda
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Benjamin R Morehouse
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | | | - Anamaria Elek
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Shani Levy
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Zhenwei Wang
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ 08349, USA
| | - Kepler S Mears
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jingjing Liu
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Dmitry Kashin
- Biolog Life Science Institute GmbH & Co. KG, Flughafendamm 9a, 28199 Bremen, Germany
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ 08349, USA
| | - Tali Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, Sdot Yam, Israel
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Barcelona, Spain
| | - Frank Schwede
- Biolog Life Science Institute GmbH & Co. KG, Flughafendamm 9a, 28199 Bremen, Germany
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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9
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Seese SE, Muheisen S, Gath N, Gross JM, Semina EV. Identification of HSPA8 as an interacting partner of MAB21L2 and an important factor in eye development. Dev Dyn 2023; 252:510-526. [PMID: 36576422 PMCID: PMC10947772 DOI: 10.1002/dvdy.560] [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: 06/19/2022] [Revised: 11/04/2022] [Accepted: 11/18/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Pathogenic variants in human MAB21L2 result in microphthalmia, anophthalmia, and coloboma. The exact molecular function of MAB21L2 is currently unknown. We conducted a series of yeast two-hybrid (Y2H) experiments to determine protein interactomes of normal human and zebrafish MAB21L2/mab21l2 as well as human disease-associated variant MAB21L2-p.(Arg51Gly) using human adult retina and zebrafish embryo libraries. RESULTS These screens identified klhl31, tnpo1, TNPO2/tnpo2, KLC2/klc2, and SPTBN1/sptbn1 as co-factors of MAB21L2/mab21l2. Several factors, including hspa8 and hspa5, were found to interact with MAB21L2-p.Arg51Gly but not wild-type MAB21L2/mab21l2 in Y2H screens. Further analyses via 1-by-1 Y2H assays, co-immunoprecipitation, and mass spectrometry revealed that both normal and variant MAB21L2 interact with HSPA5 and HSPA8. In situ hybridization detected co-expression of hspa5 and hspa8 with mab21l2 during eye development in zebrafish. Examination of zebrafish mutant hspa8hi138Tg identified reduced hspa8 expression associated with severe ocular developmental defects, including small eye, coloboma, and anterior segment dysgenesis. To investigate the effects of hspa8 deficiency on the mab21l2Arg51_Phe52del allele, corresponding zebrafish double mutants were generated and found to be more severely affected than single mutant lines. CONCLUSION This study identifies heat shock proteins as interacting partners of MAB21L2/mab21l2 and suggests a role for this interaction in vertebrate eye development.
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Affiliation(s)
- Sarah E. Seese
- Department of Pediatrics The Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Sanaa Muheisen
- Department of Pediatrics The Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Natalie Gath
- University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jeffrey M. Gross
- University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Elena V. Semina
- Department of Pediatrics The Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Children’s of Wisconsin, Milwaukee, WI 53226, USA
- Children’s Research Institute, Medical College of Wisconsin, Children’s of Wisconsin, Milwaukee, WI 53226, USA
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10
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Wang P, Wu P, Wang J, Zeng Y, Jiang Y, Wang Y, Li S, Xiao X, Zhang Q. Missense Mutations in MAB21L1: Causation of Novel Autosomal Dominant Ocular BAMD Syndrome. Invest Ophthalmol Vis Sci 2023; 64:19. [PMID: 36892533 PMCID: PMC10010443 DOI: 10.1167/iovs.64.3.19] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
Purpose Biallelic MAB21L1 variants have been reported to cause autosomal recessive cerebellar, ocular, craniofacial, and genital syndrome (COFG), whereas only five heterozygous pathogenic variants have been suspected to cause autosomal dominant (AD) microphthalmia and aniridia in eight families. This study aimed to report an AD ocular syndrome (blepharophimosis plus anterior segment and macular dysgenesis [BAMD]) syndrome based on clinical and genetic findings from patients with monoallelic MAB21L1 pathogenic variants in our cohort and reported cases. Methods Potential pathogenic variants in MAB21L1 were detected from a large in-house exome sequencing dataset. Ocular phenotypes of the patients with potential pathogenic variants in MAB21L1 were summarized, and the genotype-phenotype correlation was analyzed through a comprehensive literature review. Results Three heterozygous missense variants in MAB21L1, predicted to be damaging, were detected in 5 unrelated families, including c.152G>T in 2, c.152G>A in 2, and c.155T>G in one. All were absent from gnomAD. The variants were de novo in two families, transmitted from affected parents to offspring in two families, and with an unknown origin in the other family, demonstrating strong evidence of AD inheritance. All patients revealed similar BAMD phenotypes, including blepharophimosis, anterior segment dysgenesis, and macular dysgenesis. Genotype-phenotype analysis suggested that patients with monoallelic MAB21L1 missense variants had only ocular anomalies (BAMD), whereas patients with biallelic variants presented both ocular and extraocular symptoms. Conclusions Heterozygous pathogenic variants in MAB21L1 account for a new AD BAMD syndrome, which is completely different from COFG caused by homozygous variants in MAB21L1. Nucleotide c.152 is likely a mutation hot spot, and the encoded residue of p.Arg51 might be critical for MAB21L1.
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Affiliation(s)
- Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Pengsen Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Junwen Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yiyan Zeng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yi Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yingwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
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Li Y, Slavik KM, Morehouse BR, de Oliveira Mann CC, Mears K, Liu J, Kashin D, Schwede F, Kranzusch PJ. cGLRs are a diverse family of pattern recognition receptors in animal innate immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529553. [PMID: 36865129 PMCID: PMC9980059 DOI: 10.1101/2023.02.22.529553] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
cGAS (cyclic GMP-AMP synthase) is an enzyme in human cells that controls an immune response to cytosolic DNA. Upon binding DNA, cGAS synthesizes a nucleotide signal 2'3'-cGAMP that activates the protein STING and downstream immunity. Here we discover cGAS-like receptors (cGLRs) constitute a major family of pattern recognition receptors in animal innate immunity. Building on recent analysis in Drosophila , we use a bioinformatic approach to identify >3,000 cGLRs present in nearly all metazoan phyla. A forward biochemical screen of 140 animal cGLRs reveals a conserved mechanism of signaling including response to dsDNA and dsRNA ligands and synthesis of alternative nucleotide signals including isomers of cGAMP and cUMP-AMP. Using structural biology, we explain how synthesis of distinct nucleotide signals enables cells to control discrete cGLR-STING signaling pathways. Together our results reveal cGLRs as a widespread family of pattern recognition receptors and establish molecular rules that govern nucleotide signaling in animal immunity.
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Affiliation(s)
- Yao Li
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Kailey M. Slavik
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Benjamin R. Morehouse
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | | | - Kepler Mears
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jingjing Liu
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Dmitry Kashin
- Biolog Life Science Institute GmbH & Co. KG, Flughafendamm 9a, 28199 Bremen, Germany
| | - Frank Schwede
- Biolog Life Science Institute GmbH & Co. KG, Flughafendamm 9a, 28199 Bremen, Germany
| | - Philip J. Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Lead Contact
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12
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Klughammer J, Romanovskaia D, Nemc A, Posautz A, Seid CA, Schuster LC, Keinath MC, Lugo Ramos JS, Kosack L, Evankow A, Printz D, Kirchberger S, Ergüner B, Datlinger P, Fortelny N, Schmidl C, Farlik M, Skjærven K, Bergthaler A, Liedvogel M, Thaller D, Burger PA, Hermann M, Distel M, Distel DL, Kübber-Heiss A, Bock C. Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species. Nat Commun 2023; 14:232. [PMID: 36646694 PMCID: PMC9842680 DOI: 10.1038/s41467-022-34828-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 11/08/2022] [Indexed: 01/18/2023] Open
Abstract
Methylation of cytosines is a prototypic epigenetic modification of the DNA. It has been implicated in various regulatory mechanisms across the animal kingdom and particularly in vertebrates. We mapped DNA methylation in 580 animal species (535 vertebrates, 45 invertebrates), resulting in 2443 genome-scale DNA methylation profiles of multiple organs. Bioinformatic analysis of this large dataset quantified the association of DNA methylation with the underlying genomic DNA sequence throughout vertebrate evolution. We observed a broadly conserved link with two major transitions-once in the first vertebrates and again with the emergence of reptiles. Cross-species comparisons focusing on individual organs supported a deeply conserved association of DNA methylation with tissue type, and cross-mapping analysis of DNA methylation at gene promoters revealed evolutionary changes for orthologous genes. In summary, this study establishes a large resource of vertebrate and invertebrate DNA methylomes, it showcases the power of reference-free epigenome analysis in species for which no reference genomes are available, and it contributes an epigenetic perspective to the study of vertebrate evolution.
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Affiliation(s)
- Johanna Klughammer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria. .,Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Daria Romanovskaia
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Amelie Nemc
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Annika Posautz
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Charlotte A Seid
- Ocean Genome Legacy Center, Northeastern University Marine Science Center, Nahant, USA
| | - Linda C Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Juan Sebastian Lugo Ramos
- Max Planck Research Group Behavioral Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Lindsay Kosack
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ann Evankow
- Ocean Genome Legacy Center, Northeastern University Marine Science Center, Nahant, USA
| | - Dieter Printz
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Stefanie Kirchberger
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Bekir Ergüner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Paul Datlinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Nikolaus Fortelny
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Christian Schmidl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Medical University of Vienna, Center for Pathophysiology Infectiology and Immunology, Institute of Hygiene and Applied Immunology, Vienna, Austria
| | - Miriam Liedvogel
- Max Planck Research Group Behavioral Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Institute of Avian Research, An der Vogelwarte, Wilhelmshaven, Germany
| | - Denise Thaller
- Department for Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Marcela Hermann
- Medical University of Vienna, Department of Medical Biochemistry, Vienna, Austria
| | - Martin Distel
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Daniel L Distel
- Ocean Genome Legacy Center, Northeastern University Marine Science Center, Nahant, USA
| | - Anna Kübber-Heiss
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria. .,Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria.
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13
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Wang EJY, Chen IH, Kuo BYT, Yu CC, Lai MT, Lin JT, Lin LYT, Chen CM, Hwang T, Sheu JJC. Alterations of Cytoskeleton Networks in Cell Fate Determination and Cancer Development. Biomolecules 2022; 12:biom12121862. [PMID: 36551290 PMCID: PMC9775460 DOI: 10.3390/biom12121862] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/03/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
Cytoskeleton proteins have been long recognized as structural proteins that provide the necessary mechanical architecture for cell development and tissue homeostasis. With the completion of the cancer genome project, scientists were surprised to learn that huge numbers of mutated genes are annotated as cytoskeletal or associated proteins. Although most of these mutations are considered as passenger mutations during cancer development and evolution, some genes show high mutation rates that can even determine clinical outcomes. In addition, (phospho)proteomics study confirms that many cytoskeleton-associated proteins, e.g., β-catenin, PIK3CA, and MB21D2, are important signaling mediators, further suggesting their biofunctional roles in cancer development. With emerging evidence to indicate the involvement of mechanotransduction in stemness formation and cell differentiation, mutations in these key cytoskeleton components may change the physical/mechanical properties of the cells and determine the cell fate during cancer development. In particular, tumor microenvironment remodeling triggered by such alterations has been known to play important roles in autophagy, metabolism, cancer dormancy, and immune evasion. In this review paper, we will highlight the current understanding of how aberrant cytoskeleton networks affect cancer behaviors and cellular functions through mechanotransduction.
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Affiliation(s)
- Evan Ja-Yang Wang
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - I-Hsuan Chen
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813405, Taiwan
- Department of Pharmacy, College of Pharmacy and Health Care, Tajen University, Pingtung County 907391, Taiwan
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Brian Yu-Ting Kuo
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Chia-Cheng Yu
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813405, Taiwan
- Department of Pharmacy, College of Pharmacy and Health Care, Tajen University, Pingtung County 907391, Taiwan
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114202, Taiwan
| | - Ming-Tsung Lai
- Department of Pathology, Taichung Hospital, Ministry of Health and Welfare, Taichung 403301, Taiwan
| | - Jen-Tai Lin
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813405, Taiwan
| | - Leo Yen-Ting Lin
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Chih-Mei Chen
- Human Genetic Center, China Medical University Hospital, Taichung 404327, Taiwan
| | - Tritium Hwang
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Jim Jinn-Chyuan Sheu
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Institute of Biopharmaceutical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
- Institute of Precision Medicine, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
- Correspondence: ; Tel.: +886-7-5252000 (ext. 7102)
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14
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Meng F, Li X, Zhang J, Gao Z, Yang X, Liu Z, Liu Y, Guo T, Wang L, Yang L, Wang Z. Single amino acid variation in MAB21L1 is dominantly associated with congenital eye defects. J Med Genet 2022:jmg-2022-108506. [DOI: 10.1136/jmg-2022-108506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022]
Abstract
BackgroundDiagnosis of a genetic disease and determination of the causative molecular lesion rely on the availability of the disease-associated pedigrees. Microphthalmia is a congenital eye defect due to an insufficiently developed visual system; its prevalence is 1–3 in 10 000 live births.ObjectiveWe analysed a pedigree exhibiting autosomal dominant inheritance of microphthalmia to determine the genetic lesion; used AlphaFold2 to predict the changes in the protein’s 3-Dimensional structure; and compared wild-type and variant proteins in cultured cells or Drosophila model was used to explore the cellular or developmental function of the encoded product.ResultsWe identified a novel missense variation, F52L, in MAB21L1 that is absent in population databases and present exclusively in the individuals diagnosed with microphthalmia in this pedigree. Common structural changes were predicted for the disease-associated variants clustered at amino acids 49–52, and these variant products were also predominantly trapped in the cytoplasm of cultured human lens epithelia. To recapitulate its dominant effect in development, we expressed the Drosophila homologue corresponding to MAB21L1F52Land caused malformation of sensory organs.ConclusionMutations at the residues 49–52 of MAB21L1 compromise eye development. We recommend includingMAB21L1in the genetic testing panel for congenital eye disorders.
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15
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Hall HN, Bengani H, Hufnagel RB, Damante G, Ansari M, Marsh JA, Grimes GR, von Kriegsheim A, Moore D, McKie L, Rahmat J, Mio C, Blyth M, Keng WT, Islam L, McEntargart M, Mannens MM, Heyningen VV, Rainger J, Brooks BP, FitzPatrick DR. Monoallelic variants resulting in substitutions of MAB21L1 Arg51 Cause Aniridia and microphthalmia. PLoS One 2022; 17:e0268149. [PMID: 36413568 PMCID: PMC9681113 DOI: 10.1371/journal.pone.0268149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/06/2022] [Indexed: 11/23/2022] Open
Abstract
Classical aniridia is a congenital and progressive panocular disorder almost exclusively caused by heterozygous loss-of-function variants at the PAX6 locus. We report nine individuals from five families with severe aniridia and/or microphthalmia (with no detectable PAX6 mutation) with ultrarare monoallelic missense variants altering the Arg51 codon of MAB21L1. These mutations occurred de novo in 3/5 families, with the remaining families being compatible with autosomal dominant inheritance. Mice engineered to carry the p.Arg51Leu change showed a highly-penetrant optic disc anomaly in heterozygous animals with severe microphthalmia in homozygotes. Substitutions of the same codon (Arg51) in MAB21L2, a close homolog of MAB21L1, cause severe ocular and skeletal malformations in humans and mice. The predicted nucleotidyltransferase function of MAB21L1 could not be demonstrated using purified protein with a variety of nucleotide substrates and oligonucleotide activators. Induced expression of GFP-tagged wildtype and mutant MAB21L1 in human cells caused only modest transcriptional changes. Mass spectrometry of immunoprecipitated protein revealed that both mutant and wildtype MAB21L1 associate with transcription factors that are known regulators of PAX6 (MEIS1, MEIS2 and PBX1) and with poly(A) RNA binding proteins. Arg51 substitutions reduce the association of wild-type MAB21L1 with TBL1XR1, a component of the NCoR complex. We found limited evidence for mutation-specific interactions with MSI2/Musashi-2, an RNA-binding proteins with effects on many different developmental pathways. Given that biallelic loss-of-function variants in MAB21L1 result in a milder eye phenotype we suggest that Arg51-altering monoallelic variants most plausibly perturb eye development via a gain-of-function mechanism.
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Affiliation(s)
- Hildegard Nikki Hall
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Hemant Bengani
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Robert B. Hufnagel
- National Eye Institute, National Institutes of Health, Bethesda, MD, United States of America
| | | | - Morad Ansari
- South East Scotland Genetic Service, Western General Hospital, Edinburgh, United Kingdom
| | - Joseph A. Marsh
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Graeme R. Grimes
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Alex von Kriegsheim
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - David Moore
- South East Scotland Genetic Service, Western General Hospital, Edinburgh, United Kingdom
| | - Lisa McKie
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Jamalia Rahmat
- Ophthalmology Department, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Catia Mio
- Department of Medicine, University of Udine, Udine, Italy
| | - Moira Blyth
- University of Leeds, St. James’s University Hospital, Leeds, United Kingdom
| | - Wee Teik Keng
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Lily Islam
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, England
| | - Meriel McEntargart
- Medical Genetics, St George’s University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Marcel M. Mannens
- Genome Diagnostics laboratory, Department of Clinical Genetics, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Veronica Van Heyningen
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Joe Rainger
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Brian P. Brooks
- National Eye Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - David R. FitzPatrick
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
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16
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Diacou R, Nandigrami P, Fiser A, Liu W, Ashery-Padan R, Cvekl A. Cell fate decisions, transcription factors and signaling during early retinal development. Prog Retin Eye Res 2022; 91:101093. [PMID: 35817658 PMCID: PMC9669153 DOI: 10.1016/j.preteyeres.2022.101093] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 12/30/2022]
Abstract
The development of the vertebrate eyes is a complex process starting from anterior-posterior and dorso-ventral patterning of the anterior neural tube, resulting in the formation of the eye field. Symmetrical separation of the eye field at the anterior neural plate is followed by two symmetrical evaginations to generate a pair of optic vesicles. Next, reciprocal invagination of the optic vesicles with surface ectoderm-derived lens placodes generates double-layered optic cups. The inner and outer layers of the optic cups develop into the neural retina and retinal pigment epithelium (RPE), respectively. In vitro produced retinal tissues, called retinal organoids, are formed from human pluripotent stem cells, mimicking major steps of retinal differentiation in vivo. This review article summarizes recent progress in our understanding of early eye development, focusing on the formation the eye field, optic vesicles, and early optic cups. Recent single-cell transcriptomic studies are integrated with classical in vivo genetic and functional studies to uncover a range of cellular mechanisms underlying early eye development. The functions of signal transduction pathways and lineage-specific DNA-binding transcription factors are dissected to explain cell-specific regulatory mechanisms underlying cell fate determination during early eye development. The functions of homeodomain (HD) transcription factors Otx2, Pax6, Lhx2, Six3 and Six6, which are required for early eye development, are discussed in detail. Comprehensive understanding of the mechanisms of early eye development provides insight into the molecular and cellular basis of developmental ocular anomalies, such as optic cup coloboma. Lastly, modeling human development and inherited retinal diseases using stem cell-derived retinal organoids generates opportunities to discover novel therapies for retinal diseases.
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Affiliation(s)
- Raven Diacou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Prithviraj Nandigrami
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Wei Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ruth Ashery-Padan
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ales Cvekl
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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17
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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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18
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Yamada R, Oguri A, Fujiki K, Shirahige K, Hirate Y, Kanai-Azuma M, Takezoe H, Akimoto Y, Takahashi N, Kanai Y. MAB21L1 modulates gene expression and DNA metabolic processes in the lens placode. Dis Model Mech 2021; 14:dmm049251. [PMID: 34779479 PMCID: PMC8713989 DOI: 10.1242/dmm.049251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/09/2021] [Indexed: 11/20/2022] Open
Abstract
Mutations in human MAB21L1 cause aberrations in lens ectoderm morphogenesis and lead to congenital cerebellar, ocular, craniofacial and genital (COFG) syndrome. Murine Mab21l1-null mutations cause severe cell-autonomous defects in lens formation, leading to microphthalmia; therefore, Mab21l1-null mice are used as a mouse model for COFG syndrome. In this study, we investigated the early-onset single-cell-level phenotypes of murine Mab21l1-null lens ectoderms using electron microscopy and single-cell RNA sequencing (scRNA-seq). Electron microscopy and immunohistochemical analyses indicated endoplasmic reticulum stress at the 24- to 26-somite stage in Mab21l1-null lens placodes. scRNA-seq analysis revealed that 131 genes were downregulated and 148 were upregulated in Mab21l1-null lens ectoderms relative to the wild type. We successfully identified 21 lens-specific genes that were downregulated in Mab21l1-null cells, including three key genes involved in lens formation: Pitx3, Maf and Sfrp2. Moreover, gene ontology analysis of the 279 differentially expressed genes indicated enrichment in housekeeping genes associated with DNA/nucleotide metabolism prior to cell death. These findings suggest that MAB21L1 acts as a nuclear factor that modulates not only lens-specific gene expression but also DNA/nucleotide metabolic processes during lens placode formation.
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Affiliation(s)
- Ryuichi Yamada
- Department of Veterinary Anatomy, the University of Tokyo, Tokyo 113-8657, Japan
- Department of Applied Biological Chemistry, the University of Tokyo, Tokyo 113-8657, Japan
- RNA Company Limited, Tokyo 144-0051, Japan
| | - Akira Oguri
- Department of Applied Biological Chemistry, the University of Tokyo, Tokyo 113-8657, Japan
| | - Katsunori Fujiki
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, the University of Tokyo, Tokyo 113-0032, Japan
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, the University of Tokyo, Tokyo 113-0032, Japan
| | - Yoshikazu Hirate
- Department of Experimental Animal Model for Human Disease, Center for Experimental Animals, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Masami Kanai-Azuma
- Department of Experimental Animal Model for Human Disease, Center for Experimental Animals, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | | | - Yoshihiro Akimoto
- Department of Anatomy, Kyorin University School of Medicine, Tokyo 181-8611, Japan
| | - Naoki Takahashi
- Department of Applied Biological Chemistry, the University of Tokyo, Tokyo 113-8657, Japan
- RNA Company Limited, Tokyo 144-0051, Japan
| | - Yoshiakira Kanai
- Department of Veterinary Anatomy, the University of Tokyo, Tokyo 113-8657, Japan
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19
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Seese SE, Deml B, Muheisen S, Sorokina E, Semina EV. Genetic disruption of zebrafish mab21l1 reveals a conserved role in eye development and affected pathways. Dev Dyn 2021; 250:1056-1073. [PMID: 33570754 PMCID: PMC8349561 DOI: 10.1002/dvdy.312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The male-abnormal 21 like (MAB21L) genes are important in human ocular development. Homozygous loss of MAB21L1 leads to corneal dystrophy in all affected individuals along with cataracts and buphthalmos in some. The molecular function and downstream pathways of MAB21L factors are largely undefined. RESULTS We generated the first mab21l1 zebrafish mutant carrying a putative loss-of-function allele, c.107delA p.(Lys36Argfs*7). At the final stages of embryonic development, homozygous mab21l1c.107delA fish displayed enlarged anterior chambers and corneal thinning which progressed with age. Additional studies revealed increased cell death in the mutant corneas, transformation of the cornea into a skin-like epithelium, and progressive lens degeneration with development of fibrous masses in the anterior chamber. RNA-seq of wild-type and mutant ocular transcriptomes revealed significant changes in expression of several genes, including irf1a and b, stat1, elf3, krt17, tlr9, and loxa associated with immunity and/or corneal function. Abnormal expression of lysyl oxidases have been previously linked with corneal thinning, fibrosis, and lens defects in mammals, suggesting a role for loxa misexpression in the progressive mab21l1c.107delA eye phenotype. CONCLUSIONS Zebrafish mab21l1 is essential for normal corneal development, similar to human MAB21L1. The identified molecular changes in mab21l1c.107delA mutants provide the first clues about possible affected pathways.
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Affiliation(s)
- Sarah E. Seese
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
- Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Brett Deml
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
- Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, Wisconsin
- PreventionGenetics, Marshfield, Wisconsin
| | - Sanaa Muheisen
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Elena Sorokina
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Elena V. Semina
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
- Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, Wisconsin
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Children's of Wisconsin, Milwaukee, Wisconsin
- Children's Research Institute, Medical College of Wisconsin, Children's of Wisconsin, Milwaukee, Wisconsin
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20
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de Oliveira Mann CC, Hornung V. Molecular mechanisms of nonself nucleic acid recognition by the innate immune system. Eur J Immunol 2021; 51:1897-1910. [PMID: 34138462 DOI: 10.1002/eji.202049116] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/13/2021] [Accepted: 06/15/2021] [Indexed: 12/24/2022]
Abstract
Nucleic acids (NAs) represent one of the most important classes of molecules recognized by the innate immune system. However, NAs are not limited to pathogens, but are also present within the host. As such, the immune system has evolved an elaborate set of pathogen recognition receptors (PRRs) that employ various strategies to recognize distinct types of NAs, while reliably distinguishing between self and nonself. The here-employed strategies encompass the positioning of NA-sensing PRRs in certain subcellular compartments that potentially come in contact with pathogens but not host NAs, the existence of counterregulatory measures that keep endogenous NAs below a certain threshold, and also the specific identification of certain nonself patterns. Here, we review recent advances in the molecular mechanisms of NA recognition by TLRs, RLRs, and the cGAS-STING axis. We highlight the differences in NA-PRR interfaces that confer specificity and selectivity toward an NA ligand, as well as the NA-dependent induced conformational changes required for signal transduction.
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Affiliation(s)
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
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21
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Seese SE, Reis LM, Deml B, Griffith C, Reich A, Jamieson RV, Semina EV. Identification of missense MAB21L1 variants in microphthalmia and aniridia. Hum Mutat 2021; 42:877-890. [PMID: 33973683 PMCID: PMC8238893 DOI: 10.1002/humu.24218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/29/2021] [Accepted: 04/27/2021] [Indexed: 12/14/2022]
Abstract
Microphthalmia, coloboma, and aniridia are congenital ocular phenotypes with a strong genetic component but often unknown cause. We present a likely causative novel variant in MAB21L1, c.152G>T p.(Arg51Leu), in two family members with microphthalmia and aniridia, as well as novel or rare compound heterozygous variants of uncertain significance, c.184C>T p.(Arg62Cys)/c.-68T>C, and c.658G>C p.(Gly220Arg)/c.*529A>G, in two additional probands with microphthalmia, coloboma and/or cataracts. All variants were predicted as damaging by in silico programs. In vitro studies of coding variants revealed normal subcellular localization but variable stability for the corresponding mutant proteins. In vivo complementation assays using the zebrafish mab21l2 Q48Sfs*5 loss-of-function line demonstrated that though overexpression of wild-type MAB21L1 messenger RNA (mRNA) compensated for the loss of mab21l2, none of the coding variant mRNAs produced a statistically significant rescue, with p.(Arg51Leu) showing the highest degree of functional deficiency. Dominant variants in a close homolog of MAB21L1, MAB21L2, have been associated with microphthalmia and/or coloboma and repeatedly involved the same Arg51 residue, further supporting its pathogenicity. The possible role of p.(Arg62Cys) and p.(Gly220Arg) in microphthalmia is similarly supported by the observed functional defects, with or without an additional impact from noncoding MAB21L1 variants identified in each patient. This study suggests a broader spectrum of MAB21L1-associated disease.
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Affiliation(s)
- Sarah E. Seese
- Department of Pediatrics and Children's Research Institute, Medical College of WisconsinChildren's of WisconsinMilwaukeeWIUSA
- Department of Cell Biology, Neurobiology, and AnatomyThe Medical College of WisconsinMilwaukeeWisconsinUSA
| | - Linda M. Reis
- Department of Pediatrics and Children's Research Institute, Medical College of WisconsinChildren's of WisconsinMilwaukeeWIUSA
| | - Brett Deml
- Department of Pediatrics and Children's Research Institute, Medical College of WisconsinChildren's of WisconsinMilwaukeeWIUSA
- Present address:
PreventionGeneticsMarshfieldWisconsinUSA
| | | | | | - Robyn V. Jamieson
- Eye Genetics Research Unit, Sydney Children's Hospitals Network and Children's Medical Research InstituteUniversity of SydneySydneyNew South WalesAustralia
| | - Elena V. Semina
- Department of Pediatrics and Children's Research Institute, Medical College of WisconsinChildren's of WisconsinMilwaukeeWIUSA
- Department of Cell Biology, Neurobiology, and AnatomyThe Medical College of WisconsinMilwaukeeWisconsinUSA
- Department of Ophthalmology and Visual SciencesMedical College of WisconsinMilwaukeeWisconsinUSA
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22
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Ko TP, Wang YC, Tsai CL, Yang CS, Hou MH, Chen Y. Crystal structure and functional implication of a bacterial cyclic AMP-AMP-GMP synthetase. Nucleic Acids Res 2021; 49:4725-4737. [PMID: 33836064 PMCID: PMC8096243 DOI: 10.1093/nar/gkab165] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/24/2021] [Accepted: 04/07/2021] [Indexed: 01/10/2023] Open
Abstract
Mammalian cyclic GMP-AMP synthase (cGAS) and its homologue dinucleotide cyclase in Vibrio cholerae (VcDncV) produce cyclic dinucleotides (CDNs) that participate in the defense against viral infection. Recently, scores of new cGAS/DncV-like nucleotidyltransferases (CD-NTases) were discovered, which produce various CDNs and cyclic trinucleotides (CTNs) as second messengers. Here, we present the crystal structures of EcCdnD, a CD-NTase from Enterobacter cloacae that produces cyclic AMP-AMP-GMP, in its apo-form and in complex with ATP, ADP and AMPcPP, an ATP analogue. Despite the similar overall architecture, the protein shows significant structural variations from other CD-NTases. Adjacent to the donor substrate, another nucleotide is bound to the acceptor binding site by a non-productive mode. Isothermal titration calorimetry results also suggest the presence of two ATP binding sites. GTP alone does not bind to EcCdnD, which however binds to pppApG, a possible intermediate. The enzyme is active on ATP or a mixture of ATP and GTP, and the best metal cofactor is Mg2+. The conserved residues Asp69 and Asp71 are essential for catalysis, as indicated by the loss of activity in the mutants. Based on structural analysis and comparison with VcDncV and RNA polymerase, a tentative catalytic pathway for the CTN-producing EcCdnD is proposed.
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Affiliation(s)
- Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Chuan Wang
- Institute of New Drug Development, China Medical University, Taichung 406, Taiwan
| | - Chia-Ling Tsai
- Institute of New Drug Development, China Medical University, Taichung 406, Taiwan
| | - Chia-Shin Yang
- Institute of New Drug Development, China Medical University, Taichung 406, Taiwan
| | - Mei-Hui Hou
- Institute of New Drug Development, China Medical University, Taichung 406, Taiwan
| | - Yeh Chen
- Institute of New Drug Development, China Medical University, Taichung 406, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 406, Taiwan
- New Drug Development Center, China Medical University, Taichung 406, Taiwan
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23
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Slavik KM, Morehouse BR, Ragucci AE, Zhou W, Ai X, Chen Y, Li L, Wei Z, Bähre H, König M, Seifert R, Lee ASY, Cai H, Imler JL, Kranzusch PJ. cGAS-like receptors sense RNA and control 3'2'-cGAMP signalling in Drosophila. Nature 2021; 597:109-113. [PMID: 34261127 PMCID: PMC8410604 DOI: 10.1038/s41586-021-03743-5] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/21/2021] [Indexed: 02/07/2023]
Abstract
Cyclic GMP-AMP synthase (cGAS) is a cytosolic DNA sensor that produces the second messenger cG[2'-5']pA[3'-5']p (2'3'-cGAMP) and controls activation of innate immunity in mammalian cells1-5. Animal genomes typically encode multiple proteins with predicted homology to cGAS6-10, but the function of these uncharacterized enzymes is unknown. Here we show that cGAS-like receptors (cGLRs) are innate immune sensors that are capable of recognizing divergent molecular patterns and catalysing synthesis of distinct nucleotide second messenger signals. Crystal structures of human and insect cGLRs reveal a nucleotidyltransferase signalling core shared with cGAS and a diversified primary ligand-binding surface modified with notable insertions and deletions. We demonstrate that surface remodelling of cGLRs enables altered ligand specificity and used a forward biochemical screen to identify cGLR1 as a double-stranded RNA sensor in the model organism Drosophila melanogaster. We show that RNA recognition activates Drosophila cGLR1 to synthesize the novel product cG[3'-5']pA[2'-5']p (3'2'-cGAMP). A crystal structure of Drosophila stimulator of interferon genes (dSTING) in complex with 3'2'-cGAMP explains selective isomer recognition, and 3'2'-cGAMP induces an enhanced antiviral state in vivo that protects from viral infection. Similar to radiation of Toll-like receptors in pathogen immunity, our results establish cGLRs as a diverse family of metazoan pattern recognition receptors.
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Affiliation(s)
- Kailey M. Slavik
- grid.38142.3c000000041936754XDepartment of Microbiology, Harvard Medical School, Boston, MA USA ,grid.65499.370000 0001 2106 9910Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Benjamin R. Morehouse
- grid.38142.3c000000041936754XDepartment of Microbiology, Harvard Medical School, Boston, MA USA ,grid.65499.370000 0001 2106 9910Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Adelyn E. Ragucci
- grid.38142.3c000000041936754XDepartment of Microbiology, Harvard Medical School, Boston, MA USA ,grid.65499.370000 0001 2106 9910Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Wen Zhou
- grid.38142.3c000000041936754XDepartment of Microbiology, Harvard Medical School, Boston, MA USA ,grid.65499.370000 0001 2106 9910Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.263817.9Present Address: School of Life Sciences, Southern University of Science and Technology, Guangdong, China
| | - Xianlong Ai
- grid.410737.60000 0000 8653 1072Sino-French Hoffmann Institute, State Key Laboratory of Respiratory Disease, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Yuqiang Chen
- grid.410737.60000 0000 8653 1072Sino-French Hoffmann Institute, State Key Laboratory of Respiratory Disease, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Lihua Li
- grid.410737.60000 0000 8653 1072Sino-French Hoffmann Institute, State Key Laboratory of Respiratory Disease, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Ziming Wei
- grid.410737.60000 0000 8653 1072Sino-French Hoffmann Institute, State Key Laboratory of Respiratory Disease, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Heike Bähre
- grid.10423.340000 0000 9529 9877Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Martin König
- grid.10423.340000 0000 9529 9877Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Roland Seifert
- grid.10423.340000 0000 9529 9877Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany ,grid.10423.340000 0000 9529 9877Hannover Medical School, Institute of Pharmacology, Hannover, Germany
| | - Amy S. Y. Lee
- grid.65499.370000 0001 2106 9910Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Cell Biology, Harvard Medical School, Boston, MA USA
| | - Hua Cai
- grid.410737.60000 0000 8653 1072Sino-French Hoffmann Institute, State Key Laboratory of Respiratory Disease, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Jean-Luc Imler
- grid.410737.60000 0000 8653 1072Sino-French Hoffmann Institute, State Key Laboratory of Respiratory Disease, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China ,grid.11843.3f0000 0001 2157 9291Université de Strasbourg, CNRS UPR9022 Strasbourg, France
| | - Philip J. Kranzusch
- grid.38142.3c000000041936754XDepartment of Microbiology, Harvard Medical School, Boston, MA USA ,grid.65499.370000 0001 2106 9910Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA USA
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24
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Gracilla DE, Korla PK, Lai MT, Chiang AJ, Liou WS, Sheu JJC. Overexpression of wild type or a Q311E mutant MB21D2 promotes a pro-oncogenic phenotype in HNSCC. Mol Oncol 2020; 14:3065-3082. [PMID: 32979859 PMCID: PMC7718949 DOI: 10.1002/1878-0261.12806] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/14/2020] [Accepted: 08/04/2020] [Indexed: 02/06/2023] Open
Abstract
Cadherin‐mediated cell–cell contacts regulated by intracellular binders play critical roles in tissue homeostasis and tumorigenesis. Here, we screened mutational profiles of 312 annotated genes involved in cadherin binding in human squamous cell carcinomas and found MB21D2 to carry a unique recurrent Q311E mutation. MB21D2 overexpression was also frequently found in head and neck cancer (HNSCC) and was associated with poor clinical outcomes. Cell‐based characterizations revealed pro‐oncogenic roles for MB21D2 wild‐type (WT) and its Q311E mutant (Q311E) in cell proliferation, colony formation, sphere growth, and migration/invasion by promoting epithelial–mesenchymal transition. Conversely, MB21D2 knockdown in MB21D2‐overexpressing cells resulted in cell growth arrest and apoptosis. Xenograft tumor models with Q311E‐expressing cells formed larger and more aggressive lesions, compared to models with WT‐MB21D2‐expressing cells or an empty vector. Transcriptome and protein interactome analyses revealed enrichment of KRAS signaling by MB21D2 expression. Immunoblotting confirmed RAS elevation, along with upregulation/phosphorylation of PI3K, AKT, and CREB. Blocking RAS signaling in MB21D2‐expressing cells by manumycin significantly reduced cell growth and survival. Our study thus defined RAS signaling‐dependent pro‐oncogenic roles for MB21D2 overexpression and Q311E MB21D2 expression in HNSCC development.
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Affiliation(s)
- Daniel E Gracilla
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Praveen Kumar Korla
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Ming-Tsung Lai
- Department of Pathology, Taichung Hospital, Ministry of Health and Welfare, Taichung, Taiwan
| | - An-Jen Chiang
- Department of Obstetrics and Gynecology, Kaohsiung Veterans General Hospital, Taiwan
| | - Wen-Shiung Liou
- Department of Obstetrics and Gynecology, Kaohsiung Veterans General Hospital, Taiwan
| | - Jim Jinn-Chyuan Sheu
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan.,Department of Health and Nutrition Biotechnology, Asia University, Taichung, Taiwan.,School of Chinese Medicine, China Medical University, Taichung, Taiwan.,Department of Biotechnology, Kaohsiung Medical University, Taiwan
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25
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Boyer JA, Spangler CJ, Strauss JD, Cesmat AP, Liu P, McGinty RK, Zhang Q. Structural basis of nucleosome-dependent cGAS inhibition. Science 2020; 370:450-454. [PMID: 32913000 DOI: 10.1126/science.abd0609] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022]
Abstract
Cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) synthase (cGAS) recognizes cytosolic foreign or damaged DNA to activate the innate immune response to infection, inflammatory diseases, and cancer. By contrast, cGAS reactivity against self-DNA in the nucleus is suppressed by chromatin tethering. We report a 3.3-angstrom-resolution cryo-electron microscopy structure of cGAS in complex with the nucleosome core particle. The structure reveals that cGAS uses two conserved arginines to anchor to the nucleosome acidic patch. The nucleosome-binding interface exclusively occupies the strong double-stranded DNA (dsDNA)-binding surface on cGAS and sterically prevents cGAS from oligomerizing into the functionally active 2:2 cGAS-dsDNA state. These findings provide a structural basis for how cGAS maintains an inhibited state in the nucleus and further exemplify the role of the nucleosome in regulating diverse nuclear protein functions.
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Affiliation(s)
- Joshua A Boyer
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cathy J Spangler
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joshua D Strauss
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew P Cesmat
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Pengda Liu
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Robert K McGinty
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qi Zhang
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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26
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Cheng LC, Baboo S, Lindsay C, Brusman L, Martinez-Bartolomé S, Tapia O, Zhang X, Yates JR, Gerace L. Identification of new transmembrane proteins concentrated at the nuclear envelope using organellar proteomics of mesenchymal cells. Nucleus 2020; 10:126-143. [PMID: 31142202 PMCID: PMC6550788 DOI: 10.1080/19491034.2019.1618175] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The double membrane nuclear envelope (NE), which is contiguous with the ER, contains nuclear pore complexes (NPCs) – the channels for nucleocytoplasmic transport, and the nuclear lamina (NL) – a scaffold for NE and chromatin organization. Since numerous human diseases linked to NE proteins occur in mesenchyme-derived cells, we used proteomics to characterize NE and other subcellular fractions isolated from mesenchymal stem cells and from adipocytes and myocytes. Based on spectral abundance, we calculated enrichment scores for proteins in the NE fractions. We demonstrated by quantitative immunofluorescence microscopy that five little-characterized proteins with high enrichment scores are substantially concentrated at the NE, with Itprip exposed at the outer nuclear membrane, Smpd4 enriched at the NPC, and Mfsd10, Tmx4, and Arl6ip6 likely residing in the inner nuclear membrane. These proteins provide new focal points for studying the functions of the NE. Moreover, our datasets provide a resource for evaluating additional potential NE proteins.
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Affiliation(s)
- Li-Chun Cheng
- a Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | - Sabyasachi Baboo
- a Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | - Cory Lindsay
- a Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | - Liza Brusman
- a Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | | | - Olga Tapia
- a Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | - Xi Zhang
- a Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | - John R Yates
- a Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | - Larry Gerace
- a Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
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27
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Liu Z, Ji J, Jiang X, Shao T, Fan D, Jiang X, Lin A, Xiang L, Shao J. Characterization of cGAS homologs in innate and adaptive mucosal immunities in zebrafish gives evolutionary insights into cGAS‐STING pathway. FASEB J 2020; 34:7786-7809. [DOI: 10.1096/fj.201902833r] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 03/17/2020] [Accepted: 03/25/2020] [Indexed: 01/26/2023]
Affiliation(s)
- Zhi‐fei Liu
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province College of Life Sciences Zhejiang University Hangzhou People's Republic of China
| | - Jian‐fei Ji
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province College of Life Sciences Zhejiang University Hangzhou People's Republic of China
| | - Xiao‐feng Jiang
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province College of Life Sciences Zhejiang University Hangzhou People's Republic of China
| | - Tong Shao
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province College of Life Sciences Zhejiang University Hangzhou People's Republic of China
| | - Dong‐dong Fan
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province College of Life Sciences Zhejiang University Hangzhou People's Republic of China
| | - Xin‐hang Jiang
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province College of Life Sciences Zhejiang University Hangzhou People's Republic of China
| | - Ai‐fu Lin
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province College of Life Sciences Zhejiang University Hangzhou People's Republic of China
| | - Li‐xin Xiang
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province College of Life Sciences Zhejiang University Hangzhou People's Republic of China
| | - Jian‐zhong Shao
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province College of Life Sciences Zhejiang University Hangzhou People's Republic of China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao People's Republic of China
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Kranzusch PJ. cGAS and CD-NTase enzymes: structure, mechanism, and evolution. Curr Opin Struct Biol 2019; 59:178-187. [PMID: 31593902 PMCID: PMC7127440 DOI: 10.1016/j.sbi.2019.08.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 07/25/2019] [Accepted: 08/25/2019] [Indexed: 01/22/2023]
Abstract
Cyclic GMP-AMP synthase (cGAS) is a signaling enzyme in human cells that controls immune-sensing of cytosolic DNA. The recent discoveries of diverse structural homologs of cGAS in animals and bacteria reveal that cGAS-like signaling is surprisingly ancient and widespread in biology. Together with the Vibrio cholerae protein dinucleotide cyclase in Vibrio (DncV), cGAS and DncV homologs comprise a family of cGAS/DncV-like nucleotidyltransferase (CD-NTase) enzymes that synthesize noncanonical RNA signals including cyclic dinucleotides, cyclic trinucleotides, and linear oligonucleotides. Structural and biochemical breakthroughs provide a framework to understand how CD-NTase signaling allows cells to respond to changing environmental conditions. The CD-NTase family also includes uncharacterized human genes like MB21D2 and Mab21L1, highlighting emerging functions of cGAS-like signaling beyond innate immunity.
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Affiliation(s)
- Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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29
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Zhou Y, Lu LF, Lu XB, Li S, Zhang YA. Grass carp cGASL negatively regulates fish IFN response by targeting MITA. FISH & SHELLFISH IMMUNOLOGY 2019; 94:871-879. [PMID: 31597087 DOI: 10.1016/j.fsi.2019.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/30/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
Mammalian cyclic GMP-AMP synthase (cGAS) senses double-stranded (ds) DNA in the cytosol to activate the innate antiviral response. In the present study, a cGAS-like gene, namely cGASL, was cloned from grass carp Ctenopharyngodon idellus, and its role as a negative regulator of the IFN response was revealed. Phylogenetic analysis indicated that cGASL was evolutionarily closest to cGAS, but was not a true ortholog of cGAS. Overexpression of cGASL inhibited poly I:C-stimulated grass carp (gc)IFN1pro and ISRE activities. In addition, MITA-, but not TBK1-mediated activation of gcIFN1pro was impaired by cGASL. Co-immunoprecipitation and Western blot experiments indicated that cGASL interacted with MITA and TBK1, resulting in a reduction in the phosphorylation of MITA. Lastly, overexpression of cGASL reduced the transcriptional levels of several IFN-stimulated genes activated by MITA. Collectively, these data suggest that cGASL is a negative regulator of IFN response by targeting MITA in fish.
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Affiliation(s)
- Yu Zhou
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Long-Feng Lu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiao-Bing Lu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Shun Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
| | - Yong-An Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; State Key Laboratory of Agricultural Microbiology, College of Fisheries, Huazhong Agricultural University, Wuhan, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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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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31
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Genetics of anophthalmia and microphthalmia. Part 1: Non-syndromic anophthalmia/microphthalmia. Hum Genet 2019; 138:799-830. [PMID: 30762128 DOI: 10.1007/s00439-019-01977-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/30/2019] [Indexed: 12/22/2022]
Abstract
Eye formation is the result of coordinated induction and differentiation processes during embryogenesis. Disruption of any one of these events has the potential to cause ocular growth and structural defects, such as anophthalmia and microphthalmia (A/M). A/M can be isolated or occur with systemic anomalies, when they may form part of a recognizable syndrome. Their etiology includes genetic and environmental factors; several hundred genes involved in ocular development have been identified in humans or animal models. In humans, around 30 genes have been repeatedly implicated in A/M families, although many other genes have been described in single cases or families, and some genetic syndromes include eye anomalies occasionally as part of a wider phenotype. As a result of this broad genetic heterogeneity, with one or two notable exceptions, each gene explains only a small percentage of cases. Given the overlapping phenotypes, these genes can be most efficiently tested on panels or by whole exome/genome sequencing for the purposes of molecular diagnosis. However, despite whole exome/genome testing more than half of patients currently remain without a molecular diagnosis. The proportion of undiagnosed cases is even higher in those individuals with unilateral or milder phenotypes. Furthermore, even when a strong gene candidate is available for a patient, issues of incomplete penetrance and germinal mosaicism make diagnosis and genetic counseling challenging. In this review, we present the main genes implicated in non-syndromic human A/M phenotypes and, for practical purposes, classify them according to the most frequent or predominant phenotype each is associated with. Our intention is that this will allow clinicians to rank and prioritize their molecular analyses and interpretations according to the phenotypes of their patients.
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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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Rad A, Altunoglu U, Miller R, Maroofian R, James KN, Çağlayan AO, Najafi M, Stanley V, Boustany RM, Yeşil G, Sahebzamani A, Ercan-Sencicek G, Saeidi K, Wu K, Bauer P, Bakey Z, Gleeson JG, Hauser N, Gunel M, Kayserili H, Schmidts M. MAB21L1 loss of function causes a syndromic neurodevelopmental disorder with distinctive cerebellar, ocular, cranio facial and genital features (COFG syndrome). J Med Genet 2018; 56:332-339. [PMID: 30487245 PMCID: PMC6581149 DOI: 10.1136/jmedgenet-2018-105623] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/29/2018] [Accepted: 11/13/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Putative nucleotidyltransferase MAB21L1 is a member of an evolutionarily well-conserved family of the male abnormal 21 (MAB21)-like proteins. Little is known about the biochemical function of the protein; however, prior studies have shown essential roles for several aspects of embryonic development including the eye, midbrain, neural tube and reproductive organs. OBJECTIVE A homozygous truncating variant in MAB21L1 has recently been described in a male affected by intellectual disability, scrotal agenesis, ophthalmological anomalies, cerebellar hypoplasia and facial dysmorphism. We employed a combination of exome sequencing and homozygosity mapping to identify the underlying genetic cause in subjects with similar phenotypic features descending from five unrelated consanguineous families. RESULTS We identified four homozygous MAB21L1 loss of function variants (p.Glu281fs*20, p.Arg287Glufs*14 p.Tyr280* and p.Ser93Serfs*48) and one missense variant (p.Gln233Pro) in 10 affected individuals from 5 consanguineous families with a distinctive autosomal recessive neurodevelopmental syndrome. Cardinal features of this syndrome include a characteristic facial gestalt, corneal dystrophy, hairy nipples, underdeveloped labioscrotal folds and scrotum/scrotal agenesis as well as cerebellar hypoplasia with ataxia and variable microcephaly. CONCLUSION This report defines an ultrarare but clinically recognisable Cerebello-Oculo-Facio-Genital syndrome associated with recessive MAB21L1 variants. Additionally, our findings further support the critical role of MAB21L1 in cerebellum, lens, genitalia and as craniofacial morphogenesis.
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Affiliation(s)
- Abolfazl Rad
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, The Netherlands.,Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Umut Altunoglu
- Medical Genetics Department, İstanbul Medical Faculty, İstanbul University, Istanbul, Turkey
| | - Rebecca Miller
- Inova Cardiovascular Genomics Clinic, Inova Translational Medicine Institute, Falls Church, Virginia, USA
| | - Reza Maroofian
- Genetics and Molecular Cell Sciences Research Centre, St George's, University of London, London, UK
| | - Kiely N James
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, Rady Children's Institute for Genomic Medicine, University of California, San Diego, California, USA
| | - Ahmet Okay Çağlayan
- Department of Neurosurgery, Program on Neurogenetics, Yale School of Medicine, Yale University, New Haven, Connecticut, USA.,Medical Genetics Department, Bilim University School of Medicine, İstanbul, Turkey
| | - Maryam Najafi
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Valentina Stanley
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, Rady Children's Institute for Genomic Medicine, University of California, San Diego, California, USA
| | - Rose-Mary Boustany
- Department of Pediatrics and Adolescent Medicine, Neurogenetics Program and Division of Pediatric Neurology, American University of Beirut Medical Center Special Kids Clinic, Beirut, Lebanon.,Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Gözde Yeşil
- Medical Genetics Department, Bezmi Alem University School of Medicine, Istanbul, Turkey
| | - Afsaneh Sahebzamani
- Paediatric and Genetic Counselling Center, Kerman Welfare Organization, Kerman, Iran
| | - Gülhan Ercan-Sencicek
- Department of Neurosurgery, Program on Neurogenetics, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Kolsoum Saeidi
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran.,Department of Medical Genetics, Kerman University of Medical Sciences, Kerman, Iran
| | - Kaman Wu
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Zeineb Bakey
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, The Netherlands.,Pediatrics Genetics Division, Center for Pediatrics and Adolescent Medicine, Faculty of Medicine, Freiburg University, Freiburg, Germany
| | - Joseph G Gleeson
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, Rady Children's Institute for Genomic Medicine, University of California, San Diego, California, USA
| | - Natalie Hauser
- Inova Cardiovascular Genomics Clinic, Inova Translational Medicine Institute, Falls Church, Virginia, USA
| | - Murat Gunel
- Department of Neurosurgery, Program on Neurogenetics, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Hulya Kayserili
- Medical Genetics Department, İstanbul Medical Faculty, İstanbul University, Istanbul, Turkey.,Medical Genetics Department, Koç University School of Medicine (KUSoM), İstanbul, Turkey
| | - Miriam Schmidts
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, The Netherlands.,Pediatrics Genetics Division, Center for Pediatrics and Adolescent Medicine, Faculty of Medicine, Freiburg University, Freiburg, Germany
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Margolis SR, Wilson SC, Vance RE. Evolutionary Origins of cGAS-STING Signaling. Trends Immunol 2017; 38:733-743. [DOI: 10.1016/j.it.2017.03.004] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/19/2017] [Accepted: 03/20/2017] [Indexed: 12/25/2022]
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35
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Cvekl A, Zhang X. Signaling and Gene Regulatory Networks in Mammalian Lens Development. Trends Genet 2017; 33:677-702. [PMID: 28867048 DOI: 10.1016/j.tig.2017.08.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/27/2017] [Accepted: 08/01/2017] [Indexed: 11/16/2022]
Abstract
Ocular lens development represents an advantageous system in which to study regulatory mechanisms governing cell fate decisions, extracellular signaling, cell and tissue organization, and the underlying gene regulatory networks. Spatiotemporally regulated domains of BMP, FGF, and other signaling molecules in late gastrula-early neurula stage embryos generate the border region between the neural plate and non-neural ectoderm from which multiple cell types, including lens progenitor cells, emerge and undergo initial tissue formation. Extracellular signaling and DNA-binding transcription factors govern lens and optic cup morphogenesis. Pax6, c-Maf, Hsf4, Prox1, Sox1, and a few additional factors regulate the expression of the lens structural proteins, the crystallins. Extensive crosstalk between a diverse array of signaling pathways controls the complexity and order of lens morphogenetic processes and lens transparency.
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Affiliation(s)
- Ales Cvekl
- Departments of Genetics and Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Xin Zhang
- Departments of Ophthalmology, Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA.
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