1
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Fuller RN, Morcos A, Bustillos JG, Molina DC, Wall NR. Small non-coding RNAs and pancreatic ductal adenocarcinoma: Linking diagnosis, pathogenesis, drug resistance, and therapeutic potential. Biochim Biophys Acta Rev Cancer 2024; 1879:189153. [PMID: 38986720 DOI: 10.1016/j.bbcan.2024.189153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
This review comprehensively investigates the intricate interplay between small non-coding RNAs (sncRNAs) and pancreatic ductal adenocarcinoma (PDAC), a devastating malignancy with limited therapeutic options. Our analysis reveals the pivotal roles of sncRNAs in various facets of PDAC biology, spanning diagnosis, pathogenesis, drug resistance, and therapeutic strategies. sncRNAs have emerged as promising biomarkers for PDAC, demonstrating distinct expression profiles in diseased tissues. sncRNA differential expression patterns, often detectable in bodily fluids, hold potential for early and minimally invasive diagnostic approaches. Furthermore, sncRNAs exhibit intricate involvement in PDAC pathogenesis, regulating critical cellular processes such as proliferation, apoptosis, and metastasis. Additionally, mechanistic insights into sncRNA-mediated pathogenic pathways illuminate novel therapeutic targets and interventions. A significant focus of this review is dedicated to unraveling sncRNA mechanisms underlying drug resistance in PDAC. Understanding these mechanisms at the molecular level is imperative for devising strategies to overcome drug resistance. Exploring the therapeutic landscape, we discuss the potential of sncRNAs as therapeutic agents themselves as their ability to modulate gene expression with high specificity renders them attractive candidates for targeted therapy. In summary, this review integrates current knowledge on sncRNAs in PDAC, offering a holistic perspective on their diagnostic, pathogenic, and therapeutic relevance. By elucidating the roles of sncRNAs in PDAC biology, this review provides valuable insights for the development of novel diagnostic tools and targeted therapeutic approaches, crucial for improving the prognosis of PDAC patients.
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Affiliation(s)
- Ryan N Fuller
- Department of Basic Science, Division of Biochemistry, Center for Health Disparity and Mol. Med., Loma Linda University, Loma Linda, CA 92350, USA; Department of Radiation Medicine, James M. Slater, MD Proton Treatment and Research Center, Loma Linda University, Loma Linda, CA 92350, USA
| | - Ann Morcos
- Department of Basic Science, Division of Biochemistry, Center for Health Disparity and Mol. Med., Loma Linda University, Loma Linda, CA 92350, USA; Department of Radiation Medicine, James M. Slater, MD Proton Treatment and Research Center, Loma Linda University, Loma Linda, CA 92350, USA
| | - Joab Galvan Bustillos
- Department of Basic Science, Division of Biochemistry, Center for Health Disparity and Mol. Med., Loma Linda University, Loma Linda, CA 92350, USA; Division of Surgical Oncology, Department of Surgery, Loma Linda University, Loma Linda, CA 92350, USA
| | - David Caba Molina
- Division of Surgical Oncology, Department of Surgery, Loma Linda University, Loma Linda, CA 92350, USA
| | - Nathan R Wall
- Department of Basic Science, Division of Biochemistry, Center for Health Disparity and Mol. Med., Loma Linda University, Loma Linda, CA 92350, USA; Department of Radiation Medicine, James M. Slater, MD Proton Treatment and Research Center, Loma Linda University, Loma Linda, CA 92350, USA.
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2
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Politano D, Catalano G, Pezzotti E, Varesio C, Sirchia F, Casella A, Rognone E, Pichiecchio A, Borgatti R, Orcesi S. Expanding the Natural History of SNORD118-Related Ribosomopathy: Hints from an Early-Diagnosed Patient with Leukoencephalopathy with Calcifications and Cysts and Overview of the Literature. Genes (Basel) 2023; 14:1817. [PMID: 37761957 PMCID: PMC10531261 DOI: 10.3390/genes14091817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Leukoencephalopathy with calcifications and cysts (LCC) is a rare autosomal recessive disorder showing a pediatric or adult onset. First described in 1996 by Labrune and colleagues, it was only in 2016 that bi-allelic variants in a non-protein coding gene, SNORD118, were found as the cause for LCC, differentiating this syndrome from coats plus (CP). SNORD118 transcribes for a small nucleolar RNA, which is necessary for correct ribosome biogenesis, hence the classification of LCC among ribosomopathies. The syndrome is characterized by a combination of white matter hyperintensities, calcifications, and cysts on brain MRI with varying neurological signs. Corticosteroids, surgery, and recently bevacizumab, have been tried with unclear results since the natural history of the disease remains elusive. To date, 67 patients with a pediatric onset of disease have been described in the literature, with a clinical-radiological follow-up carried out in only eleven of them. We described the clinical-radiological follow-up from birth to almost five years of age of a late-preterm patient diagnosed with LCC and carried out a thorough overview of pediatric patients described in the literature. It is important to gather serial clinical-radiological data from other patients to depict the natural history of this disease, aiming to deeply depict genotype-phenotype correlations and make the role of new therapeutics clearer.
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Affiliation(s)
- Davide Politano
- Department of Brain and Behavior Neuroscience, University of Pavia, 27100 Pavia, Italy
- Child Neurology and Psychiatry Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Guido Catalano
- Department of Brain and Behavior Neuroscience, University of Pavia, 27100 Pavia, Italy
- Child Neurology and Psychiatry Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Elena Pezzotti
- Department of Brain and Behavior Neuroscience, University of Pavia, 27100 Pavia, Italy
- U.O. Neuropsichiatria Infanzia e Adolescenza, ASST Bergamo Est, 24068 Seriate, Italy
| | - Costanza Varesio
- Department of Brain and Behavior Neuroscience, University of Pavia, 27100 Pavia, Italy
- Child Neurology and Psychiatry Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Fabio Sirchia
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Medical Genetics Unit, IRCCS San Matteo Foundation, 27100 Pavia, Italy
| | - Antonella Casella
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Neurogenetics Research Center, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Elisa Rognone
- Neuroradiology Department, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Anna Pichiecchio
- Department of Brain and Behavior Neuroscience, University of Pavia, 27100 Pavia, Italy
- Neuroradiology Department, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Renato Borgatti
- Department of Brain and Behavior Neuroscience, University of Pavia, 27100 Pavia, Italy
- Child Neurology and Psychiatry Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Simona Orcesi
- Department of Brain and Behavior Neuroscience, University of Pavia, 27100 Pavia, Italy
- Child Neurology and Psychiatry Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
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3
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Lafontaine DLJ. In phase with the nucleolus. Cell Res 2023; 33:579-580. [PMID: 37055593 PMCID: PMC10397221 DOI: 10.1038/s41422-023-00801-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023] Open
Affiliation(s)
- Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark Campus, B-6041, Gosselies, Belgium.
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4
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Withers SE, Rowlands CF, Tapia VS, Hedley F, Mosneag IE, Crilly S, Rice GI, Badrock AP, Hayes A, Allan SM, Briggs TA, Kasher PR. Characterization of a mutant samhd1 zebrafish model implicates dysregulation of cholesterol biosynthesis in Aicardi-Goutières syndrome. Front Immunol 2023; 14:1100967. [PMID: 36949945 PMCID: PMC10025490 DOI: 10.3389/fimmu.2023.1100967] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
Aicardi-Goutières syndrome (AGS1-9) is a genetically determined encephalopathy that falls under the type I interferonopathy disease class, characterized by excessive type I interferon (IFN-I) activity, coupled with upregulation of IFN-stimulated genes (ISGs), which can be explained by the vital role these proteins play in self-non-self-discrimination. To date, few mouse models fully replicate the vast clinical phenotypes observed in AGS patients. Therefore, we investigated the use of zebrafish as an alternative species for generating a clinically relevant model of AGS. Using CRISPR-cas9 technology, we generated a stable mutant zebrafish line recapitulating AGS5, which arises from recessive mutations in SAMHD1. The resulting homozygous mutant zebrafish larvae possess a number of neurological phenotypes, exemplified by variable, but increased expression of several ISGs in the head region, a significant increase in brain cell death, microcephaly and locomotion deficits. A link between IFN-I signaling and cholesterol biosynthesis has been highlighted by others, but not previously implicated in the type I interferonopathies. Through assessment of neurovascular integrity and qPCR analysis we identified a significant dysregulation of cholesterol biosynthesis in the zebrafish model. Furthermore, dysregulation of cholesterol biosynthesis gene expression was also observed through RNA sequencing analysis of AGS patient whole blood. From this novel finding, we hypothesize that cholesterol dysregulation may play a role in AGS disease pathophysiology. Further experimentation will lend critical insight into the molecular pathophysiology of AGS and the potential links involving aberrant type I IFN signaling and cholesterol dysregulation.
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Affiliation(s)
- Sarah E. Withers
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
- Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance National Health Service (NHS) Foundation Trust, The University of Manchester, Manchester, United Kingdom
| | - Charlie F. Rowlands
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University National Health Service (NHS) Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Victor S. Tapia
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
- Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance National Health Service (NHS) Foundation Trust, The University of Manchester, Manchester, United Kingdom
| | - Frances Hedley
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
- Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance National Health Service (NHS) Foundation Trust, The University of Manchester, Manchester, United Kingdom
| | - Ioana-Emilia Mosneag
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
- Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance National Health Service (NHS) Foundation Trust, The University of Manchester, Manchester, United Kingdom
| | - Siobhan Crilly
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
- Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance National Health Service (NHS) Foundation Trust, The University of Manchester, Manchester, United Kingdom
| | - Gillian I. Rice
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University National Health Service (NHS) Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Andrew P. Badrock
- Medical Research Council (MRC) Human Genetics Unit, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew Hayes
- Genomic Technologies Core Facility, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Stuart M. Allan
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
- Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance National Health Service (NHS) Foundation Trust, The University of Manchester, Manchester, United Kingdom
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Tracy A. Briggs
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University National Health Service (NHS) Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Paul R. Kasher
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
- Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance National Health Service (NHS) Foundation Trust, The University of Manchester, Manchester, United Kingdom
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
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5
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Shan L, Xu G, Yao RW, Luan PF, Huang Y, Zhang PH, Pan YH, Zhang L, Gao X, Li Y, Cao SM, Gao SX, Yang ZH, Li S, Yang LZ, Wang Y, Wong CCL, Yu L, Li J, Yang L, Chen LL. Nucleolar URB1 ensures 3' ETS rRNA removal to prevent exosome surveillance. Nature 2023; 615:526-534. [PMID: 36890225 DOI: 10.1038/s41586-023-05767-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 01/27/2023] [Indexed: 03/10/2023]
Abstract
The nucleolus is the most prominent membraneless condensate in the nucleus. It comprises hundreds of proteins with distinct roles in the rapid transcription of ribosomal RNA (rRNA) and efficient processing within units comprising a fibrillar centre and a dense fibrillar component and ribosome assembly in a granular component1. The precise localization of most nucleolar proteins and whether their specific localization contributes to the radial flux of pre-rRNA processing have remained unknown owing to insufficient resolution in imaging studies2-5. Therefore, how these nucleolar proteins are functionally coordinated with stepwise pre-rRNA processing requires further investigation. Here we screened 200 candidate nucleolar proteins using high-resolution live-cell microscopy and identified 12 proteins that are enriched towards the periphery of the dense fibrillar component (PDFC). Among these proteins, unhealthy ribosome biogenesis 1 (URB1) is a static, nucleolar protein that ensures 3' end pre-rRNA anchoring and folding for U8 small nucleolar RNA recognition and the subsequent removal of the 3' external transcribed spacer (ETS) at the dense fibrillar component-PDFC boundary. URB1 depletion leads to a disrupted PDFC, uncontrolled pre-rRNA movement, altered pre-rRNA conformation and retention of the 3' ETS. These aberrant 3' ETS-attached pre-rRNA intermediates activate exosome-dependent nucleolar surveillance, resulting in decreased 28S rRNA production, head malformations in zebrafish and delayed embryonic development in mice. This study provides insight into functional sub-nucleolar organization and identifies a physiologically essential step in rRNA maturation that requires the static protein URB1 in the phase-separated nucleolus.
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Affiliation(s)
- Lin Shan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guang Xu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Run-Wen Yao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Peng-Fei Luan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Youkui Huang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Pei-Hong Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Hang Pan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lin Zhang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiang Gao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ying Li
- Cryo EM facility, Technology Center for Protein Sciences, School of Life Science, Tsinghua University, Beijing, China
| | - Shi-Meng Cao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shuai-Xin Gao
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing, China
| | - Zheng-Hu Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Siqi Li
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Liang-Zhong Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ying Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Catharine C L Wong
- Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
- New Cornerstone Science Laboratory, Shenzhen, China.
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6
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Waack A, Norris J, Becker K, Hoyt A, Schroeder J. Leukoencephalopathy, calcifications, and cysts: Labrune syndrome. Radiol Case Rep 2023; 18:584-590. [PMCID: PMC9703455 DOI: 10.1016/j.radcr.2022.11.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/29/2022] Open
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7
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Thalalla Gamage S, Bortolin-Cavaillé ML, Link C, Bryson K, Sas-Chen A, Schwartz S, Cavaillé J, Meier JL. Antisense pairing and SNORD13 structure guide RNA cytidine acetylation. RNA (NEW YORK, N.Y.) 2022; 28:1582-1596. [PMID: 36127124 PMCID: PMC9670809 DOI: 10.1261/rna.079254.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/02/2022] [Indexed: 05/21/2023]
Abstract
N4-acetylcytidine (ac4C) is an RNA nucleobase found in all domains of life. The establishment of ac4C in helix 45 (h45) of human 18S ribosomal RNA (rRNA) requires the combined activity of the acetyltransferase NAT10 and the box C/D snoRNA SNORD13. However, the molecular mechanisms governing RNA-guided nucleobase acetylation in humans remain unexplored. After applying comparative sequence analysis and site-directed mutagenesis to provide evidence that SNORD13 folds into three main RNA helices, we report two assays that enable the study of SNORD13-dependent RNA acetylation in human cells. First, we demonstrate that ectopic expression of SNORD13 rescues h45 in a SNORD13 knockout cell line. Next, we show that mutant snoRNAs can be used in combination with nucleotide resolution ac4C sequencing to define structure and sequence elements critical for SNORD13 function. Finally, we develop a second method that reports on the substrate specificity of endogenous NAT10-SNORD13 via mutational analysis of an ectopically expressed pre-rRNA substrate. By combining mutational analysis of these reconstituted systems with nucleotide resolution ac4C sequencing, our studies reveal plasticity in the molecular determinants underlying RNA-guided cytidine acetylation that is distinct from deposition of other well-studied rRNA modifications (e.g., pseudouridine). Overall, our studies provide a new approach to reconstitute RNA-guided cytidine acetylation in human cells as well as nucleotide resolution insights into the mechanisms governing this process.
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Affiliation(s)
| | - Marie-Line Bortolin-Cavaillé
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse III; UPS; CNRS; 31062 Cedex 9, Toulouse, France
| | - Courtney Link
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Keri Bryson
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Aldema Sas-Chen
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 6195001 Tel Aviv, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Jérôme Cavaillé
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse III; UPS; CNRS; 31062 Cedex 9, Toulouse, France
| | - Jordan L Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA
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8
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Gabryelska MM, Badrock AP, Lau JY, O'Keefe RT, Crow YJ, Kudla G. Global mapping of RNA homodimers in living cells. Genome Res 2022; 32:956-967. [PMID: 35332098 PMCID: PMC9104694 DOI: 10.1101/gr.275900.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 03/18/2022] [Indexed: 11/25/2022]
Abstract
RNA homodimerization is important for various physiological processes, including the assembly of membraneless organelles, RNA subcellular localization, and packaging of viral genomes. However, understanding RNA dimerization has been hampered by the lack of systematic in vivo detection methods. Here, we show that CLASH, PARIS, and other RNA proximity ligation methods detect RNA homodimers transcriptome-wide as "overlapping" chimeric reads that contain more than one copy of the same sequence. Analyzing published proximity ligation data sets, we show that RNA:RNA homodimers mediated by direct base-pairing are rare across the human transcriptome, but highly enriched in specific transcripts, including U8 snoRNA, U2 snRNA, and a subset of tRNAs. Mutations in the homodimerization domain of U8 snoRNA impede dimerization in vitro and disrupt zebrafish development in vivo, suggesting an evolutionarily conserved role of this domain. Analysis of virus-infected cells reveals homodimerization of SARS-CoV-2 and Zika genomes, mediated by specific palindromic sequences located within protein-coding regions of N gene in SARS-CoV-2 and NS2A gene in Zika. We speculate that regions of viral genomes involved in homodimerization may constitute effective targets for antiviral therapies.
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Affiliation(s)
- Marta M. Gabryelska
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom;,Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Andrew P. Badrock
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Jian You Lau
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Raymond T. O'Keefe
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, M13 9PL, United Kingdom
| | - Yanick J. Crow
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Grzegorz Kudla
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
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9
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Abstract
Small nucleolar RNAs (snoRNAs) are non-coding RNAs vital for ribosomal RNA (rRNA) maturation. The U8 snoRNA, encoded by the SNORD118 gene in humans, is an atypical C/D box snoRNA as it promotes rRNA cleavage rather than 2′–O–methylation and is unique to vertebrates. The U8 snoRNA is critical for cleavage events that produce the mature 5.8S and 28S rRNAs of the large ribosomal subunit. Unexpectedly, single nucleotide polymorphisms (SNPs) in the SNORD118 gene were recently found causal to the neurodegenerative disease leukoencephalopathy, brain calcifications, and cysts (LCC; aka Labrune syndrome), but its molecular pathogenesis is unclear. Here, we will review current knowledge on the function of the U8 snoRNA in ribosome biogenesis, and connect it to the preservation of brain function in humans as well as to its dysregulation in inherited white matter disease.
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Affiliation(s)
- Emily J McFadden
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Susan J Baserga
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
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10
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Paff M, Samuel N, Alsafwani N, Paul D, Diamandis P, Climans SA, Kucharczyk W, Ding MYR, Gao AF, Lozano AM. Leukoencephalopathy with brain calcifications and cysts (Labrune syndrome) case report: diagnosis and management of a rare neurological disease. BMC Neurol 2022; 22:10. [PMID: 34986804 PMCID: PMC8729138 DOI: 10.1186/s12883-021-02531-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/21/2021] [Indexed: 12/05/2022] Open
Abstract
Background Leukoencephalopathy with brain calcifications and cysts (LCC; also known as Labrune syndrome) is a rare genetic microangiopathy caused by biallelic mutations in SNORD118. The mechanisms by which loss-of-function mutations in SNORD118 lead to the phenotype of leukoencephalopathy, calcifications and intracranial cysts is unknown. Case presentation We present the histopathology of a 36-year-old woman with ataxia and neuroimaging findings of diffuse white matter abnormalities, cerebral calcifications, and parenchymal cysts, in whom the diagnosis of LCC was confirmed with genetic testing. Biopsy of frontal white matter revealed microangiopathy with small vessel occlusion and sclerosis associated with axonal loss within the white matter. Conclusions These findings support that the white matter changes seen in LCC arise as a consequence of ischemia rather than demyelination.
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Affiliation(s)
- Michelle Paff
- Department of Neurological Surgery, University of California Irvine, Irvine, CA, USA
| | - Nardin Samuel
- Division of Neurosurgery, Department of Surgery, University Health Network, Toronto, ON, USA.
| | - Noor Alsafwani
- Laboratory Medicine Program, University Health Network, Toronto, ON, USA.,Department of Pathology, College of Medicine, Imam Abdulrahman Bin Faisal University (IAU), Dammam, Saudi Arabia
| | - Darcia Paul
- Division of Neurosurgery, Department of Surgery, University Health Network, Toronto, ON, USA
| | - Phedias Diamandis
- Laboratory Medicine Program, University Health Network, Toronto, ON, USA
| | - Seth A Climans
- Division of Neurology, Department of Medicine, University Health Network, Toronto, ON, USA
| | - Walter Kucharczyk
- Joint Department of Medical Imaging, University Health Network, University of Toronto, Toronto, ON, USA
| | - Mandy Yi Rong Ding
- Division of Neurology, Department of Medicine, University Health Network, Toronto, ON, USA
| | - Andrew F Gao
- Laboratory Medicine Program, University Health Network, Toronto, ON, USA
| | - Andres M Lozano
- Division of Neurosurgery, Department of Surgery, University Health Network, Toronto, ON, USA
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11
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Barros-Silva D, Klavert J, Jenster G, Jerónimo C, Lafontaine DLJ, Martens-Uzunova ES. The role of OncoSnoRNAs and Ribosomal RNA 2'-O-methylation in Cancer. RNA Biol 2021; 18:61-74. [PMID: 34775914 PMCID: PMC8677010 DOI: 10.1080/15476286.2021.1991167] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Ribosomes are essential nanomachines responsible for all protein production in cells. Ribosome biogenesis and function are energy costly processes, they are tightly regulated to match cellular needs. In cancer, major pathways that control ribosome biogenesis and function are often deregulated to ensure cell survival and to accommodate the continuous proliferation of tumour cells. Ribosomal RNAs (rRNAs) are abundantly modified with 2'-O-methylation (Nm, ribomethylation) being one of the most common modifications. In eukaryotic ribosomes, ribomethylation is performed by the methyltransferase Fibrillarin guided by box C/D small nucleolar RNAs (snoRNAs). Accumulating evidences indicate that snoRNA expression and ribosome methylation profiles are altered in cancer. Here we review our current knowledge on differential snoRNA expression and rRNA 2ʹ-O methylation in the context of human malignancies, and discuss the consequences and opportunities for cancer diagnostics, prognostics, and therapeutics.
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Affiliation(s)
- Daniela Barros-Silva
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands.,Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal
| | - Jonathan Klavert
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (Icbas-up), Porto, Portugal
| | - Denis L J Lafontaine
- Rna Molecular Biology, Fonds De La Recherche Scientifique (F.r.s./fnrs), Université Libre De Bruxelles (Ulb), BioPark Campus, Gosselies, Belgium
| | - Elena S Martens-Uzunova
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
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12
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Jin H, Ren X, Wu H, Hou Y, Fang F. Case Report: Clinical Features of Childhood Leukoencephalopathy With Cerebral Calcifications and Cysts Due to SNORD118 Variants. Front Neurol 2021; 12:585606. [PMID: 34220662 PMCID: PMC8248351 DOI: 10.3389/fneur.2021.585606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 05/11/2021] [Indexed: 11/29/2022] Open
Abstract
Background: Leukoencephalopathy with cerebral calcifications and cysts (LCC) is a rare autosomal recessive cerebral microangiopathy. Recently, biallelic variants in a non-protein-coding gene SNORD118 have been discovered to cause LCC. Case Presentation: We here report a genetically confirmed childhood case of LCC. The patient was a 4-year-and-1-month-old boy with focal seizures. The age at onset of his seizure was 10 days after birth. The seizures were well-controlled by antiepileptic treatment but reoccurred twice due to a head impact accident and a fever, respectively. He suffered from a self-limited esotropia and unsteady running gait during the seizure onset. He had the typical neuroimaging triad of multifocal intracranial calcifications, cysts, and leukoencephalopathy. Genetic analysis indicated that he carried compound heterozygous variants of n.*9C>T and n.3C>T in SNORD118, which were inherited from his parents. Conclusion: We report a childhood LCC case with compound heterozygous variants in SNORD118. To the best of our knowledge, the patient reported in our case had the youngest onset age of LCC with a determined genotype. The triad cerebral-imaging findings of calcifications, cysts, and leukoencephalopathy provide a crucial diagnostic basis. Moreover, the gene assessment, together with the clinical investigations, should be considered for the diagnosis of LCC.
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Affiliation(s)
- Hong Jin
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xiaotun Ren
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Husheng Wu
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | | | - Fang Fang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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13
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Baldini L, Charpentier B, Labialle S. Emerging Data on the Diversity of Molecular Mechanisms Involving C/D snoRNAs. Noncoding RNA 2021; 7:ncrna7020030. [PMID: 34066559 PMCID: PMC8162545 DOI: 10.3390/ncrna7020030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/15/2022] Open
Abstract
Box C/D small nucleolar RNAs (C/D snoRNAs) represent an ancient family of small non-coding RNAs that are classically viewed as housekeeping guides for the 2′-O-methylation of ribosomal RNA in Archaea and Eukaryotes. However, an extensive set of studies now argues that they are involved in mechanisms that go well beyond this function. Here, we present these pieces of evidence in light of the current comprehension of the molecular mechanisms that control C/D snoRNA expression and function. From this inventory emerges that an accurate description of these activities at a molecular level is required to let the snoRNA field enter in a second age of maturity.
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Affiliation(s)
| | - Bruno Charpentier
- Correspondence: (B.C.); (S.L.); Tel.: +33-3-72-74-66-27 (B.C.); +33-3-72-74-66-51 (S.L.)
| | - Stéphane Labialle
- Correspondence: (B.C.); (S.L.); Tel.: +33-3-72-74-66-27 (B.C.); +33-3-72-74-66-51 (S.L.)
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14
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Crow YJ, Marshall H, Rice GI, Seabra L, Jenkinson EM, Baranano K, Battini R, Berger A, Blair E, Blauwblomme T, Bolduc F, Boddaert N, Buckard J, Burnett H, Calvert S, Caumes R, Ng ACH, Chiang D, Clifford DB, Cordelli DM, de Burca A, Demic N, Desguerre I, De Waele L, Di Fonzo A, Dunham SR, Dyack S, Elmslie F, Ferrand M, Fisher G, Karimiani EG, Ghoumid J, Gibbon F, Goel H, Hilmarsen HT, Hughes I, Jacob A, Jones EA, Kumar R, Leventer RJ, MacDonald S, Maroofian R, Mehta SG, Metz I, Monfrini E, Neumann D, Noetzel M, O'Driscoll M, Õunap K, Panzer A, Parikh S, Prabhakar P, Ramond F, Sandford R, Saneto R, Soh C, Stutterd CA, Subramanian GM, Talbot K, Thomas RH, Toro C, Touraine R, Wakeling E, Wassmer E, Whitney A, Livingston JH, O'Keefe RT, Badrock AP. Leukoencephalopathy with calcifications and cysts: Genetic and phenotypic spectrum. Am J Med Genet A 2021; 185:15-25. [PMID: 33029936 DOI: 10.1002/ajmg.a.61907] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/03/2020] [Accepted: 09/16/2020] [Indexed: 12/19/2022]
Abstract
Biallelic mutations in SNORD118, encoding the small nucleolar RNA U8, cause leukoencephalopathy with calcifications and cysts (LCC). Given the difficulty in interpreting the functional consequences of variants in nonprotein encoding genes, and the high allelic polymorphism across SNORD118 in controls, we set out to provide a description of the molecular pathology and clinical spectrum observed in a cohort of patients with LCC. We identified 64 affected individuals from 56 families. Age at presentation varied from 3 weeks to 67 years, with disease onset after age 40 years in eight patients. Ten patients had died. We recorded 44 distinct, likely pathogenic, variants in SNORD118. Fifty two of 56 probands were compound heterozygotes, with parental consanguinity reported in only three families. Forty nine of 56 probands were either heterozygous (46) or homozygous (three) for a mutation involving one of seven nucleotides that facilitate a novel intramolecular interaction between the 5' end and 3' extension of precursor-U8. There was no obvious genotype-phenotype correlation to explain the marked variability in age at onset. Complementing recently published functional analyses in a zebrafish model, these data suggest that LCC most often occurs due to combinatorial severe and milder mutations, with the latter mostly affecting 3' end processing of precursor-U8.
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Affiliation(s)
- Yanick J Crow
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Laboratory of Neurogenetics and Neuroinflammation, Institut Imagine, Université de Paris, Paris, France
| | - Heather Marshall
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Gillian I Rice
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Luis Seabra
- Laboratory of Neurogenetics and Neuroinflammation, Institut Imagine, Université de Paris, Paris, France
| | - Emma M Jenkinson
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Kristin Baranano
- Department of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Roberta Battini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Andrea Berger
- Department of Neuropediatrics, Kliniken Nordoberpfalz AG, Germany
| | - Edward Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Thomas Blauwblomme
- Paediatric Neurosurgery Department, Necker-Enfants Malades Hospital, APHP, Université de Paris, Paris, France
| | - Francois Bolduc
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Natalie Boddaert
- Paediatric Radiology Department, Hôpital Necker Enfants Malades, AP-HP, University de Paris, INSERM U1163, Institut Imagine, Paris, France
| | - Johannes Buckard
- Department of Neuropediatrics, Sozialpädiatrisches Zentrum am EVK Düsseldorf, Düsseldorf, Germany
| | | | - Sophie Calvert
- Neurosciences Department, Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - Roseline Caumes
- Clinique de Génétique Guy Fontaine, CHU Lille, Lille, France
| | - Andy Cheuk-Him Ng
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Diana Chiang
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - David B Clifford
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Duccio M Cordelli
- Child Neurology and Psychiatry Unit, Department of Medical and Surgical Sciences (DIMEC), S. Orsola Hospital, University of Bologna, Italy
| | - Anna de Burca
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Natasha Demic
- Department of Neurology, Vestfold Hospital, Tønsberg, Norway
| | - Isabelle Desguerre
- Department of Paediatric Neurology, Université de Paris, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Liesbeth De Waele
- Department of Paediatric Neurology, University Hospitals Leuven, Leuven, Belgium
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Alessio Di Fonzo
- Foundation IRCCS Ca 'Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
- Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - S Richard Dunham
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sarah Dyack
- Division of Medical Genetics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Frances Elmslie
- South West Thames Regional Genetics Service, St George's, University of London, London, UK
| | | | - Gemma Fisher
- Department of Paediatric Neurology, University Hospital of Wales, Cardiff, UK
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St. George's University of London, London, UK
- Innovative Medical Research Center, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Jamal Ghoumid
- Clinique de Génétique Guy Fontaine, CHU Lille, Lille, France
| | - Frances Gibbon
- Department of Paediatric Neurology, University Hospital of Wales, Cardiff, UK
| | - Himanshu Goel
- Hunter Genetics, Hunter New England Local Health District, Waratah, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, Australia
| | - Hilde T Hilmarsen
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Imelda Hughes
- Department of Paediatric Neurology, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Anu Jacob
- Department of Neurology, The Walton Centre NHS Trust, Liverpool, UK
- Department of Neurology, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Elizabeth A Jones
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Clinical Genetic Service, Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Ram Kumar
- Department of Paediatric Neurology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Richard J Leventer
- Department of Neurology Royal Children's Hospital, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Shelley MacDonald
- Maritime Medical Genetics, IWK Health Centre, Halifax, Nova Scotia, Canada
| | - Reza Maroofian
- Department of Neuromuscular Disorders, University College London Queen Square Institute of Neurology, London, UK
| | - Sarju G Mehta
- East Anglian Regional Genetics Service, Addenbrookes Hospital, Cambridge, UK
| | - Imke Metz
- Department of Neuropathology, University Medical Center, Georg August University, Göttingen, Germany
| | - Edoardo Monfrini
- Foundation IRCCS Ca 'Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
- Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Daniela Neumann
- Klinikum Wilhelmshaven, Department of Neuropediatrics, Germany
| | - Michael Noetzel
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Washington, USA
| | - Mary O'Driscoll
- West Midlands Regional Clinical Genetics Service, Birmingham Health Partners, Birmingham Women's Hospital NHS Foundation Trust, Birmingham, UK
| | - Katrin Õunap
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Axel Panzer
- Paediatric Neurology, DRK Kliniken Berlin-Westend, Berlin, Germany
| | - Sumit Parikh
- Neurogenetics Program, Center for Pediatric Neurology, Neurosciences Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Prab Prabhakar
- Department of Paediatric Neurology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Francis Ramond
- Service de Génétique, CHU-Hôpital Nord, Saint Etienne, France
| | - Richard Sandford
- Academic Department of Medical Genetics, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Russell Saneto
- Neuroscience Institute, Division of Paediatric Neurology, Seattle Children's Hospital and University of Washington, Seattle, Washington, USA
- Department of Neurology, Seattle Children's Hospital and University of Washington, Seattle, Washington, USA
| | - Calvin Soh
- Radiology Department, Manchester University Foundation NHS Trust, Manchester, UK
| | | | - Gopinath M Subramanian
- Department of Paediatric Neurology, John Hunter Children's Hospital, New Lambton Heights, New South Wales, Australia
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, UK
| | - Rhys H Thomas
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Camilo Toro
- NIH Undiagnosed Diseases Program (UDP), National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Renaud Touraine
- Neuroscience Institute, Division of Paediatric Neurology, Seattle Children's Hospital and University of Washington, Seattle, Washington, USA
| | - Emma Wakeling
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Evangeline Wassmer
- Department of Paediatric Neurology, Birmingham Children's Hospital, Birmingham, UK
| | - Andrea Whitney
- University Hospital Southampton NHS Foundation Trust, Department of Paediatric Neurology, Southampton, UK
| | - John H Livingston
- Department of Paediatric Neurology, Leeds General Infirmary, Leeds, UK
| | - Raymond T O'Keefe
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Andrew P Badrock
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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15
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Uggenti C, Lepelley A, Depp M, Badrock AP, Rodero MP, El-Daher MT, Rice GI, Dhir S, Wheeler AP, Dhir A, Albawardi W, Frémond ML, Seabra L, Doig J, Blair N, Martin-Niclos MJ, Della Mina E, Rubio-Roldán A, García-Pérez JL, Sproul D, Rehwinkel J, Hertzog J, Boland-Auge A, Olaso R, Deleuze JF, Baruteau J, Brochard K, Buckley J, Cavallera V, Cereda C, De Waele LMH, Dobbie A, Doummar D, Elmslie F, Koch-Hogrebe M, Kumar R, Lamb K, Livingston JH, Majumdar A, Lorenço CM, Orcesi S, Peudenier S, Rostasy K, Salmon CA, Scott C, Tonduti D, Touati G, Valente M, van der Linden H, Van Esch H, Vermelle M, Webb K, Jackson AP, Reijns MAM, Gilbert N, Crow YJ. cGAS-mediated induction of type I interferon due to inborn errors of histone pre-mRNA processing. Nat Genet 2020; 52:1364-1372. [PMID: 33230297 DOI: 10.1038/s41588-020-00737-3] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/09/2020] [Indexed: 12/25/2022]
Abstract
Inappropriate stimulation or defective negative regulation of the type I interferon response can lead to autoinflammation. In genetically uncharacterized cases of the type I interferonopathy Aicardi-Goutières syndrome, we identified biallelic mutations in LSM11 and RNU7-1, which encode components of the replication-dependent histone pre-mRNA-processing complex. Mutations were associated with the misprocessing of canonical histone transcripts and a disturbance of linker histone stoichiometry. Additionally, we observed an altered distribution of nuclear cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS) and enhanced interferon signaling mediated by the cGAS-stimulator of interferon genes (STING) pathway in patient-derived fibroblasts. Finally, we established that chromatin without linker histone stimulates cyclic guanosine monophosphate-adenosine monophosphate (cGAMP) production in vitro more efficiently. We conclude that nuclear histones, as key constituents of chromatin, are essential in suppressing the immunogenicity of self-DNA.
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Affiliation(s)
- Carolina Uggenti
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Alice Lepelley
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France
| | - Marine Depp
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Andrew P Badrock
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Mathieu P Rodero
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France
| | - Marie-Thérèse El-Daher
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Gillian I Rice
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Somdutta Dhir
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Ann P Wheeler
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Ashish Dhir
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Waad Albawardi
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Marie-Louise Frémond
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France
| | - Luis Seabra
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France
| | - Jennifer Doig
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Natalie Blair
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Maria José Martin-Niclos
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France
| | - Erika Della Mina
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France
| | - Alejandro Rubio-Roldán
- Centre for Genomics and Oncological Research (GENyO), Pfizer-University of Granada-Andalusian Regional Government, Parque Tecnico de la Ciencia de Salud, Granada, Spain
| | - Jose L García-Pérez
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
- Centre for Genomics and Oncological Research (GENyO), Pfizer-University of Granada-Andalusian Regional Government, Parque Tecnico de la Ciencia de Salud, Granada, Spain
| | - Duncan Sproul
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jonny Hertzog
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Anne Boland-Auge
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de Recherche en Génomique Humaine, Évry, France
| | - Robert Olaso
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de Recherche en Génomique Humaine, Évry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de Recherche en Génomique Humaine, Évry, France
| | - Julien Baruteau
- University College London Great Ormond Street Institute of Child Health, London, UK
| | - Karine Brochard
- Service de Médecine Interne Néphrologie Pédiatrique, Hôpital des Enfants, Toulouse, France
| | - Jonathan Buckley
- Department of Paediatric Nephrology, University of Cape Town, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
| | - Vanessa Cavallera
- Child Neurology and Psychiatry Unit, Istituto di Ricovero e Cura a Carattere Scientifico, Mondino Foundation, Pavia, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Center, Istituto di Ricovero e Cura a Carattere Scientifico, Mondino Foundation, Pavia, Italy
| | | | - Angus Dobbie
- Yorkshire Clinical Genetics Service, Chapel Allerton Hospital, Leeds, UK
| | - Diane Doummar
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Département de Neuropédiatrie, Centre de Référence de Neurogénétique et Mouvements Anormaux de l'Enfant, Hôpital Armand Trousseau, Paris, France
| | - Frances Elmslie
- South West Thames Regional Genetics Service, St George's, University of London, London, UK
| | - Margarete Koch-Hogrebe
- Department of Paediatric Neurology, Children's Hospital Datteln, Witten/Herdecke University, Datteln, Germany
| | - Ram Kumar
- Department of Paediatric Neurology, Alder Hey Children's National Health Service Foundation Trust, Liverpool, UK
| | - Kate Lamb
- Department of Paediatrics, Gloucestershire Royal Hospital, Gloucester, UK
| | - John H Livingston
- Department of Paediatric Neurology, Leeds Teaching Hospitals National Health Service Trust, Leeds, UK
| | - Anirban Majumdar
- Department of Paediatric Neurology, Bristol Children's Hospital, Bristol, UK
| | - Charles Marques Lorenço
- Faculdade de Medicina - Centro Universitário Estácio de Ribeirão Preto, Ribeirão Preto, Brazil
| | - Simona Orcesi
- Child Neurology and Psychiatry Unit, Istituto di Ricovero e Cura a Carattere Scientifico, Mondino Foundation, Pavia, Italy
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
| | - Sylviane Peudenier
- Centre de Référence des Déficiences Intellectuelles de Causes Rares et Polyhandicap, Centre Hospitalier Régional Universitaire de Brest, Brest, France
| | - Kevin Rostasy
- Department of Paediatric Neurology, Children's Hospital Datteln, Witten/Herdecke University, Datteln, Germany
| | - Caroline A Salmon
- Department of Paediatrics, Royal Surrey County Hospital, Guildford, UK
| | - Christiaan Scott
- University of Cape Town, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
| | - Davide Tonduti
- Center for diagnosis and treatment of Leukodystrophies, Pediatric Neurology Unit, V. Buzzi Children's Hospital, Milano, Italy
| | - Guy Touati
- Reference Center for Inborn Errors of Metabolism-Department of Pediatrics, Hôpital des Enfants-Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Marialuisa Valente
- Genomic and Post-Genomic Center, Istituto di Ricovero e Cura a Carattere Scientifico, Mondino Foundation, Pavia, Italy
| | - Hélio van der Linden
- Department of Paediatric Neurology, Neurological Institute of Goiânia, Goiânia, Brazil
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Marie Vermelle
- Department of Paediatrics, Centre Hospitalier de Dunkerque, Dunkerque, France
| | - Kate Webb
- University of Cape Town, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
| | - Andrew P Jackson
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Martin A M Reijns
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Nick Gilbert
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Yanick J Crow
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK.
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France.
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