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Gianferante DM, Mendez KJW, Cole S, Gadalla SM, Alter BP, Savage SA, Giri N. Genotype-phenotype associations in individuals with Diamond Blackfan anaemia. EJHAEM 2024; 5:1117-1124. [PMID: 39691264 PMCID: PMC11647742 DOI: 10.1002/jha2.1031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Accepted: 09/11/2024] [Indexed: 12/19/2024]
Abstract
Introduction Diamond Blackfan anaemia (DBA) is a rare disorder characterized by failure of red blood cell production, congenital abnormalities and cancer predisposition, primarily caused by pathogenic germline variants in genes encoding ribosomal proteins. Methods We conducted a genotype-phenotype and outcome study of 121 patients with DBA spanning the 20-year history of the National Cancer Institute's Inherited Bone Marrow Failure Syndromes study. Patient phenotypes were compared by large versus small ribosomal protein genes, across genes with >5 cases (RPS19, RPS29, RPS26 and RPL35A) and by type of pathogenic variants (hypomorphic versus null, large deletions versus others). Results A pathogenic germline variant was identified in 71% of patients (n = 86/121) from 54 families. After adjusting for multiple testing, we found that patients with RPS29 variants were least likely to need treatment for anaemia while those with large ribosomal protein subunit variants had a higher proportion of intellectual disability and gastrointestinal abnormalities compared with small ribosomal protein subunit variants (p < 3.5 × 10-4). There were no statistically significant differences in overall survival or cancer incidence among patients with large or small ribosomal subunit genes. Conclusion This detailed genotype-phenotype study of DBA improves our understanding of the role of germline genetics in the clinical manifestations that may help guide the management of people with DBA.
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Affiliation(s)
- D. Matthew Gianferante
- Clinical Genetics Branch, Division of Cancer Epidemiology and GeneticsNational Cancer Institute, NIH, RockvilleBethesdaMarylandUSA
- Department of PediatricsUniformed Services University of the Health SciencesBethesdaMarylandUSA
| | - Kyra J. W. Mendez
- Clinical Genetics Branch, Division of Cancer Epidemiology and GeneticsNational Cancer Institute, NIH, RockvilleBethesdaMarylandUSA
| | - Sarah Cole
- Clinical Genetics Branch, Division of Cancer Epidemiology and GeneticsNational Cancer Institute, NIH, RockvilleBethesdaMarylandUSA
- Department of PediatricsUniformed Services University of the Health SciencesBethesdaMarylandUSA
- Department of Cancer Epidemiology and GeneticsWalter Reed National Military Medical CenterBethesdaMarylandUSA
| | - Shahinaz M. Gadalla
- Clinical Genetics Branch, Division of Cancer Epidemiology and GeneticsNational Cancer Institute, NIH, RockvilleBethesdaMarylandUSA
| | - Blanche P. Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and GeneticsNational Cancer Institute, NIH, RockvilleBethesdaMarylandUSA
| | - Sharon A. Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and GeneticsNational Cancer Institute, NIH, RockvilleBethesdaMarylandUSA
| | - Neelam Giri
- Clinical Genetics Branch, Division of Cancer Epidemiology and GeneticsNational Cancer Institute, NIH, RockvilleBethesdaMarylandUSA
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2
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Schieweck R, Götz M. Pan-cellular organelles and suborganelles-from common functions to cellular diversity? Genes Dev 2024; 38:98-114. [PMID: 38485267 PMCID: PMC10982711 DOI: 10.1101/gad.351337.123] [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] [Indexed: 04/02/2024]
Abstract
Cell diversification is at the base of increasing multicellular organism complexity in phylogeny achieved during ontogeny. However, there are also functions common to all cells, such as cell division, cell migration, translation, endocytosis, exocytosis, etc. Here we revisit the organelles involved in such common functions, reviewing recent evidence of unexpected differences of proteins at these organelles. For instance, centrosomes or mitochondria differ significantly in their protein composition in different, sometimes closely related, cell types. This has relevance for development and disease. Particularly striking is the high amount and diversity of RNA-binding proteins at these and other organelles, which brings us to review the evidence for RNA at different organelles and suborganelles. We include a discussion about (sub)organelles involved in translation, such as the nucleolus and ribosomes, for which unexpected cell type-specific diversity has also been reported. We propose here that the heterogeneity of these organelles and compartments represents a novel mechanism for regulating cell diversity. One reason is that protein functions can be multiplied by their different contributions in distinct organelles, as also exemplified by proteins with moonlighting function. The specialized organelles still perform pan-cellular functions but in a cell type-specific mode, as discussed here for centrosomes, mitochondria, vesicles, and other organelles. These can serve as regulatory hubs for the storage and transport of specific and functionally important regulators. In this way, they can control cell differentiation, plasticity, and survival. We further include examples highlighting the relevance for disease and propose to examine organelles in many more cell types for their possible differences with functional relevance.
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Affiliation(s)
- Rico Schieweck
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, 38123 Povo, Italy;
- Biomedical Center (BMC), Department of Physiological Genomics, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Magdalena Götz
- Biomedical Center (BMC), Department of Physiological Genomics, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany;
- Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, 82152 Planegg-Martinsried, Germany
- SYNERGY, Excellence Cluster of Systems Neurology, Biomedical Center, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
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3
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Catalanotto C, Barbato C, Cogoni C, Benelli D. The RNA-Binding Function of Ribosomal Proteins and Ribosome Biogenesis Factors in Human Health and Disease. Biomedicines 2023; 11:2969. [PMID: 38001969 PMCID: PMC10669870 DOI: 10.3390/biomedicines11112969] [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: 10/10/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
The ribosome is a macromolecular complex composed of RNA and proteins that interact through an integrated and interconnected network to preserve its ancient core activities. In this review, we emphasize the pivotal role played by RNA-binding proteins as a driving force in the evolution of the current form of the ribosome, underscoring their importance in ensuring accurate protein synthesis. This category of proteins includes both ribosomal proteins and ribosome biogenesis factors. Impairment of their RNA-binding activity can also lead to ribosomopathies, which is a group of disorders characterized by defects in ribosome biogenesis that are detrimental to protein synthesis and cellular homeostasis. A comprehensive understanding of these intricate processes is essential for elucidating the mechanisms underlying the resulting diseases and advancing potential therapeutic interventions.
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Affiliation(s)
- Caterina Catalanotto
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (C.C.); (C.C.)
| | - Christian Barbato
- National Research Council (CNR), Department of Sense Organs DOS, Institute of Biochemistry and Cell Biology (IBBC), Sapienza University of Rome, 00185 Rome, Italy;
| | - Carlo Cogoni
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (C.C.); (C.C.)
| | - Dario Benelli
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (C.C.); (C.C.)
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4
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Li J, Su Y, Chen L, Lin Y, Ru K. Identification of novel mutations in patients with Diamond-Blackfan anemia and literature review of RPS10 and RPS26 mutations. Int J Lab Hematol 2023; 45:766-773. [PMID: 37376976 DOI: 10.1111/ijlh.14126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023]
Abstract
INTRODUCTION Diamond-Blackfan anemia (DBA) is a rare congenital bone marrow failure syndrome characterized by erythroid aplasia, physical malformation, and cancer predisposition. Twenty ribosomal protein genes and three non-ribosomal protein genes have been identified associated with DBA. METHODS To investigate the presence of novel mutations and gain a deeper understanding of the molecular mechanisms of disease, targeted next-generation sequencing was performed in 12 patients with clinically suspected DBA. Literatures were retrieved with complete clinical information published in English by November 2022. The clinical features, treatment, and RPS10/RPS26 mutations were analyzed. RESULTS Among the 12 patients, 11 mutations were identified and 5 of them were novel (RPS19, p.W52S; RPS10, p.P106Qfs*11; RPS26, p.R28*; RPL5, p.R35*; RPL11, p.T44Lfs*40). Including 2 patients in this study, 13 patients with RPS10 mutations and 38 patients with RPS26 mutations were reported from 4 and 6 countries, respectively. The incidences of physical malformation in patients with RPS10 and RPS26 mutations (22% and 36%, respectively) were lower than the overall incidence in DBA patients (~50%). Patients with RPS26 mutations had a worse response rate of steroid therapy than RPS10 (47% vs. 87.5%), but preferred RBC transfusions (67% vs. 44%, p = 0.0253). CONCLUSION Our findings add to the DBA pathogenic variant database and demonstrate the clinical presentations of the DBA patients with RPS10/RPS26 mutations. It shows that next-generation sequencing is a powerful tool for the diagnosis of genetic diseases such as DBA.
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Affiliation(s)
- Jing Li
- SINO-US Diagnostics, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Yongfeng Su
- Department of Hematology for Seniors, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Long Chen
- SINO-US Diagnostics, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Yani Lin
- SINO-US Diagnostics, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Kun Ru
- SINO-US Diagnostics, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
- Department of Pathology and Lab Medicine, Shandong Cancer Hospital, Jinan, Shandong, China
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5
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Savage SA, Jones K, Teshome K, Lori A, McReynolds LJ, Niewisch MR. Next-generation sequencing errors due to genetic variation in WRAP53 encoding TCAB1 on chromosome 17. Hum Mutat 2022; 43:1856-1859. [PMID: 36116037 PMCID: PMC9771914 DOI: 10.1002/humu.24469] [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: 06/15/2022] [Revised: 08/17/2022] [Accepted: 09/12/2022] [Indexed: 01/24/2023]
Abstract
Next-generation sequencing (NGS) is a valuable tool, but has limitations in sequencing through repetitive runs of single nucleotides (homopolymers). Pathogenic germline variants in WRAP53 encoding telomere Cajal body protein 1 (TCAB1) are a known cause of dyskeratosis congenita. We identified a significant NGS error in WRAP53, c.1562dup, p.Ala522Glyfs*8 (rs755116516 G>-/GG/GGG) that did not validate by Sanger sequencing. This error occurs because rs755116516 G>-/GG/GGG (Chr17:7,606,714) is polymorphic, and variants at this site challenge the ability of NGS to accurately call the correct number of nucleotides in a homopolymer run. This was further complicated by the fact that chr17:7,606,721 (rs769202794) is multiallelic G>A, C, T, and that chr17:7,606,722 is also multiallelic (rs7640C>A/G/T and rs373064567C>delC). In addition to the expert interpretation of potentially clinically actionable variants, it recommended that all variants in regions of the genome with homopolymers be validated by Sanger sequencing before clinical action.
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Affiliation(s)
- Sharon A. Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kedest Teshome
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Lisa J. McReynolds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Marena R. Niewisch
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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6
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McElreavey K, Pailhoux E, Bashamboo A. DHX37 and 46,XY DSD: A New Ribosomopathy? Sex Dev 2022; 16:194-206. [PMID: 35835064 DOI: 10.1159/000522004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/04/2022] [Indexed: 11/19/2022] Open
Abstract
Recently, a series of recurrent missense variants in the RNA-helicase DHX37 have been reported associated with either 46,XY gonadal dysgenesis, 46,XY testicular regression syndrome (TRS), or anorchia. All affected children have non-syndromic forms of disorders/differences of sex development (DSD). These variants, which involve highly conserved amino acids within known functional domains of the protein, are predicted by in silico tools to have a deleterious effect on helicase function. DHX37 is required for ribosome biogenesis in eukaryotes, and how these variants cause DSD is unclear. The relationship between DHX37 and human congenital disorders is complex as compound heterozygous as well as de novo heterozygous missense variants in DHX37 are also associated with a complex congenital developmental syndrome (NEDBAVC, neurodevelopmental disorder with brain anomalies and with or without vertebral or cardiac anomalies; OMIM 618731), consisting of microcephaly, global developmental delay, seizures, facial dysmorphia, and kidney and cardiac anomalies. Here, we will give a brief overview of ribosome biogenesis and the role of DHX37 in this process. We will discuss variants in DHX37, their contribution to human disease in the general context of human ribosomopathies, and the possible disease mechanisms that may be involved.
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Affiliation(s)
- Kenneth McElreavey
- Human Developmental Genetics, CNRS UMR3738, Institut Pasteur, Paris, France
| | - Eric Pailhoux
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Anu Bashamboo
- Human Developmental Genetics, CNRS UMR3738, Institut Pasteur, Paris, France
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7
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Roy NBA, Da Costa L, Russo R, Bianchi P, Mañú-Pereira MDM, Fermo E, Andolfo I, Clark B, Proven M, Sanchez M, van Wijk R, van der Zwaag B, Layton M, Rees D, Iolascon A. The use of next-generation sequencing in the diagnosis of rare inherited anaemias: A Joint BSH/EHA Good Practice Paper. Br J Haematol 2022; 198:459-477. [PMID: 35661144 DOI: 10.1111/bjh.18191] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 12/27/2022]
Affiliation(s)
- Noémi B A Roy
- Department of Haematology, Oxford University Hospitals, NHS Foundation Trust, Oxford, UK.,NIHR BRC Blood Theme, Oxford, UK
| | | | - Roberta Russo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Paola Bianchi
- UOS Fisiopatologia delle Anemie, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico Milano, Milan, Italy
| | | | - Elisa Fermo
- UOS Fisiopatologia delle Anemie, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico Milano, Milan, Italy
| | - Immacolata Andolfo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | | | - Melanie Proven
- Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Mayka Sanchez
- Department of Basic Sciences, Iron metabolism: Regulation and Diseases, Universitat Internacional de Catalunya (UIC), Barcelona, Spain.,BloodGenetics S.L. Diagnostics in Inherited Blood Diseases, Barcelona, Spain
| | - Richard van Wijk
- Central Diagnostic Laboratory, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Bert van der Zwaag
- Central Diagnostic Laboratory, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Mark Layton
- Imperial College London, Hammersmith Hospital, London, UK
| | - David Rees
- King's College Hospital, King's College London, UK
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
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8
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The Use of Next-generation Sequencing in the Diagnosis of Rare Inherited Anaemias: A Joint BSH/EHA Good Practice Paper. Hemasphere 2022; 6:e739. [PMID: 35686139 PMCID: PMC9170004 DOI: 10.1097/hs9.0000000000000739] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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9
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Hiregange DG, Rivalta A, Yonath A, Zimmerman E, Bashan A, Yonath H. Mutations in RPS19 may affect ribosome function and biogenesis in Diamond Blackfan Anemia. FEBS Open Bio 2022; 12:1419-1434. [PMID: 35583751 PMCID: PMC9249338 DOI: 10.1002/2211-5463.13444] [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: 03/29/2022] [Revised: 05/04/2022] [Accepted: 05/17/2022] [Indexed: 11/12/2022] Open
Abstract
Ribosomes, the cellular organelles translating the genetic code to proteins, are assemblies of RNA chains and many proteins (RPs) arranged in precise fine-tuned interwoven structures. Mutated ribosomal genes cause ribosomopathies, including Diamond Blackfan Anemia (DBA, a rare heterogeneous red-cell aplasia connected to ribosome malfunction) or failed biogenesis. Combined bioinformatical, structural, and predictive analyses of potential consequences of possibly expressed mutations in eS19, the protein product of the highly mutated RPS19, suggests that mutations in its exposed surface could alter its positioning during assembly and consequently prevent biogenesis, implying a natural selective strategy to avoid malfunctions in ribosome assembly. A search for RPS19 pseudogenes indicated >90% sequence identity with the wild type, hinting at its expression in cases of absent or truncated gene products.
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Affiliation(s)
| | - Andre Rivalta
- The Department of Chemical and Structural Biology, Weizmann Institute of Science, Israel
| | - Ada Yonath
- The Department of Chemical and Structural Biology, Weizmann Institute of Science, Israel
| | - Ella Zimmerman
- The Department of Chemical and Structural Biology, Weizmann Institute of Science, Israel
| | - Anat Bashan
- The Department of Chemical and Structural Biology, Weizmann Institute of Science, Israel
| | - Hagith Yonath
- Internal Medicine A and Genetics Institute Sheba Medical Center, and Sackler School of Medicine, Tel Aviv University, Israel
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10
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Zhou X, Liu Z, He T, Zhang C, Jiang M, Jin Y, Wu Z, Gu C, Zhang W, Yang X. DDX10 promotes the proliferation and metastasis of colorectal cancer cells via splicing RPL35. Cancer Cell Int 2022; 22:58. [PMID: 35109823 PMCID: PMC8812018 DOI: 10.1186/s12935-022-02478-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/19/2022] [Indexed: 12/24/2022] Open
Abstract
Background Colorectal cancer (CRC) has become the second deadliest cancer in the world and severely threatens human health. An increasing number of studies have focused on the role of the RNA helicase DEAD-box (DDX) family in CRC. However, the mechanism of DDX10 in CRC has not been elucidated. Methods In our study, we analysed the expression data of CRC samples from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Subsequently, we performed cytological experiments and animal experiments to explore the role of DDX10 in CRC cells. Furthermore, we performed Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and protein–protein interaction (PPI) network analyses. Finally, we predicted the interacting protein of DDX10 by LC–MS/MS and verified it by coimmunoprecipitation (Co-IP) and qPCR. Results In the present study, we identified that DDX10 mRNA was extremely highly expressed in CRC tissues compared with normal colon tissues in the TCGA and GEO databases. The protein expression of DDX10 was measured by immunochemistry (IHC) in 17 CRC patients. The biological roles of DDX10 were explored via cell and molecular biology experiments in vitro and in vivo and cell cycle assays. We found that DDX10 knockdown markedly reduced CRC cell proliferation, migration and invasion. Then, we constructed a PPI network with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING). GO and KEGG enrichment analysis and gene set enrichment analysis (GSEA) showed that DDX10 was closely related to RNA splicing and E2F targets. Using LC–MS/MS and Co-IP assays, we discovered that RPL35 is the interacting protein of DDX10. In addition, we hypothesize that RPL35 is related to the E2F pathway and the immune response in CRC. Conclusions In conclusion, provides a better understanding of the molecular mechanisms of DDX10 in CRC and provides a potential biomarker for the diagnosis and treatment of CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02478-1.
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Affiliation(s)
- Xin Zhou
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, Jiangsu, China
| | - Zhihong Liu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, Jiangsu, China
| | - Tengfei He
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, Jiangsu, China
| | - Cuifeng Zhang
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, Jiangsu, China
| | - Manman Jiang
- Soochow University, 1 Shizi Street, Suzhou, China
| | - Yuxiao Jin
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, Jiangsu, China
| | - Ziyu Wu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, Jiangsu, China
| | - Changji Gu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, Jiangsu, China
| | - Wei Zhang
- Department of Radiotherapy, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, Jiangsu, China.
| | - Xiaodong Yang
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, Jiangsu, China.
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11
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Lebaron S, O’Donohue M, Smith SC, Engleman KL, Juusola J, Safina NN, Thiffault I, Saunders CJ, Gleizes P. Functionally impaired
RPL8
variants associated with Diamond‐Blackfan anemia and a Diamond‐Blackfan anemia‐like phenotype. Hum Mutat 2021; 43:389-402. [DOI: 10.1002/humu.24323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Simon Lebaron
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI) University of Toulouse, CNRS, UT3 Toulouse France
| | - Marie‐Françoise O’Donohue
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI) University of Toulouse, CNRS, UT3 Toulouse France
| | - Scott C. Smith
- Department of Pathology and Laboratory Medicine Children's Mercy Hospital Kansas City MO USA
- Current address: SUNY Upstate Medical University Syracuse NY USA
| | - Kendra L. Engleman
- Division of Clinical Genetics Children's Mercy Hospital Kansas City MO USA
- Department of Pediatrics Children’s Mercy Hospital Kansas City MO USA
| | | | - Nicole N. Safina
- Division of Clinical Genetics Children's Mercy Hospital Kansas City MO USA
- Department of Pediatrics Children’s Mercy Hospital Kansas City MO USA
- Current address: Division of Medical Genetics and Genomics, Stead Family University of Iowa Children’s Hospital, The University of Iowa Carver College of Medicine Iowa City IA USA
| | - Isabelle Thiffault
- Department of Pathology and Laboratory Medicine Children's Mercy Hospital Kansas City MO USA
- University of Missouri‐Kansas City School of Medicine Kansas City MO USA
- Center for Pediatric Genomic Medicine Children’s Mercy Hospital Kansas City MO USA
| | - Carol J. Saunders
- Department of Pathology and Laboratory Medicine Children's Mercy Hospital Kansas City MO USA
- University of Missouri‐Kansas City School of Medicine Kansas City MO USA
- Center for Pediatric Genomic Medicine Children’s Mercy Hospital Kansas City MO USA
| | - Pierre‐Emmanuel Gleizes
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI) University of Toulouse, CNRS, UT3 Toulouse France
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12
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Colli LM, Jessop L, Myers TA, Camp SY, Machiela MJ, Choi J, Cunha R, Onabajo O, Mills GC, Schmid V, Brodie SA, Delattre O, Mole DR, Purdue MP, Yu K, Brown KM, Chanock SJ. Altered regulation of DPF3, a member of the SWI/SNF complexes, underlies the 14q24 renal cancer susceptibility locus. Am J Hum Genet 2021; 108:1590-1610. [PMID: 34390653 PMCID: PMC8456159 DOI: 10.1016/j.ajhg.2021.07.009] [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: 04/06/2021] [Accepted: 07/22/2021] [Indexed: 12/11/2022] Open
Abstract
Our study investigated the underlying mechanism for the 14q24 renal cell carcinoma (RCC) susceptibility risk locus identified by a genome-wide association study (GWAS). The sentinel single-nucleotide polymorphism (SNP), rs4903064, at 14q24 confers an allele-specific effect on expression of the double PHD fingers 3 (DPF3) of the BAF SWI/SNF complex as assessed by massively parallel reporter assay, confirmatory luciferase assays, and eQTL analyses. Overexpression of DPF3 in renal cell lines increases growth rates and alters chromatin accessibility and gene expression, leading to inhibition of apoptosis and activation of oncogenic pathways. siRNA interference of multiple DPF3-deregulated genes reduces growth. Our results indicate that germline variation in DPF3, a component of the BAF complex, part of the SWI/SNF complexes, can lead to reduced apoptosis and activation of the STAT3 pathway, both critical in RCC carcinogenesis. In addition, we show that altered DPF3 expression in the 14q24 RCC locus could influence the effectiveness of immunotherapy treatment for RCC by regulating tumor cytokine secretion and immune cell activation.
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MESH Headings
- Carcinogenesis/genetics
- Carcinogenesis/immunology
- Carcinogenesis/pathology
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/immunology
- Carcinoma, Renal Cell/pathology
- Carcinoma, Renal Cell/therapy
- Cell Line, Tumor
- Chromatin/chemistry
- Chromatin/immunology
- Chromatin Assembly and Disassembly/immunology
- Chromosomes, Human, Pair 14
- Cytokines/genetics
- Cytokines/immunology
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/immunology
- Gene Expression Regulation
- Genetic Loci
- Genetic Predisposition to Disease
- Genome, Human
- Genome-Wide Association Study
- High-Throughput Nucleotide Sequencing
- Humans
- Immunotherapy/methods
- Kidney Neoplasms/genetics
- Kidney Neoplasms/immunology
- Kidney Neoplasms/pathology
- Kidney Neoplasms/therapy
- Polymorphism, Single Nucleotide
- STAT3 Transcription Factor/genetics
- STAT3 Transcription Factor/immunology
- T-Lymphocytes, Cytotoxic
- Transcription Factors/genetics
- Transcription Factors/immunology
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Affiliation(s)
- Leandro M Colli
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; Department of Medical Imaging, Hematology, and Oncology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP 14040-900, Brazil
| | - Lea Jessop
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Timothy A Myers
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Sabrina Y Camp
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Renato Cunha
- Department of Medical Imaging, Hematology, and Oncology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP 14040-900, Brazil; Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Olusegun Onabajo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Grace C Mills
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Virginia Schmid
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Seth A Brodie
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Olivier Delattre
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris 75248, France
| | - David R Mole
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA.
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13
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Takafuji S, Mori T, Nishimura N, Yamamoto N, Uemura S, Nozu K, Terui K, Toki T, Ito E, Muramatsu H, Takahashi Y, Matsuo M, Yamamura T, Iijima K. Usefulness of functional splicing analysis to confirm precise disease pathogenesis in Diamond-Blackfan anemia caused by intronic variants in RPS19. Pediatr Hematol Oncol 2021; 38:515-527. [PMID: 33622161 DOI: 10.1080/08880018.2021.1887984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Diamond-Blackfan anemia (DBA) is mainly caused by pathogenic variants in ribosomal proteins and 22 responsible genes have been identified to date. The most common causative gene of DBA is RPS19 [NM_001022.4]. Nearly 180 RPS19 variants have been reported, including three deep intronic variants outside the splicing consensus sequence (c.72-92A > G, c.356 + 18G > C, and c.411 + 6G > C). We also identified one case with a c.412-3C > G intronic variant. Without conducting transcript analysis, the pathogenicity of these variants is unknown. However, it is difficult to assess transcripts because of their fragility. In such cases, in vitro functional splicing assays can be used to assess pathogenicity. Here, we report functional splicing analysis results of four RPS19 deep intronic variants identified in our case and in previously reported cases. One splicing consensus variant (c.411 + 1G > A) was also examined as a positive control. Aberrant splicing with a 2-bp insertion between exons 5 and 6 was identified in the patient samples and minigene assay results also identified exon 6 skipping in our case. The exon 6 skipping transcript was confirmed by further evaluation using quantitative RT-PCR. Additionally, minigene assay analysis of three reported deep intronic variants revealed that none of them showed aberrant splicing and that these variants were not considered to be pathogenic. In conclusion, the minigene assay is a useful method for functional splicing analysis of inherited disease.
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Affiliation(s)
- Satoru Takafuji
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takeshi Mori
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Noriyuki Nishimura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Nobuyuki Yamamoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Suguru Uemura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kiminori Terui
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Tsutomu Toki
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Etsuro Ito
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masafumi Matsuo
- Locomotion Biology Research Center, Kobe Gakuin University, Kobe, Japan
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
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14
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Kang J, Brajanovski N, Chan KT, Xuan J, Pearson RB, Sanij E. Ribosomal proteins and human diseases: molecular mechanisms and targeted therapy. Signal Transduct Target Ther 2021; 6:323. [PMID: 34462428 PMCID: PMC8405630 DOI: 10.1038/s41392-021-00728-8] [Citation(s) in RCA: 157] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 07/12/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Ribosome biogenesis and protein synthesis are fundamental rate-limiting steps for cell growth and proliferation. The ribosomal proteins (RPs), comprising the structural parts of the ribosome, are essential for ribosome assembly and function. In addition to their canonical ribosomal functions, multiple RPs have extra-ribosomal functions including activation of p53-dependent or p53-independent pathways in response to stress, resulting in cell cycle arrest and apoptosis. Defects in ribosome biogenesis, translation, and the functions of individual RPs, including mutations in RPs have been linked to a diverse range of human congenital disorders termed ribosomopathies. Ribosomopathies are characterized by tissue-specific phenotypic abnormalities and higher cancer risk later in life. Recent discoveries of somatic mutations in RPs in multiple tumor types reinforce the connections between ribosomal defects and cancer. In this article, we review the most recent advances in understanding the molecular consequences of RP mutations and ribosomal defects in ribosomopathies and cancer. We particularly discuss the molecular basis of the transition from hypo- to hyper-proliferation in ribosomopathies with elevated cancer risk, a paradox termed "Dameshek's riddle." Furthermore, we review the current treatments for ribosomopathies and prospective therapies targeting ribosomal defects. We also highlight recent advances in ribosome stress-based cancer therapeutics. Importantly, insights into the mechanisms of resistance to therapies targeting ribosome biogenesis bring new perspectives into the molecular basis of cancer susceptibility in ribosomopathies and new clinical implications for cancer therapy.
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Affiliation(s)
- Jian Kang
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Natalie Brajanovski
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Keefe T. Chan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Jiachen Xuan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Richard B. Pearson
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, VIC Australia
| | - Elaine Sanij
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Clinical Pathology, University of Melbourne, Melbourne, VIC Australia ,grid.1073.50000 0004 0626 201XSt. Vincent’s Institute of Medical Research, Fitzroy, VIC Australia
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15
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Brodie SA, Khincha PP, Giri N, Bouk AJ, Steinberg M, Dai J, Jessop L, Donovan FX, Chandrasekharappa SC, de Andrade KC, Maric I, Ellis SR, Mirabello L, Alter BP, Savage SA. Pathogenic germline IKZF1 variant alters hematopoietic gene expression profiles. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006015. [PMID: 34162668 PMCID: PMC8327879 DOI: 10.1101/mcs.a006015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 05/28/2021] [Indexed: 12/03/2022] Open
Abstract
IKZF1 encodes Ikaros, a zinc finger–containing transcription factor crucial to the development of the hematopoietic system. Germline pathogenic variants in IKZF1 have been reported in patients with acute lymphocytic leukemia and immunodeficiency syndromes. Diamond–Blackfan anemia (DBA) is a rare inherited bone marrow failure syndrome characterized by erythroid hypoplasia, associated with a spectrum of congenital anomalies and an elevated risk of certain cancers. DBA is usually caused by heterozygous pathogenic variants in genes that function in ribosomal biogenesis; however, in many cases the genetic etiology is unknown. We identified a germline IKZF1 variant, rs757907717 C > T, in identical twins with DBA-like features and autoimmune gastrointestinal disease. rs757907717 C > T results in a p.R381C amino acid change in the IKZF1 Ik-x isoform (p.R423C on isoform Ik-1), which we show is associated with altered global gene expression and perturbation of transcriptional networks involved in hematopoietic system development. These data suggest that this missense substitution caused a DBA-like syndrome in this family because of alterations in hematopoiesis, including dysregulation of networks essential for normal erythropoiesis and the immune system.
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Affiliation(s)
- Seth A Brodie
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 20850, USA
| | - Payal P Khincha
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Clinical Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Neelam Giri
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Clinical Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Aaron J Bouk
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 20850, USA
| | - Mia Steinberg
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 20850, USA
| | - Jieqiong Dai
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 20850, USA
| | - Lea Jessop
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Clinical Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Frank X Donovan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Clinical Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Clinical Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kelvin C de Andrade
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Clinical Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Irina Maric
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Steven R Ellis
- Department of Biochemistry and Molecular Biology, University of Louisville, Louisville, Kentucky 40292, USA
| | - Lisa Mirabello
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Clinical Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Blanche P Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Clinical Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Clinical Center, National Institutes of Health, Bethesda, Maryland 20892, USA
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16
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Gay DM, Lund AH, Jansson MD. Translational control through ribosome heterogeneity and functional specialization. Trends Biochem Sci 2021; 47:66-81. [PMID: 34312084 DOI: 10.1016/j.tibs.2021.07.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/18/2021] [Accepted: 07/01/2021] [Indexed: 12/31/2022]
Abstract
The conceptual origins of ribosome specialization can be traced back to the earliest days of molecular biology. Yet, this field has only recently begun to gather momentum, with numerous studies identifying distinct heterogeneous ribosome populations across multiple species and model systems. It is proposed that some of these compositionally distinct ribosomes may be functionally specialized and able to regulate the translation of specific mRNAs. Identification and functional characterization of specialized ribosomes has the potential to elucidate a novel layer of gene expression control, at the level of translation, where the ribosome itself is a key regulatory player. In this review, we discuss different sources of ribosome heterogeneity, evidence for ribosome specialization, and also the future directions of this exciting field.
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Affiliation(s)
- David M Gay
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anders H Lund
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Martin D Jansson
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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17
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Gianferante MD, Wlodarski MW, Atsidaftos E, Da Costa L, Delaporta P, Farrar JE, Goldman FD, Hussain M, Kattamis A, Leblanc T, Lipton JM, Niemeyer CM, Pospisilova D, Quarello P, Ramenghi U, Sankaran VG, Vlachos A, Volejnikova J, Alter BP, Savage SA, Giri N. Genotype-phenotype association and variant characterization in Diamond-Blackfan anemia caused by pathogenic variants in RPL35A. Haematologica 2021; 106:1303-1310. [PMID: 32241839 PMCID: PMC8094096 DOI: 10.3324/haematol.2020.246629] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Indexed: 01/02/2023] Open
Abstract
Diamond Blackfan anemia (DBA) is predominantly an autosomal dominant inherited red cell aplasia primarily caused by pathogenic germline variants in ribosomal protein genes. DBA due to pathogenic RPL35A variants has been associated with large 3q29 deletions and phenotypes not common in DBA. We conducted a multi-institutional genotypephenotype study of 45 patients with DBA associated with pathogenic RPL35A germline variants and curated the variant data on 21 additional cases from the literature. Genotype-phenotype analyses were conducted comparing patients with large deletions versus all other pathogenic variants in RPL35A. Twenty-two of the 45 cases had large deletions in RPL35A. After adjusting for multiple tests, a statistically significant association was observed between patients with a large deletion and steroid-resistant anemia, neutropenia, craniofacial abnormalities, chronic gastrointestinal problems, and intellectual disabilities (P<0.01) compared with all other pathogenic variants. Non-large deletion pathogenic variants were spread across RPL35Awith no apparent hot spot and 56% of the individual family variants were observed more than once. In this, the largest known study of DBA patients with pathogenic RPL35A variants, we determined that patients with large deletions have a more severe phenotype that is clinically different from those with non-large deletion variants. Genes of interest also deleted in the 3q29 region that could be associated with some of these phenotypic features include LMLN and IQCG. Management of DBA due to large RPL35A deletions may be challenging due to complex problems and require comprehensive assessments by multiple specialists including immunological, gastrointestinal, and developmental evaluations to provide optimal multidisciplinary care.
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Affiliation(s)
- Matthew D Gianferante
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | | | - Evangelia Atsidaftos
- Feinstein Institute of Medical Research, Cohen Children's Medical Center, NY, USA
| | - Lydie Da Costa
- Service Hematologie Biologique, Hopital Robert-Debré, Université de Paris, France
| | - Polyxeni Delaporta
- First Department of Pediatrics, National and Kapodistrian University of Athens, Greece
| | - Jason E Farrar
- Arkansas Children Research Institute, University of Arkansas, Little Rock, USA
| | | | - Maryam Hussain
- Feinstein Institute of Medical Research, Cohen Children's Medical Center, NY, USA
| | - Antonis Kattamis
- First Department of Pediatrics, National and Kapodistrian University of Athens, Greece
| | - Thierry Leblanc
- Service Hematologie Biologique, Hopital Robert-Debré, Université de Paris, France
| | - Jeffrey M Lipton
- Feinstein Institute of Medical Research, Cohen Children's Medical Center, NY, USA
| | | | | | | | - Ugo Ramenghi
- Pediatric and Public Health Science, University of Torino, Torino, Italy
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Adrianna Vlachos
- Feinstein Institute of Medical Research, Cohen Children's Medical Center, NY, USA
| | - Jana Volejnikova
- Palacky University and University Hospital, Olomouc, Czech Republic
| | - Blanche P Alter
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Neelam Giri
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
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18
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The Use of B-Cell Polysome Profiling to Validate Novel RPL5 (uL18) and RPL26 (uL24) Variants in Diamond-Blackfan Anemia. J Pediatr Hematol Oncol 2021; 43:e336-e340. [PMID: 33122585 DOI: 10.1097/mph.0000000000001980] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/19/2020] [Indexed: 11/25/2022]
Abstract
Diamond-Blackfan anemia (DBA) is a rare bone marrow failure syndrome usually caused by heterozygous variants in ribosomal proteins (RP) and which leads to severe anemia. Genetic studies in DBA rely primarily on multigene panels that often result in variants of unknown significance. Our objective was to optimize polysome profiling to functionally validate new large subunit RP variants. We determined the optimal experimental conditions for B-cell polysome profiles then performed this analysis on 2 children with DBA and novel missense RPL5 (uL18) and RPL26 (uL24) variants of unknown significance. Both patients had reduced 60S and 80S fractions when compared with an unaffected parent consistent with a large ribosomal subunit defect. Polysome profiling using primary B-cells is an adjunctive tool that can assist in validation of large subunit RP variants of uncertain significance. Further studies are necessary to validate this method in patients with known DBA mutations, small RP subunit variants, and silent carriers.
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19
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Boussaid I, Le Goff S, Floquet C, Gautier EF, Raimbault A, Viailly PJ, Al Dulaimi D, Burroni B, Dusanter-Fourt I, Hatin I, Mayeux P, Cosson B, Fontenay M. Integrated analyses of translatome and proteome identify the rules of translation selectivity in RPS14-deficient cells. Haematologica 2021; 106:746-758. [PMID: 32327500 PMCID: PMC7927886 DOI: 10.3324/haematol.2019.239970] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Indexed: 12/24/2022] Open
Abstract
In ribosomopathies, the Diamond-Blackfan anemia (DBA) or 5q- syndrome, ribosomal protein (RP) genes are affected by mutation or deletion, resulting in bone marrow erythroid hypoplasia. Unbalanced production of ribosomal subunits leading to a limited ribosome cellular content regulates translation at the expense of the master erythroid transcription factor GATA1. In RPS14-deficient cells mimicking 5q- syndrome erythroid defects, we show that the transcript length, codon bias of the coding sequence (CDS) and 3’UTR (untranslated region) structure are the key determinants of translation. In these cells, short transcripts with a structured 3’UTR and high codon adaptation index (CAI) showed a decreased translation efficiency. Quantitative analysis of the whole proteome confirmed that the post-transcriptional changes depended on the transcript characteristics that governed the translation efficiency in conditions of low ribosome availability. In addition, proteins involved in normal erythroid differentiation share most determinants of translation selectivity. Our findings thus indicate that impaired erythroid maturation due to 5q- syndrome may proceed from a translational selectivity at the expense of the erythroid differentiation program, and suggest that an interplay between the CDS and UTR may regulate mRNA translation.
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Affiliation(s)
- Ismael Boussaid
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris
| | - Salomé Le Goff
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris,Laboratoire d’Excellence du Globule Rouge GR-Ex, Université de Paris, Paris
| | - Célia Floquet
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris
| | - Emilie-Fleur Gautier
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris,Centre-Université de Paris Cochin, Service de Pathologie, Paris, France
| | - Anna Raimbault
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris
| | - Pierre-Julien Viailly
- Centre Henri-Becquerel, Institut de Recherche et d’Innovation Biomedicale de Haute Normandie, INSERM U1245, Rouen
| | - Dina Al Dulaimi
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris
| | - Barbara Burroni
- Assistance Publique-Hôpitaux de Paris, Centre-Université de Paris - Cochin, Service de Pathologie, Paris
| | | | - Isabelle Hatin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université de Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex
| | - Patrick Mayeux
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris,Laboratoire d’Excellence du Globule Rouge GR-Ex, Université de Paris, Paris,Centre-Université de Paris Cochin, Service de Pathologie, Paris, France
| | - Bertrand Cosson
- Université de Paris, Epigenetics and Cell Fate, CNRS UMR 7216, Paris
| | - Michaela Fontenay
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris,Laboratoire d’Excellence du Globule Rouge GR-Ex, Université de Paris, Paris,Centre-Université de Paris Cochin, Service de Pathologie, Paris, France.,Centre Henri-Becquerel, Institut de Recherche et d’Innovation Biomedicale de Haute Normandie, INSERM U1245, Rouen,Assistance Publique- Hôpitaux de Paris, Centre-Université de Paris - Hôpital Cochin, Service d’Hématologie Biologique, Paris, France
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20
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Bellott DW, Page DC. Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals. Genome Res 2021; 31:198-210. [PMID: 33479023 PMCID: PMC7849413 DOI: 10.1101/gr.268516.120] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/04/2020] [Indexed: 12/18/2022]
Abstract
Different ancestral autosomes independently evolved into sex chromosomes in snakes, birds, and mammals. In snakes and birds, females are ZW and males are ZZ; in mammals, females are XX and males are XY. Although X and Z Chromosomes retain nearly all ancestral genes, sex-specific W and Y Chromosomes suffered extensive genetic decay. In both birds and mammals, the genes that survived on sex-specific chromosomes are enriched for broadly expressed, dosage-sensitive regulators of gene expression, subject to strong purifying selection. To gain deeper insight into the processes that govern survival on sex-specific chromosomes, we carried out a meta-analysis of survival across 41 species-three snakes, 24 birds, and 14 mammals-doubling the number of ancestral genes under investigation and increasing our power to detect enrichments among survivors relative to nonsurvivors. Of 2564 ancestral genes, representing an eighth of the ancestral amniote genome, only 324 survive on present-day sex-specific chromosomes. Survivors are enriched for dosage-sensitive developmental processes, particularly development of neural crest-derived structures, such as the face. However, there was no enrichment for expression in sex-specific tissues, involvement in sex determination or gonadogenesis pathways, or conserved sex-biased expression. Broad expression and dosage sensitivity contributed independently to gene survival, suggesting that pleiotropy imposes additional constraints on the evolution of dosage compensation. We propose that maintaining the viability of the heterogametic sex drove gene survival on amniote sex-specific chromosomes, and that subtle modulation of the expression of survivor genes and their autosomal orthologs has disproportionately large effects on development and disease.
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Affiliation(s)
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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21
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Mirabello L, Zhu B, Koster R, Karlins E, Dean M, Yeager M, Gianferante M, Spector LG, Morton LM, Karyadi D, Robison LL, Armstrong GT, Bhatia S, Song L, Pankratz N, Pinheiro M, Gastier-Foster JM, Gorlick R, de Toledo SRC, Petrilli AS, Patino-Garcia A, Lecanda F, Gutierrez-Jimeno M, Serra M, Hattinger C, Picci P, Scotlandi K, Flanagan AM, Tirabosco R, Amary MF, Kurucu N, Ilhan IE, Ballinger ML, Thomas DM, Barkauskas DA, Mejia-Baltodano G, Valverde P, Hicks BD, Zhu B, Wang M, Hutchinson AA, Tucker M, Sampson J, Landi MT, Freedman ND, Gapstur S, Carter B, Hoover RN, Chanock SJ, Savage SA. Frequency of Pathogenic Germline Variants in Cancer-Susceptibility Genes in Patients With Osteosarcoma. JAMA Oncol 2021; 6:724-734. [PMID: 32191290 DOI: 10.1001/jamaoncol.2020.0197] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Importance Osteosarcoma, the most common malignant bone tumor in children and adolescents, occurs in a high number of cancer predisposition syndromes that are defined by highly penetrant germline mutations. The germline genetic susceptibility to osteosarcoma outside of familial cancer syndromes remains unclear. Objective To investigate the germline genetic architecture of 1244 patients with osteosarcoma. Design, Setting, and Participants Whole-exome sequencing (n = 1104) or targeted sequencing (n = 140) of the DNA of 1244 patients with osteosarcoma from 10 participating international centers or studies was conducted from April 21, 2014, to September 1, 2017. The results were compared with the DNA of 1062 individuals without cancer assembled internally from 4 participating studies who underwent comparable whole-exome sequencing and 27 173 individuals of non-Finnish European ancestry who were identified through the Exome Aggregation Consortium (ExAC) database. In the analysis, 238 high-interest cancer-susceptibility genes were assessed followed by testing of the mutational burden across 736 additional candidate genes. Principal component analyses were used to identify 732 European patients with osteosarcoma and 994 European individuals without cancer, with outliers removed for patient-control group comparisons. Patients were subsequently compared with individuals in the ExAC group. All data were analyzed from June 1, 2017, to July 1, 2019. Main Outcomes and Measures The frequency of rare pathogenic or likely pathogenic genetic variants. Results Among 1244 patients with osteosarcoma (mean [SD] age at diagnosis, 16 [8.9] years [range, 2-80 years]; 684 patients [55.0%] were male), an analysis restricted to individuals with European ancestry indicated a significantly higher pathogenic or likely pathogenic variant burden in 238 high-interest cancer-susceptibility genes among patients with osteosarcoma compared with the control group (732 vs 994, respectively; P = 1.3 × 10-18). A pathogenic or likely pathogenic cancer-susceptibility gene variant was identified in 281 of 1004 patients with osteosarcoma (28.0%), of which nearly three-quarters had a variant that mapped to an autosomal-dominant gene or a known osteosarcoma-associated cancer predisposition syndrome gene. The frequency of a pathogenic or likely pathogenic cancer-susceptibility gene variant was 128 of 1062 individuals (12.1%) in the control group and 2527 of 27 173 individuals (9.3%) in the ExAC group. A higher than expected frequency of pathogenic or likely pathogenic variants was observed in genes not previously linked to osteosarcoma (eg, CDKN2A, MEN1, VHL, POT1, APC, MSH2, and ATRX) and in the Li-Fraumeni syndrome-associated gene, TP53. Conclusions and Relevance In this study, approximately one-fourth of patients with osteosarcoma unselected for family history had a highly penetrant germline mutation requiring additional follow-up analysis and possible genetic counseling with cascade testing.
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Affiliation(s)
- Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Roelof Koster
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Eric Karlins
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Matthew Gianferante
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Logan G Spector
- Department of Pediatrics, University of Minnesota, Minneapolis
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Danielle Karyadi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Nathan Pankratz
- Department of Pediatrics, University of Minnesota, Minneapolis
| | - Maisa Pinheiro
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Julie M Gastier-Foster
- Department of Pathology and Pediatrics, Nationwide Children's Hospital, The Ohio State University, Columbus
| | - Richard Gorlick
- Department of Pediatrics, University of Texas MD Anderson Cancer Center, Houston
| | - Silvia Regina Caminada de Toledo
- Laboratorio de Genetica, Instituto de Oncologia Pediatrica, Grupo de Apoio ao Adolescente e a Crianca com Cancer/Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Antonio S Petrilli
- Laboratorio de Genetica, Instituto de Oncologia Pediatrica, Grupo de Apoio ao Adolescente e a Crianca com Cancer/Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Ana Patino-Garcia
- Solid Tumor Division, Department of Pediatrics, University Clinic of Navarra and Center for Applied Medical Research, Navarra Institute for Health Research, Pamplona, Spain.,Center for Applied Medical Research, University of Navarra, Instituto de Investigacion Sanitaria de Navarra, and Centro de Investigacion Biomedica en Red Cancer, Pamplona, Spain
| | - Fernando Lecanda
- Solid Tumor Division, Department of Pediatrics, University Clinic of Navarra and Center for Applied Medical Research, Navarra Institute for Health Research, Pamplona, Spain.,Center for Applied Medical Research, University of Navarra, Instituto de Investigacion Sanitaria de Navarra, and Centro de Investigacion Biomedica en Red Cancer, Pamplona, Spain
| | - Miriam Gutierrez-Jimeno
- Solid Tumor Division, Department of Pediatrics, University Clinic of Navarra and Center for Applied Medical Research, Navarra Institute for Health Research, Pamplona, Spain
| | - Massimo Serra
- Laboratory of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Claudia Hattinger
- Laboratory of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Piero Picci
- Laboratory of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Adrienne M Flanagan
- Research Department of Pathology, UCL Cancer Institute, London, United Kingdom.,Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, United Kingdom
| | - Roberto Tirabosco
- Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, United Kingdom
| | - Maria Fernanda Amary
- Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, United Kingdom
| | - Nilgün Kurucu
- Department of Pediatric Oncology, A.Y. Ankara Oncology Training and Research Hospital, Yenimahalle, Ankara, Turkey
| | - Inci Ergurhan Ilhan
- Department of Pediatric Oncology, A.Y. Ankara Oncology Training and Research Hospital, Yenimahalle, Ankara, Turkey
| | - Mandy L Ballinger
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - David M Thomas
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Donald A Barkauskas
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles
| | | | | | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Mingyi Wang
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Amy A Hutchinson
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Margaret Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Joshua Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Maria T Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Susan Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia
| | - Brian Carter
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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22
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Sawyer JK, Kabiri Z, Montague RA, Allen SR, Stewart R, Paramore SV, Cohen E, Zaribafzadeh H, Counter CM, Fox DT. Exploiting codon usage identifies intensity-specific modifiers of Ras/MAPK signaling in vivo. PLoS Genet 2020; 16:e1009228. [PMID: 33296356 PMCID: PMC7752094 DOI: 10.1371/journal.pgen.1009228] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/21/2020] [Accepted: 10/27/2020] [Indexed: 01/05/2023] Open
Abstract
Signal transduction pathways are intricately fine-tuned to accomplish diverse biological processes. An example is the conserved Ras/mitogen-activated-protein-kinase (MAPK) pathway, which exhibits context-dependent signaling output dynamics and regulation. Here, by altering codon usage as a novel platform to control signaling output, we screened the Drosophila genome for modifiers specific to either weak or strong Ras-driven eye phenotypes. Our screen enriched for regions of the genome not previously connected with Ras phenotypic modification. We mapped the underlying gene from one modifier to the ribosomal gene RpS21. In multiple contexts, we show that RpS21 preferentially influences weak Ras/MAPK signaling outputs. These data show that codon usage manipulation can identify new, output-specific signaling regulators, and identify RpS21 as an in vivo Ras/MAPK phenotypic regulator. Cellular communication is critical in controlling the growth of organs and must be carefully regulated to prevent disease. The Ras signaling pathway is frequently used for cellular communication of tissue growth regulation but can operate at different signaling strengths. Here, we used a novel strategy to identify genes that specifically tune weak or strong Ras signaling states. We find that the gene RpS21 preferentially tunes weak Ras signaling states.
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Affiliation(s)
- Jessica K. Sawyer
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Zahra Kabiri
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Ruth A. Montague
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Scott R. Allen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Rebeccah Stewart
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Sarah V. Paramore
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Erez Cohen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Hamed Zaribafzadeh
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Christopher M. Counter
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- * E-mail: (CMC); (DTF)
| | - Donald T. Fox
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- * E-mail: (CMC); (DTF)
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23
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Human mutational constraint as a tool to understand biology of rare and emerging bone marrow failure syndromes. Blood Adv 2020; 4:5232-5245. [PMID: 33104793 DOI: 10.1182/bloodadvances.2020002687] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/16/2020] [Indexed: 12/17/2022] Open
Abstract
Inherited bone marrow failure (IBMF) syndromes are rare blood disorders characterized by hematopoietic cell dysfunction and predisposition to hematologic malignancies. Despite advances in the understanding of molecular pathogenesis of these heterogeneous diseases, genetic variant interpretation, genotype-phenotype correlation, and outcome prognostication remain difficult. As new IBMF and other myelodysplastic syndrome (MDS) predisposition genes continue to be discovered (frequently in small kindred studies), there is an increasing need for a systematic framework to evaluate penetrance and prevalence of mutations in genes associated with IBMF phenotypes. To address this need, we analyzed population-based genomic data from >125 000 individuals in the Genome Aggregation Database for loss-of-function (LoF) variants in 100 genes associated with IBMF. LoF variants in genes associated with IBMF/MDS were present in 0.426% of individuals. Heterozygous LoF variants in genes in which haploinsufficiency is associated with IBMF/MDS were identified in 0.422% of the population; homozygous LoF variants associated with autosomal recessive IBMF/MDS diseases were identified in only .004% of the cohort. Using age distribution of LoF variants and 2 measures of mutational constraint, LOEUF ("loss-of-function observed/expected upper bound fraction") and pLI ("probability of being loss-of-function intolerance"), we evaluated the pathogenicity, tolerance, and age-related penetrance of LoF mutations in specific genes associated with IBMF syndromes. This analysis led to insights into rare IBMF diseases, including syndromes associated with DHX34, MDM4, RAD51, SRP54, and WIPF1. Our results provide an important population-based framework for the interpretation of LoF variant pathogenicity in rare and emerging IBMF syndromes.
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24
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Venturi G, Montanaro L. How Altered Ribosome Production Can Cause or Contribute to Human Disease: The Spectrum of Ribosomopathies. Cells 2020; 9:E2300. [PMID: 33076379 PMCID: PMC7602531 DOI: 10.3390/cells9102300] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 12/22/2022] Open
Abstract
A number of different defects in the process of ribosome production can lead to a diversified spectrum of disorders that are collectively identified as ribosomopathies. The specific factors involved may either play a role only in ribosome biogenesis or have additional extra-ribosomal functions, making it difficult to ascribe the pathogenesis of the disease specifically to an altered ribosome biogenesis, even if the latter is clearly affected. We reviewed the available literature in the field from this point of view with the aim of distinguishing, among ribosomopathies, the ones due to specific alterations in the process of ribosome production from those characterized by a multifactorial pathogenesis.
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Affiliation(s)
- Giulia Venturi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy;
- Center for Applied Biomedical Research, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy;
- Center for Applied Biomedical Research, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
- Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, 40138 Bologna, Italy
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25
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Petibon C, Malik Ghulam M, Catala M, Abou Elela S. Regulation of ribosomal protein genes: An ordered anarchy. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1632. [PMID: 33038057 PMCID: PMC8047918 DOI: 10.1002/wrna.1632] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/08/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023]
Abstract
Ribosomal protein genes are among the most highly expressed genes in most cell types. Their products are generally essential for ribosome synthesis, which is the cornerstone for cell growth and proliferation. Many cellular resources are dedicated to producing ribosomal proteins and thus this process needs to be regulated in ways that carefully balance the supply of nascent ribosomal proteins with the demand for new ribosomes. Ribosomal protein genes have classically been viewed as a uniform interconnected regulon regulated in eukaryotic cells by target of rapamycin and protein kinase A pathway in response to changes in growth conditions and/or cellular status. However, recent literature depicts a more complex picture in which the amount of ribosomal proteins produced varies between genes in response to two overlapping regulatory circuits. The first includes the classical general ribosome‐producing program and the second is a gene‐specific feature responsible for fine‐tuning the amount of ribosomal proteins produced from each individual ribosomal gene. Unlike the general pathway that is mainly controlled at the level of transcription and translation, this specific regulation of ribosomal protein genes is largely achieved through changes in pre‐mRNA splicing efficiency and mRNA stability. By combining general and specific regulation, the cell can coordinate ribosome production, while allowing functional specialization and diversity. Here we review the many ways ribosomal protein genes are regulated, with special focus on the emerging role of posttranscriptional regulatory events in fine‐tuning the expression of ribosomal protein genes and its role in controlling the potential variation in ribosome functions. This article is categorized under:Translation > Ribosome Biogenesis Translation > Ribosome Structure/Function Translation > Translation Regulation
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Affiliation(s)
- Cyrielle Petibon
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Mustafa Malik Ghulam
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Mathieu Catala
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Sherif Abou Elela
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
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26
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Ribosomopathies: New Therapeutic Perspectives. Cells 2020; 9:cells9092080. [PMID: 32932838 PMCID: PMC7564184 DOI: 10.3390/cells9092080] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 12/13/2022] Open
Abstract
Ribosomopathies are a group of rare diseases in which genetic mutations cause defects in either ribosome biogenesis or function, given specific phenotypes. Ribosomal proteins, and multiple other factors that are necessary for ribosome biogenesis (rRNA processing, assembly of subunits, export to cytoplasm), can be affected in ribosomopathies. Despite the need for ribosomes in all cell types, these diseases result mainly in tissue-specific impairments. Depending on the type of ribosomopathy and its pathogenicity, there are many potential therapeutic targets. The present manuscript will review our knowledge of ribosomopathies, discuss current treatments, and introduce the new therapeutic perspectives based on recent research. Diamond–Blackfan anemia, currently treated with blood transfusion prior to steroids, could be managed with a range of new compounds, acting mainly on anemia, such as L-leucine. Treacher Collins syndrome could be managed by various treatments, but it has recently been shown that proteasomal inhibition by MG132 or Bortezomib may improve cranial skeleton malformations. Developmental defects resulting from ribosomopathies could be also treated pharmacologically after birth. It might thus be possible to treat certain ribosomopathies without using multiple treatments such as surgery and transplants. Ribosomopathies remain an open field in the search for new therapeutic approaches based on our recent understanding of the role of ribosomes and progress in gene therapy for curing genetic disorders.
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27
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Jahan D, Al Hasan MM, Haque M. Diamond-Blackfan anemia with mutation in RPS19: A case report and an overview of published pieces of literature. J Pharm Bioallied Sci 2020; 12:163-170. [PMID: 32742115 PMCID: PMC7373105 DOI: 10.4103/jpbs.jpbs_234_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 11/04/2022] Open
Abstract
Introduction Diamond-Blackfan anemia (DBA), one of a rare group of inherited bone marrow failure syndromes, is characterized by red cell failure, the presence of congenital anomalies, and cancer predisposition. It can be caused by mutations in the RPS19 gene (25% of the cases). Methods This case report describes a 10-month-old boy who presented with 2 months' history of gradually increasing weakness and pallor. Results The patient was diagnosed as a case of DBA based on peripheral blood finding, bone marrow aspiration with trephine biopsy reports, and genetic mutation analysis of the RPS19 gene. His father refused hematopoietic stem cell transplantation for financial constraints. Patient received prednisolone therapy with oral folic acid and iron supplements. Conclusion Hemoglobin raised from 6.7 to 9.8g/dL after 1 month of therapeutic intervention.
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Affiliation(s)
- Dilshad Jahan
- Department of Hematology, Apollo Hospitals, Dhaka, Bangladesh
| | | | - Mainul Haque
- Unit of Pharmacology, Faculty of Medicine and Defence Health, Universiti Pertahanan Nasional Malaysia (National Defence University of Malaysia), Kuala Lumpur, Malaysia
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28
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Ribosomes: An Exciting Avenue in Stem Cell Research. Stem Cells Int 2020; 2020:8863539. [PMID: 32695182 PMCID: PMC7362291 DOI: 10.1155/2020/8863539] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 02/07/2023] Open
Abstract
Stem cell research has focused on genomic studies. However, recent evidence has indicated the involvement of epigenetic regulation in determining the fate of stem cells. Ribosomes play a crucial role in epigenetic regulation, and thus, we focused on the role of ribosomes in stem cells. Majority of living organisms possess ribosomes that are involved in the translation of mRNA into proteins and promote cellular proliferation and differentiation. Ribosomes are stable molecular machines that play a role with changes in the levels of RNA during translation. Recent research suggests that specific ribosomes actively regulate gene expression in multiple cell types, such as stem cells. Stem cells have the potential for self-renewal and differentiation into multiple lineages and, thus, require high efficiency of translation. Ribosomes induce cellular transdifferentiation and reprogramming, and disrupted ribosome synthesis affects translation efficiency, thereby hindering stem cell function leading to cell death and differentiation. Stem cell function is regulated by ribosome-mediated control of stem cell-specific gene expression. In this review, we have presented a detailed discourse on the characteristics of ribosomes in stem cells. Understanding ribosome biology in stem cells will provide insights into the regulation of stem cell function and cellular reprogramming.
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29
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Wilkes MC, Siva K, Chen J, Varetti G, Youn MY, Chae H, Ek F, Olsson R, Lundbäck T, Dever DP, Nishimura T, Narla A, Glader B, Nakauchi H, Porteus MH, Repellin CE, Gazda HT, Lin S, Serrano M, Flygare J, Sakamoto KM. Diamond Blackfan anemia is mediated by hyperactive Nemo-like kinase. Nat Commun 2020; 11:3344. [PMID: 32620751 PMCID: PMC7334220 DOI: 10.1038/s41467-020-17100-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 05/26/2020] [Indexed: 01/30/2023] Open
Abstract
Diamond Blackfan Anemia (DBA) is a congenital bone marrow failure syndrome associated with ribosomal gene mutations that lead to ribosomal insufficiency. DBA is characterized by anemia, congenital anomalies, and cancer predisposition. Treatment for DBA is associated with significant morbidity. Here, we report the identification of Nemo-like kinase (NLK) as a potential target for DBA therapy. To identify new DBA targets, we screen for small molecules that increase erythroid expansion in mouse models of DBA. This screen identified a compound that inhibits NLK. Chemical and genetic inhibition of NLK increases erythroid expansion in mouse and human progenitors, including bone marrow cells from DBA patients. In DBA models and patient samples, aberrant NLK activation is initiated at the Megakaryocyte/Erythroid Progenitor (MEP) stage of differentiation and is not observed in non-erythroid hematopoietic lineages or healthy erythroblasts. We propose that NLK mediates aberrant erythropoiesis in DBA and is a potential target for therapy. Diamond Blackfan Anemia (DBA) is a congenital bone marrow failure syndrome that is associated with anemia. Here, the authors examine the role of Nemo-like kinase (NLK) in erythroid cells in the pathogenesis of DBA and as a potential target for therapy.
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Affiliation(s)
- M C Wilkes
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - K Siva
- Department of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, 22184, Sweden
| | - J Chen
- Department of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, 22184, Sweden
| | - G Varetti
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028, Spain.,Barcelona Institute of Science and Technology (BIST), Barcelona, 08028, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08028, Spain
| | - M Y Youn
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - H Chae
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - F Ek
- Chemical Biology and Therapeutics Group, Department of Medical Science, Lund University, Lund, 22184, Sweden
| | - R Olsson
- Chemical Biology and Therapeutics Group, Department of Medical Science, Lund University, Lund, 22184, Sweden
| | - T Lundbäck
- Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Department for Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - D P Dever
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - T Nishimura
- Department of Genetics, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - A Narla
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - B Glader
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - H Nakauchi
- Department of Genetics, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - M H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - C E Repellin
- Biosciences Division, SRI International, Menlo Park, CA, 94025, USA
| | - H T Gazda
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - S Lin
- Department of Molecular, Cell and Development Biology, University of California, Los Angeles, CA, 90095, USA
| | - M Serrano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028, Spain.,Barcelona Institute of Science and Technology (BIST), Barcelona, 08028, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08028, Spain
| | - J Flygare
- Department of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, 22184, Sweden
| | - K M Sakamoto
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA.
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Nonsense Suppression Therapy: New Hypothesis for the Treatment of Inherited Bone Marrow Failure Syndromes. Int J Mol Sci 2020; 21:ijms21134672. [PMID: 32630050 PMCID: PMC7369780 DOI: 10.3390/ijms21134672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/29/2020] [Accepted: 06/29/2020] [Indexed: 12/13/2022] Open
Abstract
Inherited bone marrow failure syndromes (IBMFS) are a group of cancer-prone genetic diseases characterized by hypocellular bone marrow with impairment in one or more hematopoietic lineages. The pathogenesis of IBMFS involves mutations in several genes which encode for proteins involved in DNA repair, telomere biology and ribosome biogenesis. The classical IBMFS include Shwachman–Diamond syndrome (SDS), Diamond–Blackfan anemia (DBA), Fanconi anemia (FA), dyskeratosis congenita (DC), and severe congenital neutropenia (SCN). IBMFS are associated with high risk of myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), and solid tumors. Unfortunately, no specific pharmacological therapies have been highly effective for IBMFS. Hematopoietic stem cell transplantation provides a cure for aplastic or myeloid neoplastic complications. However, it does not affect the risk of solid tumors. Since approximately 28% of FA, 24% of SCN, 21% of DBA, 20% of SDS, and 17% of DC patients harbor nonsense mutations in the respective IBMFS-related genes, we discuss the use of the nonsense suppression therapy in these diseases. We recently described the beneficial effect of ataluren, a nonsense suppressor drug, in SDS bone marrow hematopoietic cells ex vivo. A similar approach could be therefore designed for treating other IBMFS. In this review we explain in detail the new generation of nonsense suppressor molecules and their mechanistic roles. Furthermore, we will discuss strengths and limitations of these molecules which are emerging from preclinical and clinical studies. Finally we discuss the state-of-the-art of preclinical and clinical therapeutic studies carried out for IBMFS.
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31
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Choe HK, Cho J. Comprehensive Genome-Wide Approaches to Activity-Dependent Translational Control in Neurons. Int J Mol Sci 2020; 21:ijms21051592. [PMID: 32111062 PMCID: PMC7084349 DOI: 10.3390/ijms21051592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 02/06/2023] Open
Abstract
Activity-dependent regulation of gene expression is critical in experience-mediated changes in the brain. Although less appreciated than transcriptional control, translational control is a crucial regulatory step of activity-mediated gene expression in physiological and pathological conditions. In the first part of this review, we overview evidence demonstrating the importance of translational controls under the context of synaptic plasticity as well as learning and memory. Then, molecular mechanisms underlying the translational control, including post-translational modifications of translation factors, mTOR signaling pathway, and local translation, are explored. We also summarize how activity-dependent translational regulation is associated with neurodevelopmental and psychiatric disorders, such as autism spectrum disorder and depression. In the second part, we highlight how recent application of high-throughput sequencing techniques has added insight into genome-wide studies on translational regulation of neuronal genes. Sequencing-based strategies to identify molecular signatures of the active neuronal population responding to a specific stimulus are discussed. Overall, this review aims to highlight the implication of translational control for neuronal gene regulation and functions of the brain and to suggest prospects provided by the leading-edge techniques to study yet-unappreciated translational regulation in the nervous system.
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Affiliation(s)
- Han Kyoung Choe
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
- Correspondence: (H.K.C.); (J.C.)
| | - Jun Cho
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
- Correspondence: (H.K.C.); (J.C.)
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32
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Chen C, Lu M, Lin S, Qin W. The nuclear gene rpl18 regulates erythroid maturation via JAK2-STAT3 signaling in zebrafish model of Diamond-Blackfan anemia. Cell Death Dis 2020; 11:135. [PMID: 32075953 PMCID: PMC7031319 DOI: 10.1038/s41419-020-2331-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/04/2020] [Accepted: 02/04/2020] [Indexed: 11/09/2022]
Abstract
Diamond-Blackfan anemia (DBA) is a rare, inherited bone marrow failure syndrome, characterized by red blood cell aplasia, developmental abnormalities, and enhanced risk of malignancy. However, the underlying pathogenesis of DBA is yet to be understood. Recently, mutations in the gene encoding ribosomal protein (RP) L18 were identified in DBA patients. RPL18 is a crucial component of the ribosomal large subunit but its role in hematopoiesis remains unknown. To genetically model the ribosomal defect identified in DBA, we generated a rpl18 mutant line in zebrafish, using CRISPR/Cas9 system. Molecular characterization of this mutant line demonstrated that Rpl18 deficiency mirrored the erythroid defects of DBA, namely a lack of mature red blood cells. Rpl18 deficiency caused an increase in p53 activation and JAK2-STAT3 activity. Furthermore, we found inhibitors of JAK2 or STAT3 phosphorylation could rescue anemia in rpl18 mutants. Our research provides a new in vivo model of Rpl18 deficiency and suggests involvement of signal pathway of JAK2-STAT3 in the DBA pathogenesis.
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Affiliation(s)
- Cheng Chen
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Mengjia Lu
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Shuo Lin
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Wei Qin
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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33
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Lezzerini M, Penzo M, O’Donohue MF, Marques dos Santos Vieira C, Saby M, Elfrink HL, Diets IJ, Hesse AM, Couté Y, Gastou M, Nin-Velez A, Nikkels PGJ, Olson AN, Zonneveld-Huijssoon E, Jongmans MCJ, Zhang G, van Weeghel M, Houtkooper RH, Wlodarski MW, Kuiper RP, Bierings MB, van der Werff ten Bosch J, Leblanc T, Montanaro L, Dinman JD, Da Costa L, Gleizes PE, MacInnes AW. Ribosomal protein gene RPL9 variants can differentially impair ribosome function and cellular metabolism. Nucleic Acids Res 2020; 48:770-787. [PMID: 31799629 PMCID: PMC6954397 DOI: 10.1093/nar/gkz1042] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/17/2019] [Accepted: 11/19/2019] [Indexed: 12/20/2022] Open
Abstract
Variants in ribosomal protein (RP) genes drive Diamond-Blackfan anemia (DBA), a bone marrow failure syndrome that can also predispose individuals to cancer. Inherited and sporadic RP gene variants are also linked to a variety of phenotypes, including malignancy, in individuals with no anemia. Here we report an individual diagnosed with DBA carrying a variant in the 5'UTR of RPL9 (uL6). Additionally, we report two individuals from a family with multiple cancer incidences carrying a RPL9 missense variant. Analysis of cells from these individuals reveals that despite the variants both driving pre-rRNA processing defects and 80S monosome reduction, the downstream effects are remarkably different. Cells carrying the 5'UTR variant stabilize TP53 and impair the growth and differentiation of erythroid cells. In contrast, ribosomes incorporating the missense variant erroneously read through UAG and UGA stop codons of mRNAs. Metabolic profiles of cells carrying the 5'UTR variant reveal an increased metabolism of amino acids and a switch from glycolysis to gluconeogenesis while those of cells carrying the missense variant reveal a depletion of nucleotide pools. These findings indicate that variants in the same RP gene can drive similar ribosome biogenesis defects yet still have markedly different downstream consequences and clinical impacts.
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Affiliation(s)
- Marco Lezzerini
- Amsterdam UMC, University of Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Marianna Penzo
- Laboratorio di Patologia Clinica, Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale and Centro di Ricerca Biomedica Applicata (CRBA), Policlinico Universitario di S. Orsola, Università di Bologna,Via Massarenti 9, 40138 Bologna, Italy
| | - Marie-Françoise O’Donohue
- LBME, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | | | - Manon Saby
- INSERM UMR S1134, F-75015, Paris, France
| | - Hyung L Elfrink
- Amsterdam UMC, University of Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Laboratory Genetic Metabolic Diseases, Core Facility Metabolomics, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Illja J Diets
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anne-Marie Hesse
- University Grenoble Alpes, CEA, INSERM, IRIG, BGE, F-38000 Grenoble, France
| | - Yohann Couté
- University Grenoble Alpes, CEA, INSERM, IRIG, BGE, F-38000 Grenoble, France
| | - Marc Gastou
- Paris University, Paris, France
- Laboratory of Excellence for Red Cell, LABEX GR-Ex, F-75015, Paris, France
- Institute Gustave Roussy, Inserm unit U1170, F-94800 Villejuif, France
| | - Alexandra Nin-Velez
- Department of Comparative Biology and Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Peter G J Nikkels
- Department of Pathology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Alexandra N Olson
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marjolijn C J Jongmans
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands
- Princess Maxima Center for Pediatric Oncology and Utrecht University Children's Hospital, Utrecht, The Netherlands
| | - GuangJun Zhang
- Department of Comparative Biology and Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Michel van Weeghel
- Amsterdam UMC, University of Amsterdam, Laboratory Genetic Metabolic Diseases, Core Facility Metabolomics, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Riekelt H Houtkooper
- Amsterdam UMC, University of Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Marcin W Wlodarski
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, D-79106 Freiburg, Germany
- St. Jude's Children Research Hospital, Memphis, TN, USA
| | - Roland P Kuiper
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands
| | - Marc B Bierings
- Princess Maxima Center for Pediatric Oncology and Utrecht University Children's Hospital, Utrecht, The Netherlands
| | | | - Thierry Leblanc
- Pediatric Hematology/Oncology Service, Robert Debré Hospital, F-75019 Paris, France
| | - Lorenzo Montanaro
- Laboratorio di Patologia Clinica, Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale and Centro di Ricerca Biomedica Applicata (CRBA), Policlinico Universitario di S. Orsola, Università di Bologna,Via Massarenti 9, 40138 Bologna, Italy
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Lydie Da Costa
- INSERM UMR S1134, F-75015, Paris, France
- Paris University, Paris, France
- Laboratory of Excellence for Red Cell, LABEX GR-Ex, F-75015, Paris, France
- Hematology Lab, Robert Debré Hospital, F-75019 Paris, France
| | - Pierre-Emmanuel Gleizes
- LBME, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Alyson W MacInnes
- Amsterdam UMC, University of Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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34
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Bai H, Liu L, An K, Lu X, Harrison M, Zhao Y, Yan R, Lu Z, Li S, Lin S, Liang F, Qin W. CRISPR/Cas9-mediated precise genome modification by a long ssDNA template in zebrafish. BMC Genomics 2020; 21:67. [PMID: 31964350 PMCID: PMC6974980 DOI: 10.1186/s12864-020-6493-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/14/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene targeting by homology-directed repair (HDR) can precisely edit the genome and is a versatile tool for biomedical research. However, the efficiency of HDR-based modification is still low in many model organisms including zebrafish. Recently, long single-stranded DNA (lssDNA) molecules have been developed as efficient alternative donor templates to mediate HDR for the generation of conditional mouse alleles. Here we report a method, zLOST (zebrafish long single-stranded DNA template), which utilises HDR with a long single-stranded DNA template to produce more efficient and precise mutations in zebrafish. RESULTS The efficiency of knock-ins was assessed by phenotypic rescue at the tyrosinase (tyr) locus and confirmed by sequencing. zLOST was found to be a successful optimised rescue strategy: using zLOST containing a tyr repair site, we restored pigmentation in at least one melanocyte in close to 98% of albino tyr25del/25del embryos, although more than half of the larvae had only a small number of pigmented cells. Sequence analysis showed that there was precise HDR dependent repair of the tyr locus in these rescued pigmented embryos. Furthermore, quantification of zLOST knock-in efficiency at the rps14, nop56 and th loci by next generation sequencing demonstrated that zLOST showed a clear improvement. We utilised the HDR efficiency of zLOST to precisely model specific human disease mutations in zebrafish with ease. Finally, we determined that this method can achieve a germline transmission rate of up to 31.8%. CONCLUSIONS In summary, these results show that zLOST is a useful method of zebrafish genome editing, particularly for generating desired mutations by targeted DNA knock-in through HDR.
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Affiliation(s)
- Haipeng Bai
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Lijun Liu
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Ke An
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Xiaochan Lu
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Michael Harrison
- The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Yanqiu Zhao
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Ruibin Yan
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Zhijie Lu
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong, 510631, People's Republic of China
| | - Song Li
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Shuo Lin
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Fang Liang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong, 510631, People's Republic of China.
| | - Wei Qin
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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Volejnikova J, Vojta P, Urbankova H, Mojzíkova R, Horvathova M, Hochova I, Cermak J, Blatny J, Sukova M, Bubanska E, Feketeova J, Prochazkova D, Horakova J, Hajduch M, Pospisilova D. Czech and Slovak Diamond-Blackfan Anemia (DBA) Registry update: Clinical data and novel causative genetic lesions. Blood Cells Mol Dis 2019; 81:102380. [PMID: 31855845 DOI: 10.1016/j.bcmd.2019.102380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/08/2019] [Accepted: 11/08/2019] [Indexed: 12/23/2022]
Abstract
Diamond-Blackfan anemia (DBA) is a rare congenital erythroid aplasia, underlied by haploinsufficient mutations in genes coding for ribosomal proteins (RP) in approximately 70% of cases. DBA is frequently associated with somatic malformations, endocrine dysfunction and with an increased predisposition to cancer. Here we present clinical and genetic characteristics of 62 patients from 52 families enrolled in the Czech and Slovak DBA Registry. Whole exome sequencing (WES) and array comparative genomic hybridization (aCGH) were employed to identify causative mutations in newly diagnosed patients and in cases with previously unrecognized molecular pathology. RP mutation detection rate was 81% (50/62 patients). This included 8 novel point mutations and 4 large deletions encompassing some of the RP genes. Malignant or predisposing condition developed in 8/62 patients (13%): myelodysplastic syndrome in 3 patients; breast cancer in 2 patients; colorectal cancer plus ocular tumor, diffuse large B-cell lymphoma and multiple myeloma each in one case. These patients exclusively harbored RPL5, RPL11 or RPS19 mutations. Array CGH is beneficial for detection of novel mutations in DBA due to its capacity to detect larger chromosomal aberrations. Despite the importance of genotype-phenotype correlation in DBA, phenotypic differences among family members harboring an identical mutation were observed.
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Affiliation(s)
- Jana Volejnikova
- Department of Pediatrics, Faculty of Medicine and Dentistry, Palacky University and University Hospital Olomouc, I. P. Pavlova 6, 77900 Olomouc, Czech Republic; Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 1333/5, 77900 Olomouc, Czech Republic
| | - Petr Vojta
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 1333/5, 77900 Olomouc, Czech Republic
| | - Helena Urbankova
- Department of Hemato-Oncology, Faculty of Medicine and Dentistry, Palacky University and University Hospital Olomouc, I. P. Pavlova 6, 77900 Olomouc, Czech Republic
| | - Renata Mojzíkova
- Department of Biology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 3, 77900 Olomouc, Czech Republic
| | - Monika Horvathova
- Department of Biology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 3, 77900 Olomouc, Czech Republic
| | - Ivana Hochova
- Department of Hematology, Second Faculty of Medicine, Charles University and University Hospital Motol Prague, V Uvalu 84, 15006 Prague, Czech Republic
| | - Jaroslav Cermak
- Institute of Hematology and Blood Transfusion, U Nemocnice 2094/1, 12820 Prague, Czech Republic
| | - Jan Blatny
- Department of Pediatric Hematology, Masaryk University and University Hospital Brno, Jihlavská 20, 62500 Brno, Czech Republic
| | - Martina Sukova
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol Prague, V Uvalu 84, 15006 Prague, Czech Republic
| | - Eva Bubanska
- Department of Pediatric Oncology and Hematology, Children's Faculty Hospital Banska Bystrica, Ludovit Svoboda Square 4, 97409 Banska Bystrica, Slovakia
| | - Jaroslava Feketeova
- Department of Pediatric Oncology and Hematology, Children Teaching Hospital Kosice, Trieda SNP 457/1, 04011 Kosice, Slovakia
| | - Daniela Prochazkova
- Department of Pediatrics, Masaryk Hospital Usti nad Labem, Socialni pece 3316/12A, 40113 Usti nad Labem, Czech Republic
| | - Julia Horakova
- Department of Pediatric Hematology and Oncology, Faculty of Medicine, Comenius University and University Hospital Bratislava, Limbova 1, 83340 Bratislava, Slovakia
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska 1333/5, 77900 Olomouc, Czech Republic
| | - Dagmar Pospisilova
- Department of Pediatrics, Faculty of Medicine and Dentistry, Palacky University and University Hospital Olomouc, I. P. Pavlova 6, 77900 Olomouc, Czech Republic.
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Aspesi A, Borsotti C, Follenzi A. Emerging Therapeutic Approaches for Diamond Blackfan Anemia. Curr Gene Ther 2019; 18:327-335. [PMID: 30411682 PMCID: PMC6637096 DOI: 10.2174/1566523218666181109124538] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/02/2018] [Accepted: 11/09/2018] [Indexed: 01/05/2023]
Abstract
Diamond Blackfan Anemia (DBA) is an inherited erythroid aplasia with onset in childhood. Patients carry heterozygous mutations in one of 19 Ribosomal Protein (RP) genes, that lead to defective ribosome biogenesis and function. Standard treatments include steroids or blood transfusions but the only definitive cure is allogeneic Hematopoietic Stem Cell Transplantation (HSCT). Although advances in HSCT have greatly improved the success rate over the last years, the risk of adverse events and mor-tality is still significant. Clinical trials employing gene therapy are now in progress for a variety of monogenic diseases and the development of innovative stem cell-based strategies may open new alternatives for DBA treatment as well. In this review, we summarize the most recent progress toward the implementation of new thera-peutic approaches for this disorder. We present different DNA- and RNA-based technologies as well as new candidate pharmacological treatments and discuss their relevance and potential applicability for the cure of DBA.
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Affiliation(s)
- Anna Aspesi
- Department of Health Sciences, University of Eastern Piedmont Amedeo Avogadro, Novara, Italy
| | - Chiara Borsotti
- Department of Health Sciences, University of Eastern Piedmont Amedeo Avogadro, Novara, Italy
| | - Antonia Follenzi
- Department of Health Sciences, University of Eastern Piedmont Amedeo Avogadro, Novara, Italy
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Su H, Tang X, Zhang X, Liu L, Jing L, Pan D, Sun W, He H, Yang C, Zhao D, Zhang H, Qi B. Comparative proteomics analysis reveals the difference during antler regeneration stage between red deer and sika deer. PeerJ 2019; 7:e7299. [PMID: 31346498 PMCID: PMC6642628 DOI: 10.7717/peerj.7299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/14/2019] [Indexed: 12/21/2022] Open
Abstract
Deer antler, as the only mammalian regenerative appendage, provides an optimal model to study regenerative medicine. Antler harvested from red deer or sika deer were mainly study objects used to disclose the mechanism underlying antler regeneration over past decades. A previous study used proteomic technology to reveal the signaling pathways of antler stem cell derived from red deer. Moreover, transcriptome of antler tip from sika deer provide us with the essential genes, which regulated antler development and regeneration. However, antler comparison between red deer and sika deer has not been well studied. In our current study, proteomics were employed to analyze the biological difference of antler regeneration between sika deer and red deer. The proteomics profile was completed by searching the UniProt database, and differentially expressed proteins were identified by bioinformatic software. Thirty-six proteins were highly expressed in red deer antler, while 144 proteins were abundant in sika deer. GO and KEGG analysis revealed that differentially expressed proteins participated in the regulation of several pathways including oxidative phosphorylation, ribosome, extracellular matrix interaction, and PI3K-Akt pathway.
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Affiliation(s)
- Hang Su
- Practice Innovations Center, Changchun University of Chinese Medicine, Changchun, China
| | - Xiaolei Tang
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Xiaocui Zhang
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Li Liu
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Li Jing
- Practice Innovations Center, Changchun University of Chinese Medicine, Changchun, China
| | - Daian Pan
- School of Clinical Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Weijie Sun
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Huinan He
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Chonghui Yang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Daqing Zhao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - He Zhang
- School of Clinical Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Bin Qi
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
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The Best for the Most Important: Maintaining a Pristine Proteome in Stem and Progenitor Cells. Stem Cells Int 2019; 2019:1608787. [PMID: 31191665 PMCID: PMC6525796 DOI: 10.1155/2019/1608787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/05/2019] [Indexed: 12/19/2022] Open
Abstract
Pluripotent stem cells give rise to reproductively enabled offsprings by generating progressively lineage-restricted multipotent stem cells that would differentiate into lineage-committed stem and progenitor cells. These lineage-committed stem and progenitor cells give rise to all adult tissues and organs. Adult stem and progenitor cells are generated as part of the developmental program and play critical roles in tissue and organ maintenance and/or regeneration. The ability of pluripotent stem cells to self-renew, maintain pluripotency, and differentiate into a multicellular organism is highly dependent on sensing and integrating extracellular and extraorganismal cues. Proteins perform and integrate almost all cellular functions including signal transduction, regulation of gene expression, metabolism, and cell division and death. Therefore, maintenance of an appropriate mix of correctly folded proteins, a pristine proteome, is essential for proper stem cell function. The stem cells' proteome must be pristine because unfolded, misfolded, or otherwise damaged proteins would interfere with unlimited self-renewal, maintenance of pluripotency, differentiation into downstream lineages, and consequently with the development of properly functioning tissue and organs. Understanding how various stem cells generate and maintain a pristine proteome is therefore essential for exploiting their potential in regenerative medicine and possibly for the discovery of novel approaches for maintaining, propagating, and differentiating pluripotent, multipotent, and adult stem cells as well as induced pluripotent stem cells. In this review, we will summarize cellular networks used by various stem cells for generation and maintenance of a pristine proteome. We will also explore the coordination of these networks with one another and their integration with the gene regulatory and signaling networks.
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Abstract
Long thought to be too big and too ubiquitous to fail, we now know that human cells can fail to make sufficient amounts of ribosomes, causing a number of diseases collectively known as ribosomopathies. The best characterized ribosomopathies, with the exception of Treacher Collins syndrome, are inherited bone marrow failure syndromes, each of which has a marked increase in cancer predisposition relative to the general population. Although rare, emerging data reveal that the inherited bone marrow failure syndromes may be underdiagnosed on the basis of classical symptomology, leaving undiagnosed patients with these syndromes at an elevated risk of cancer without adequate counselling and surveillance. The link between the inherited ribosomopathies and cancer has led to greater awareness that somatic mutations in factors involved in ribosome biogenesis may also be drivers in sporadic cancers. Our goal here is to compare and contrast the pathophysiological mechanisms underpinning ribosomopathies to gain a better understanding of the mechanisms that predispose these disorders to cancer.
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Affiliation(s)
- Anna Aspesi
- Department of Health Sciences, University of Piemonte Orientale, Novara, Italy
| | - Steven R Ellis
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA.
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Abstract
Bone and marrow are the two facets of the same organ, in which bone and hematopoietic cells coexist and interact. Marrow and skeletal tissue influence each-other and a variety of genetic disorders directly targets both of them, which may result in combined hematopoietic failure and skeletal malformations. Other conditions primarily affect one organ with secondary influences on the other. For instance, various forms of congenital anemias reduce bone mass and induce osteoporosis, while osteoclast failure in osteopetrosis prevents marrow development reducing medullary cavities and causing anemia and pancytopenia. Understanding the pathophysiology of these conditions may facilitate diagnosis and management, although many disorders are presently incurable. This article describes several congenital bone diseases and their relationship to hematopoietic tissue.
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Affiliation(s)
- Anna Teti
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy.
| | - Steven L Teitelbaum
- Department of Medicine, Division of Bone and Mineral Diseases, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology and Immunology, Division of Anatomic and Molecular Pathology, Washington University School of Medicine, St. Louis, MO, USA
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Claassen D, Boals M, Bowling KM, Cooper GM, Cox J, Hershfield M, Lewis S, Wlodarski M, Weiss MJ, Estepp JH. Complexities of genetic diagnosis illustrated by an atypical case of congenital hypoplastic anemia. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a003384. [PMID: 30559313 PMCID: PMC6318771 DOI: 10.1101/mcs.a003384] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/29/2018] [Indexed: 11/24/2022] Open
Abstract
Diamond-Blackfan Anemia (DBA) is a rare polygenic disorder defined by congenital hypoplastic anemia with marked decrease or absence of bone marrow erythroid precursors. Identifying the specific genetic etiology is important for counseling and clinical management. A 6-yr-old boy with a clinical diagnosis of DBA has been followed by our pediatric hematology team since birth. His clinical course includes transfusion-dependent hypoplastic anemia and progressive autoimmune cytopenias. Genetic testing failed to identify a causative mutation in any of the classical DBA-associated genes. He and his parents underwent trio whole-exome sequencing (WES) with no genetic etiology identified initially. Clinical persistence and suspicion led to testing for adenosine deaminase 2 (ADA2) activity and whole-genome sequencing (WGS) that identified compound heterozygous pathogenic mutations in the ADA2-encoding CECR1 gene, a recently appreciated etiology for congenital hypoplastic anemia. This case illustrates current challenges in genetic testing and how they can be overcome by multidisciplinary expertise in clinical medicine and genomics.
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Affiliation(s)
- David Claassen
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Michelle Boals
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Jennifer Cox
- St. Jude Affiliate Clinic, Huntsville Hospital for Women and Children, Huntsville, Alabama 35801, USA
| | - Michael Hershfield
- Department of Medicine and Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Sara Lewis
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Marcin Wlodarski
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Jeremie H Estepp
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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Ulirsch JC, Verboon JM, Kazerounian S, Guo MH, Yuan D, Ludwig LS, Handsaker RE, Abdulhay NJ, Fiorini C, Genovese G, Lim ET, Cheng A, Cummings BB, Chao KR, Beggs AH, Genetti CA, Sieff CA, Newburger PE, Niewiadomska E, Matysiak M, Vlachos A, Lipton JM, Atsidaftos E, Glader B, Narla A, Gleizes PE, O'Donohue MF, Montel-Lehry N, Amor DJ, McCarroll SA, O'Donnell-Luria AH, Gupta N, Gabriel SB, MacArthur DG, Lander ES, Lek M, Da Costa L, Nathan DG, Korostelev AA, Do R, Sankaran VG, Gazda HT. The Genetic Landscape of Diamond-Blackfan Anemia. Am J Hum Genet 2018; 103:930-947. [PMID: 30503522 PMCID: PMC6288280 DOI: 10.1016/j.ajhg.2018.10.027] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/29/2018] [Indexed: 01/19/2023] Open
Abstract
Diamond-Blackfan anemia (DBA) is a rare bone marrow failure disorder that affects 7 out of 1,000,000 live births and has been associated with mutations in components of the ribosome. In order to characterize the genetic landscape of this heterogeneous disorder, we recruited a cohort of 472 individuals with a clinical diagnosis of DBA and performed whole-exome sequencing (WES). We identified relevant rare and predicted damaging mutations for 78% of individuals. The majority of mutations were singletons, absent from population databases, predicted to cause loss of function, and located in 1 of 19 previously reported ribosomal protein (RP)-encoding genes. Using exon coverage estimates, we identified and validated 31 deletions in RP genes. We also observed an enrichment for extended splice site mutations and validated their diverse effects using RNA sequencing in cell lines obtained from individuals with DBA. Leveraging the size of our cohort, we observed robust genotype-phenotype associations with congenital abnormalities and treatment outcomes. We further identified rare mutations in seven previously unreported RP genes that may cause DBA, as well as several distinct disorders that appear to phenocopy DBA, including nine individuals with biallelic CECR1 mutations that result in deficiency of ADA2. However, no new genes were identified at exome-wide significance, suggesting that there are no unidentified genes containing mutations readily identified by WES that explain >5% of DBA-affected case subjects. Overall, this report should inform not only clinical practice for DBA-affected individuals, but also the design and analysis of rare variant studies for heterogeneous Mendelian disorders.
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Affiliation(s)
- Jacob C Ulirsch
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Jeffrey M Verboon
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shideh Kazerounian
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael H Guo
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel Yuan
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Leif S Ludwig
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert E Handsaker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nour J Abdulhay
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Claudia Fiorini
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elaine T Lim
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aaron Cheng
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Beryl B Cummings
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine R Chao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alan H Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Casie A Genetti
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Colin A Sieff
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Peter E Newburger
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Edyta Niewiadomska
- Department of Pediatric Hematology/Oncology, Medical University of Warsaw, Warsaw, Poland
| | - Michal Matysiak
- Department of Pediatric Hematology/Oncology, Medical University of Warsaw, Warsaw, Poland
| | - Adrianna Vlachos
- Feinstein Institute for Medical Research, Manhasset, NY; Division of Hematology/Oncology and Stem Cell Transplantation, Cohen Children's Medical Center, New Hyde Park, NY; Hofstra Northwell School of Medicine, Hempstead, NY 11030, USA
| | - Jeffrey M Lipton
- Feinstein Institute for Medical Research, Manhasset, NY; Division of Hematology/Oncology and Stem Cell Transplantation, Cohen Children's Medical Center, New Hyde Park, NY; Hofstra Northwell School of Medicine, Hempstead, NY 11030, USA
| | - Eva Atsidaftos
- Feinstein Institute for Medical Research, Manhasset, NY; Division of Hematology/Oncology and Stem Cell Transplantation, Cohen Children's Medical Center, New Hyde Park, NY; Hofstra Northwell School of Medicine, Hempstead, NY 11030, USA
| | - Bertil Glader
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 02114, USA
| | - Anupama Narla
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 02114, USA
| | - Pierre-Emmanuel Gleizes
- Laboratory of Eukaryotic Molecular Biology, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France
| | - Marie-Françoise O'Donohue
- Laboratory of Eukaryotic Molecular Biology, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France
| | - Nathalie Montel-Lehry
- Laboratory of Eukaryotic Molecular Biology, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Anne H O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stacey B Gabriel
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Eric S Lander
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lydie Da Costa
- University Paris VII Denis DIDEROT, Faculté de Médecine Xavier Bichat, 75019 Paris, France; Laboratory of Excellence for Red Cell, LABEX GR-Ex, 75015 Paris, France
| | - David G Nathan
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Ron Do
- Department of Genetics and Genomic Sciences and The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
| | - Hanna T Gazda
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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Roberti D, Conforti R, Giugliano T, Brogna B, Tartaglione I, Casale M, Piluso G, Perrotta S. A Novel 12q13.2-q13.3 Microdeletion Syndrome With Combined Features of Diamond Blackfan Anemia, Pierre Robin Sequence and Klippel Feil Deformity. Front Genet 2018; 9:549. [PMID: 30524470 PMCID: PMC6262175 DOI: 10.3389/fgene.2018.00549] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/26/2018] [Indexed: 11/21/2022] Open
Abstract
Diamond-Blackfan anemia (DBA) is a rare congenital erythroid aplasia with a highly heterogeneous genetic background; it usually occurs in infancy. Approximately 30–40% of patients have other associated congenital anomalies; in particular, facial anomalies, such as cleft palate, are part of about 10% of the DBA clinical presentations. Pierre Robin sequence (PRS) is a heterogeneous condition, defined by the presence of the triad of glossoptosis, micrognathia and cleft palate; it occurs in 1/8500 to 1/14,000 births. Klippel Feil (KF) syndrome is a complex of both osseous and visceral anomalies, characterized mainly by congenital development defects of the cervical spine. We describe the case of a 22-years-old woman affected by DBA, carrying a de novo deletion about 500 Kb-long at 12q13.2-q13.3 that included RPS26 and, at least, others 25 flanking genes. The patient showed craniofacial anomalies due to PRS and suffered for KF deformities (type II). Computed Tomography study of cranio-cervical junction (CCJ) drew out severe bone malformations and congenital anomalies as atlanto-occipital assimilation (AOA), arcuate foramen and occipito-condylar hyperplasia. Foramen magnum was severely reduced. Atlanto-axial instability (AAI) was linked to atlanto-occipital assimilation, congenital vertebral fusion and occipito-condyle bone hyperplasia. Basilar invagination and platybasia were ruled out on CT and Magnetic Resonance Imaging (MRI) studies. Furthermore, the temporal Bone CT study showed anomalies of external auditory canals, absent mastoid pneumatization, chronic middle ear otitis and abnormal course of the facial nerve bones canal. The described phenotype might be related to the peculiar deletion affecting the patient, highlighting that genes involved in the in the breakdown of extracellular matrix (MMP19), in cell cycle regulation (CDK2), vesicular trafficking (RAB5B), in ribonucleoprotein complexes formation (ZC3H10) and muscles function (MYL6 and MYL6B) could be potentially related to bone-developmental disorders. Moreover, it points out that multiple associated ribosomal deficits might play a role in DBA-related phenotypes, considering the simultaneous deletion of three of them in the index case (RPS26, PA2G4 and RPL41), and it confirms the association among SLC39A5 functional disruption and severe myopia. This report highlights the need for a careful genetic evaluation and a detailed phenotype-genotype correlation in each complex malformative syndrome.
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Affiliation(s)
- Domenico Roberti
- Department of Woman, Child and General and Specialized Surgery, University of Campania "L. Vanvitelli" Naples, Italy
| | - Renata Conforti
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Naples, Italy
| | - Teresa Giugliano
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Naples, Italy
| | - Barbara Brogna
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Naples, Italy
| | - Immacolata Tartaglione
- Department of Woman, Child and General and Specialized Surgery, University of Campania "L. Vanvitelli" Naples, Italy
| | - Maddalena Casale
- Department of Woman, Child and General and Specialized Surgery, University of Campania "L. Vanvitelli" Naples, Italy
| | - Giulio Piluso
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Naples, Italy
| | - Silverio Perrotta
- Department of Woman, Child and General and Specialized Surgery, University of Campania "L. Vanvitelli" Naples, Italy
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Gianferante DM, Rotunno M, Dean M, Zhou W, Hicks BD, Wyatt K, Jones K, Wang M, Zhu B, Goldstein AM, Mirabello L. Whole-exome sequencing of nevoid basal cell carcinoma syndrome families and review of Human Gene Mutation Database PTCH1 mutation data. Mol Genet Genomic Med 2018; 6:1168-1180. [PMID: 30411536 PMCID: PMC6305672 DOI: 10.1002/mgg3.498] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/05/2018] [Accepted: 10/02/2018] [Indexed: 12/22/2022] Open
Abstract
Background Nevoid basal cell carcinoma syndrome (NBCCS) is an autosomal dominant disorder with variable expression and nearly complete penetrance. PTCH1 is the major susceptibility locus and has no known hot spots or genotype–phenotype relationships. Methods We evaluated 18 NBCCS National Cancer Institute (NCI) families plus PTCH1 data on 333 NBCCS disease‐causing mutations (DM) reported in the Human Gene Mutation Database (HGMD). National Cancer Institute families underwent comprehensive genomic evaluation, and clinical data were extracted from NCI and HGMD cases. Genotype–phenotype relationships were analyzed using Fisher's exact tests focusing on mutation type and PTCH1 domains. Results PTCH1 pathogenic mutations were identified in 16 of 18 NCI families, including three previously mutation‐negative families. PTCH1 mutations were spread across the gene with no hot spot. After adjustment for multiple tests, a statistically significant genotype–phenotype association was observed for developmental delay and gross deletion–insertions (p = 9.0 × 10−6), and suggestive associations between falx cerebri calcification and all transmembrane domains (p = 0.002) and severe outcomes and gross deletion–insertions (p = 4.0 × 10−4). Conclusion Overall, 89% of our NCI families had a pathogenic PTCH1 mutation. The identification of PTCH1 mutations in previously mutation‐negative families underscores the importance of repeated testing when new technologies become available. Additional clinical information linked to mutation databases would enhance follow‐up and future studies of genotype–phenotype relationships.
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Affiliation(s)
- D Matthew Gianferante
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Melissa Rotunno
- Division of Cancer Control and Population Science, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Weiyin Zhou
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Belynda D Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Kathleen Wyatt
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Mingyi Wang
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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45
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Aubert M, O'Donohue MF, Lebaron S, Gleizes PE. Pre-Ribosomal RNA Processing in Human Cells: From Mechanisms to Congenital Diseases. Biomolecules 2018; 8:biom8040123. [PMID: 30356013 PMCID: PMC6315592 DOI: 10.3390/biom8040123] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 12/15/2022] Open
Abstract
Ribosomal RNAs, the most abundant cellular RNA species, have evolved as the structural scaffold and the catalytic center of protein synthesis in every living organism. In eukaryotes, they are produced from a long primary transcript through an intricate sequence of processing steps that include RNA cleavage and folding and nucleotide modification. The mechanisms underlying this process in human cells have long been investigated, but technological advances have accelerated their study in the past decade. In addition, the association of congenital diseases to defects in ribosome synthesis has highlighted the central place of ribosomal RNA maturation in cell physiology regulation and broadened the interest in these mechanisms. Here, we give an overview of the current knowledge of pre-ribosomal RNA processing in human cells in light of recent progress and discuss how dysfunction of this pathway may contribute to the physiopathology of congenital diseases.
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Affiliation(s)
- Maxime Aubert
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Simon Lebaron
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
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Griffin JN, Sondalle SB, Robson A, Mis EK, Griffin G, Kulkarni SS, Deniz E, Baserga SJ, Khokha MK. RPSA, a candidate gene for isolated congenital asplenia, is required for pre-rRNA processing and spleen formation in Xenopus. Development 2018; 145:145/20/dev166181. [PMID: 30337486 DOI: 10.1242/dev.166181] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/13/2018] [Indexed: 12/14/2022]
Abstract
A growing number of tissue-specific inherited disorders are associated with impaired ribosome production, despite the universal requirement for ribosome function. Recently, mutations in RPSA, a protein component of the small ribosomal subunit, were discovered to underlie approximately half of all isolated congenital asplenia cases. However, the mechanisms by which mutations in this ribosome biogenesis factor lead specifically to spleen agenesis remain unknown, in part due to the lack of a suitable animal model for study. Here we reveal that RPSA is required for normal spleen development in the frog, Xenopus tropicalis Depletion of Rpsa in early embryonic development disrupts pre-rRNA processing and ribosome biogenesis, and impairs expression of the key spleen patterning genes nkx2-5, bapx1 and pod1 in the spleen anlage. Importantly, we also show that whereas injection of human RPSA mRNA can rescue both pre-rRNA processing and spleen patterning, injection of human mRNA bearing a common disease-associated mutation cannot. Together, we present the first animal model of RPSA-mediated asplenia and reveal a crucial requirement for RPSA in pre-rRNA processing and molecular patterning during early Xenopus development.
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Affiliation(s)
- John N Griffin
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Samuel B Sondalle
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Andrew Robson
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Emily K Mis
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Gerald Griffin
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Saurabh S Kulkarni
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Engin Deniz
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Susan J Baserga
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA .,Departments of Molecular Biophysics and Biochemistry, and Therapeutic Radiology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA .,Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
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47
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James CC, Smyth JW. Alternative mechanisms of translation initiation: An emerging dynamic regulator of the proteome in health and disease. Life Sci 2018; 212:138-144. [PMID: 30290184 DOI: 10.1016/j.lfs.2018.09.054] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/18/2018] [Accepted: 09/27/2018] [Indexed: 01/06/2023]
Abstract
Eukaryotic mRNAs were historically thought to rely exclusively on recognition and binding of their 5' cap by initiation factors to effect protein translation. While internal ribosome entry sites (IRESs) are well accepted as necessary for the cap-independent translation of many viral genomes, there is now recognition that eukaryotic mRNAs also undergo non-canonical modes of translation initiation. Recently, high-throughput assays have identified thousands of mammalian transcripts with translation initiation occurring at non-canonical start codons, upstream of and within protein coding regions. In addition to IRES-mediated events, regulatory mechanisms of translation initiation have been described involving alternate 5' cap recognition, mRNA sequence elements, and ribosome selection. These mechanisms ensure translation of specific mRNAs under conditions where cap-dependent translation is shut down and contribute to pathological states including cardiac hypertrophy and cancer. Such global and gene-specific dynamic regulation of translation presents us with an increasing number of novel therapeutic targets. While these newly discovered modes of translation initiation have been largely studied in isolation, it is likely that several act on the same mRNA and exquisite coordination is necessary to maintain 'normal' translation. In this short review, we summarize the current state of knowledge of these alternative mechanisms of eukaryotic protein translation, their contribution to normal and pathological cell biology, and the potential of targeting translation initiation therapeutically in human disease.
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Affiliation(s)
- Carissa C James
- Virginia Tech Carilion Research Institute and School of Medicine, Roanoke, VA, USA; Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA, USA; Center for Heart and Regenerative Medicine, Virginia Tech Carilion Research Institute, Roanoke, VA, USA
| | - James W Smyth
- Virginia Tech Carilion Research Institute and School of Medicine, Roanoke, VA, USA; Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA; Center for Heart and Regenerative Medicine, Virginia Tech Carilion Research Institute, Roanoke, VA, USA.
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48
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Jongmans MCJ, Diets IJ, Quarello P, Garelli E, Kuiper RP, Pfundt R. Somatic reversion events point towards RPL4 as a novel disease gene in a condition resembling Diamond-Blackfan anemia. Haematologica 2018; 103:e607-e609. [PMID: 30213830 DOI: 10.3324/haematol.2018.200683] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Marjolijn C J Jongmans
- Department of Human Genetics, Radboud university medical center and Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands .,Department of Medical Genetics, University Medical Center Utrecht, the Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Illja J Diets
- Department of Human Genetics, Radboud university medical center and Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Paola Quarello
- Paediatric Onco-Haematology, Stem Cell Transplantation and Cellular Therapy Division, Regina Margherita Children's Hospital, Torino, Italy
| | - Emanuela Garelli
- Department of Public Health and Paediatric Sciences, University of Torino, Italy
| | - Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud university medical center and Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
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49
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Abstract
Diamond–Blackfan anemia (DBA) is a rare congenital hypoplastic anemia characterized by a block in erythropoiesis at the progenitor stage, although the exact stage at which this occurs remains to be fully defined. DBA presents primarily during infancy with macrocytic anemia and reticulocytopenia with 50% of cases associated with a variety of congenital malformations. DBA is most frequently due to a sporadic mutation (55%) in genes encoding several different ribosomal proteins, although there are many cases where there is a family history of the disease with varying phenotypes. The erythroid tropism of the disease is still a matter of debate for a disease related to a defect in global ribosome biogenesis. Assessment of biological features in conjunction with genetic testing has increased the accuracy of the diagnosis of DBA. However, in certain cases, it continues to be difficult to firmly establish a diagnosis. This review will focus on the diagnosis of DBA along with a description of new advances in our understanding of the pathophysiology and treatment recommendations for DBA.
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Affiliation(s)
- Lydie Da Costa
- Université Paris 7 Denis Diderot-Sorbonne, Paris, France.,AP-HP, Hematology laboratory, Robert Debré Hospital, Paris, France.,INSERM UMR1134, Paris, France.,Laboratory of Excellence for Red Cell, LABEX GR-Ex, Paris, France
| | - Anupama Narla
- Stanford University School of Medicine, Stanford, USA
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50
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Incomplete penetrance for isolated congenital asplenia in humans with mutations in translated and untranslated RPSA exons. Proc Natl Acad Sci U S A 2018; 115:E8007-E8016. [PMID: 30072435 DOI: 10.1073/pnas.1805437115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Isolated congenital asplenia (ICA) is the only known human developmental defect exclusively affecting a lymphoid organ. In 2013, we showed that private deleterious mutations in the protein-coding region of RPSA, encoding ribosomal protein SA, caused ICA by haploinsufficiency with complete penetrance. We reported seven heterozygous protein-coding mutations in 8 of the 23 kindreds studied, including 6 of the 8 multiplex kindreds. We have since enrolled 33 new kindreds, 5 of which are multiplex. We describe here 11 new heterozygous ICA-causing RPSA protein-coding mutations, and the first two mutations in the 5'-UTR of this gene, which disrupt mRNA splicing. Overall, 40 of the 73 ICA patients (55%) and 23 of the 56 kindreds (41%) carry mutations located in translated or untranslated exons of RPSA. Eleven of the 43 kindreds affected by sporadic disease (26%) carry RPSA mutations, whereas 12 of the 13 multiplex kindreds (92%) carry RPSA mutations. We also report that 6 of 18 (33%) protein-coding mutations and the two (100%) 5'-UTR mutations display incomplete penetrance. Three mutations were identified in two independent kindreds, due to a hotspot or a founder effect. Finally, RPSA ICA-causing mutations were demonstrated to be de novo in 7 of the 23 probands. Mutations in RPSA exons can affect the translated or untranslated regions and can underlie ICA with complete or incomplete penetrance.
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