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Stillinovic M, Sarangdhar MA, Andina N, Tardivel A, Greub F, Bombaci G, Ansermet C, Zatti M, Saha D, Xiong J, Sagae T, Yokogawa M, Osawa M, Heller M, Keogh A, Keller I, Angelillo-Scherrer A, Allam R. Ribonuclease inhibitor and angiogenin system regulates cell type-specific global translation. SCIENCE ADVANCES 2024; 10:eadl0320. [PMID: 38820160 DOI: 10.1126/sciadv.adl0320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/30/2024] [Indexed: 06/02/2024]
Abstract
Translation of mRNAs is a fundamental process that occurs in all cell types of multicellular organisms. Conventionally, it has been considered a default step in gene expression, lacking specific regulation. However, recent studies have documented that certain mRNAs exhibit cell type-specific translation. Despite this, it remains unclear whether global translation is controlled in a cell type-specific manner. By using human cell lines and mouse models, we found that deletion of the ribosome-associated protein ribonuclease inhibitor 1 (RNH1) decreases global translation selectively in hematopoietic-origin cells but not in the non-hematopoietic-origin cells. RNH1-mediated cell type-specific translation is mechanistically linked to angiogenin-induced ribosomal biogenesis. Collectively, this study unravels the existence of cell type-specific global translation regulators and highlights the complex translation regulation in vertebrates.
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Affiliation(s)
- Martina Stillinovic
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Mayuresh Anant Sarangdhar
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Nicola Andina
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Aubry Tardivel
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Frédéric Greub
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Giuseppe Bombaci
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Camille Ansermet
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Marco Zatti
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Dipanjali Saha
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Jieyu Xiong
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Takeru Sagae
- Graduate School of Pharmaceutical Sciences, Keio University, Minato-ku, Tokyo, Japan
| | - Mariko Yokogawa
- Graduate School of Pharmaceutical Sciences, Keio University, Minato-ku, Tokyo, Japan
| | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, Keio University, Minato-ku, Tokyo, Japan
| | - Manfred Heller
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Adrian Keogh
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Irene Keller
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Anne Angelillo-Scherrer
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Ramanjaneyulu Allam
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
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Xiao R, Zhang L, Xin Z, Zhu J, Zhang Q, Zheng G, Chu S, Wu J, Zhang L, Wan Y, Chen X, Yuan W, Zhang Z, Zhu X, Fang X. Disruption of mitochondrial energy metabolism is a putative pathogenesis of Diamond-Blackfan anemia. iScience 2024; 27:109172. [PMID: 38414864 PMCID: PMC10897903 DOI: 10.1016/j.isci.2024.109172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/23/2023] [Accepted: 02/06/2024] [Indexed: 02/29/2024] Open
Abstract
Energy metabolism in the context of erythropoiesis and related diseases remains largely unexplored. Here, we developed a primary cell model by differentiating hematopoietic stem progenitor cells toward the erythroid lineage and suppressing the mitochondrial oxidative phosphorylation (OXPHOS) pathway. OXPHOS suppression led to differentiation failure of erythroid progenitors and defects in ribosome biogenesis. Ran GTPase-activating protein 1 (RanGAP1) was identified as a target of mitochondrial OXPHOS for ribosomal defects during erythropoiesis. Overexpression of RanGAP1 largely alleviated erythroid defects resulting from OXPHOS suppression. Coenzyme Q10, an activator of OXPHOS, largely rescued erythroid defects and increased RanGAP1 expression. Patients with Diamond-Blackfan anemia (DBA) exhibited OXPHOS suppression and a concomitant suppression of ribosome biogenesis. RNA-seq analysis implied that the substantial mutation (approximately 10%) in OXPHOS genes accounts for OXPHOS suppression in these patients. Conclusively, OXPHOS disruption and the associated disruptive mitochondrial energy metabolism are linked to the pathogenesis of DBA.
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Affiliation(s)
- Rudan Xiao
- Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing 100101, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Lijuan Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing 100101, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Zijuan Xin
- Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing 100101, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Junwei Zhu
- Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing 100101, P.R. China
| | - Qian Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing 100101, P.R. China
| | - Guangmin Zheng
- Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing 100101, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Siyun Chu
- Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing 100101, P.R. China
| | - Jing Wu
- Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing 100101, P.R. China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, P.R. China
| | - Lu Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing 100101, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Yang Wan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Xiaojuan Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Weiping Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Zhaojun Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing 100101, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, P.R. China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, P.R. China
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, P.R. China
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Xiangdong Fang
- Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation, Beijing 100101, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, P.R. China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, P.R. China
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, P.R. China
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3
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Warden CD, Wu X. Critical Differential Expression Assessment for Individual Bulk RNA-Seq Projects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579728. [PMID: 38405814 PMCID: PMC10888899 DOI: 10.1101/2024.02.10.579728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Finding the right balance of quality and quantity can be important, and it is essential that project quality does not drop below the level where important main conclusions are missed or misstated. We use knock-out and over-expression studies as a simplification to test recovery of a known causal gene in RNA-Seq cell line experiments. When single-end RNA-Seq reads are aligned with STAR and quantified with htseq-count, we found potential value in testing the use of the Generalized Linear Model (GLM) implementation of edgeR with robust dispersion estimation more frequently for either single-variate or multi-variate 2-group comparisons (with the possibility of defining criteria less stringent than |fold-change| > 1.5 and FDR < 0.05). When considering a limited number of patient sample comparisons with larger sample size, there might be some decreased variability between methods (except for DESeq1). However, at the same time, the ranking of the gene identified using immunohistochemistry (for ER/PR/HER2 in breast cancer samples from The Cancer Genome Atlas) showed as possible shift in performance compared to the cell line comparisons, potentially highlighting utility for standard statistical tests and/or limma-based analysis with larger sample sizes. If this continues to be true in additional studies and comparisons, then that could be consistent with the possibility that it may be important to allocate time for potential methods troubleshooting for genomics projects. Analysis of public data presented in this study does not consider all experimental designs, and presentation of downstream analysis is limited. So, any estimate from this simplification would be an underestimation of the true need for some methods testing for every project. Additionally, this set of independent cell line experiments has a limitation in being able to determine the frequency of missing a highly important gene if the problem is rare (such as 10% or lower). For example, if there was an assumption that only one method can be tested for "initial" analysis, then it is not completely clear to the extent that using edgeR-robust might perform better than DESeq2 in the cell line experiments. Importantly, we do not wish to cause undue concern, and we believe that it should often be possible to define a gene expression differential expression workflow that is suitable for some purposes for many samples. Nevertheless, at the same time, we provide a variety of measures that we believe emphasize the need to critically assess every individual project and maximize confidence in published results.
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Affiliation(s)
- Charles D Warden
- Integrative Genomics Core, Department of Molecular and Cellular Biology, City of Hope National Medical Center, Duarte, CA
| | - Xiwei Wu
- Integrative Genomics Core, Department of Molecular and Cellular Biology, City of Hope National Medical Center, Duarte, CA
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Sarangdhar MA, Andina N, Allam R. Human molecular genetics sheds light on the physiological significance of ribonuclease inhibitor (RNH1). Eur J Hum Genet 2023:10.1038/s41431-023-01362-4. [PMID: 37085604 PMCID: PMC10400534 DOI: 10.1038/s41431-023-01362-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023] Open
Affiliation(s)
- Mayuresh Anant Sarangdhar
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
| | - Nicola Andina
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Ramanjaneyulu Allam
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
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5
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Ribonuclease inhibitor 1 (RNH1) deficiency cause congenital cataracts and global developmental delay with infection-induced psychomotor regression and anemia. Eur J Hum Genet 2023:10.1038/s41431-023-01327-7. [PMID: 36935417 PMCID: PMC10400601 DOI: 10.1038/s41431-023-01327-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 03/21/2023] Open
Abstract
Ribonuclease inhibitor 1, also known as angiogenin inhibitor 1, encoded by RNH1, is a ubiquitously expressed leucine-rich repeat protein, which is highly conserved in mammalian species. Inactivation of rnh1 in mice causes an embryonically lethal anemia, but the exact biological function of RNH1 in humans remains unknown and no human genetic disease has so far been associated with RNH1. Here, we describe a family with two out of seven siblings affected by a disease characterized by congenital cataract, global developmental delay, myopathy and psychomotor deterioration, seizures and periodic anemia associated with upper respiratory tract infections. A homozygous splice-site variant (c.615-2A > C) in RNH1 segregated with the disease. Sequencing of RNA derived from patient fibroblasts and cDNA analysis of skeletal muscle mRNA showed aberrant splicing with skipping of exon 7. Western blot analysis revealed a total lack of the RNH1 protein. Functional analysis revealed that patient fibroblasts were more sensitive to RNase A exposure, and this phenotype was reversed by transduction with a lentivirus expressing RNH1 to complement patient cells. Our results demonstrate that loss-of-function of RNH1 in humans is associated with a multiorgan developmental disease with recessive inheritance. It may be speculated that the infection-induced deterioration resulted from an increased susceptibility toward extracellular RNases and/or other inflammatory responses normally kept in place by the RNase inhibitor RNH1.
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Exploring the mechanistic link between SF3B1 mutation and ring sideroblast formation in myelodysplastic syndrome. Sci Rep 2022; 12:14562. [PMID: 36028755 PMCID: PMC9418223 DOI: 10.1038/s41598-022-18921-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/22/2022] [Indexed: 12/02/2022] Open
Abstract
Acquired sideroblastic anemia, characterized by bone marrow ring sideroblasts (RS), is predominantly associated with myelodysplastic syndrome (MDS). Although somatic mutations in splicing factor 3b subunit 1 (SF3B1), which is involved in the RNA splicing machinery, are frequently found in MDS-RS, the detailed mechanism contributing to RS formation is unknown. To explore the mechanism, we established human umbilical cord blood-derived erythroid progenitor-2 (HUDEP-2) cells stably expressing SF3B1K700E. SF3B1K700E expressing cells showed higher proportion of RS than the control cells along with erythroid differentiation, indicating the direct contribution of mutant SF3B1 expression in erythroblasts to RS formation. In SF3B1K700E expressing cells, ABCB7 and ALAS2, known causative genes for congenital sideroblastic anemia, were downregulated. Additionally, mis-splicing of ABCB7 was observed in SF3B1K700E expressing cells. ABCB7-knockdown HUDEP-2 cells revealed an increased frequency of RS formation along with erythroid differentiation, demonstrating the direct molecular link between ABCB7 defects and RS formation. ALAS2 protein levels were obviously decreased in ABCB7-knockdown cells, indicating decreased ALAS2 translation owing to impaired Fe–S cluster export by ABCB7 defects. Finally, RNA-seq analysis of MDS clinical samples demonstrated decreased expression of ABCB7 by the SF3B1 mutation. Our findings contribute to the elucidation of the complex mechanisms of RS formation in MDS-RS.
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Bombaci G, Sarangdhar MA, Andina N, Tardivel A, Yu ECW, Mackie GM, Pugh M, Ozan VB, Banz Y, Spinetti T, Hirzel C, Youd E, Schefold JC, Taylor G, Gazdhar A, Bonadies N, Angelillo-Scherrer A, Schneider P, Maslowski KM, Allam R. LRR-protein RNH1 dampens the inflammasome activation and is associated with COVID-19 severity. Life Sci Alliance 2022; 5:5/6/e202101226. [PMID: 35256513 PMCID: PMC8922048 DOI: 10.26508/lsa.202101226] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/12/2022] Open
Abstract
RNH1 prevents inflammation by inhibiting inflammasome activation through controlling caspase-1 protein levels. In COVID-19 patients, RNH1 expression levels were negatively associated with disease severity and inflammation, suggesting a role for RNH1 in SARS-CoV-2–mediated inflammation and pathology. Inflammasomes are cytosolic innate immune sensors of pathogen infection and cellular damage that induce caspase-1–mediated inflammation upon activation. Although inflammation is protective, uncontrolled excessive inflammation can cause inflammatory diseases and can be detrimental, such as in coronavirus disease (COVID-19). However, the underlying mechanisms that control inflammasome activation are incompletely understood. Here we report that the leucine-rich repeat (LRR) protein ribonuclease inhibitor (RNH1), which shares homology with LRRs of NLRP (nucleotide-binding oligomerization domain, leucine-rich repeat, and pyrin domain containing) proteins, attenuates inflammasome activation. Deletion of RNH1 in macrophages increases interleukin (IL)-1β production and caspase-1 activation in response to inflammasome stimulation. Mechanistically, RNH1 decreases pro-IL-1β expression and induces proteasome-mediated caspase-1 degradation. Corroborating this, mouse models of monosodium urate (MSU)-induced peritonitis and lipopolysaccharide (LPS)-induced endotoxemia, which are dependent on caspase-1, respectively, show increased neutrophil infiltration and lethality in Rnh1−/− mice compared with wild-type mice. Furthermore, RNH1 protein levels were negatively related with disease severity and inflammation in hospitalized COVID-19 patients. We propose that RNH1 is a new inflammasome regulator with relevance to COVID-19 severity.
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Affiliation(s)
- Giuseppe Bombaci
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Mayuresh Anant Sarangdhar
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Nicola Andina
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Aubry Tardivel
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Eric Chi-Wang Yu
- Department of Biochemistry, University of Lausanne, Lausanne, Switzerland
| | - Gillian M Mackie
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Matthew Pugh
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Vedat Burak Ozan
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Yara Banz
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Thibaud Spinetti
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Cedric Hirzel
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Esther Youd
- School of Medicine, Dentistry and Nursing, Forensic Medicine and Science. University of Glasgow, Scotland, UK
| | - Joerg C Schefold
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Graham Taylor
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Amiq Gazdhar
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Nicolas Bonadies
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Anne Angelillo-Scherrer
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Pascal Schneider
- Department of Biochemistry, University of Lausanne, Lausanne, Switzerland
| | - Kendle M Maslowski
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Ramanjaneyulu Allam
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
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Wen JT, Huang ZH, Li QH, Chen X, Qin HL, Zhao Y. Research progress on the tsRNA classification, function, and application in gynecological malignant tumors. Cell Death Discov 2021; 7:388. [PMID: 34907180 PMCID: PMC8671397 DOI: 10.1038/s41420-021-00789-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/18/2021] [Accepted: 11/29/2021] [Indexed: 12/21/2022] Open
Abstract
A large number of small non-coding RNAs derived from tRNAs, called tRNA-derived small RNA (tsRNAs), have been identified by high-throughput RNA sequencing of cell lines. Further research has revealed that they are not produced via random tRNA degradation, but through degradation by specific nuclease cleavages, such as Elac Ribonuclease Z 2 (ELAC2)/RNase Z, RNase L, Dicer, and angiogenin (ANG), the tsRNAs can be classified into the following types based on the location from which they have been derived from the parental tRNA: tRF-1s, tRF-3s, tRF-5s, tiRNA, and tRF-2s/i-tRFs. Moreover, tsRNAs are a type of small RNAs with diverse functions, including gene expression regulation, anti-apoptosis, translation inhibition, participation in epigenetic regulation, initial virus reverse transcription, promote virus replication and cell-to-cell communication. Certain types of tsRNAs are overexpressed in cancer tissues, but are underexpressed in normal tissues. Therefore, the relationship between tsRNAs and the occurrence and development of cancer has attracted significant research attention. Research advancements have contributed to further discoveries of the biological activities of tsRNAs, but the mechanisms of their biogenesis and functions have not been fully elucidated. This article reviews the classification and biological functions of tsRNAs, and introduces the research progress in gynecological malignancies.
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Affiliation(s)
- Jing-Tao Wen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Zheng-Hao Huang
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Qian-Hui Li
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Xi Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Hong-Lei Qin
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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9
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Saba JA, Liakath-Ali K, Green R, Watt FM. Translational control of stem cell function. Nat Rev Mol Cell Biol 2021; 22:671-690. [PMID: 34272502 DOI: 10.1038/s41580-021-00386-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 12/22/2022]
Abstract
Stem cells are characterized by their ability to self-renew and differentiate into many different cell types. Research has focused primarily on how these processes are regulated at a transcriptional level. However, recent studies have indicated that stem cell behaviour is strongly coupled to the regulation of protein synthesis by the ribosome. In this Review, we discuss how different translation mechanisms control the function of adult and embryonic stem cells. Stem cells are characterized by low global translation rates despite high levels of ribosome biogenesis. The maintenance of pluripotency, the commitment to a specific cell fate and the switch to cell differentiation depend on the tight regulation of protein synthesis and ribosome biogenesis. Translation regulatory mechanisms that impact on stem cell function include mTOR signalling, ribosome levels, and mRNA and tRNA features and amounts. Understanding these mechanisms important for stem cell self-renewal and differentiation may also guide our understanding of cancer grade and metastasis.
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Affiliation(s)
- James A Saba
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kifayathullah Liakath-Ali
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Fiona M Watt
- King's College London Centre for Stem Cells and Regenerative Medicine, Guy's Hospital, London, UK.
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10
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Lin X, Dinglin X, Cao S, Zheng S, Wu C, Chen W, Li Q, Hu Q, Zheng F, Wu Z, Lin DC, Yao Y, Xu X, Xie Z, Liu Q, Yao H, Hu H. Enhancer-Driven lncRNA BDNF-AS Induces Endocrine Resistance and Malignant Progression of Breast Cancer through the RNH1/TRIM21/mTOR Cascade. Cell Rep 2021; 31:107753. [PMID: 32521278 DOI: 10.1016/j.celrep.2020.107753] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/20/2020] [Accepted: 05/19/2020] [Indexed: 12/12/2022] Open
Abstract
Epigenomic alterations can give rise to various tumor-promoting properties, including therapeutic resistance of cancer cells. Here, we identify an lncRNA, BDNF-AS, whose overexpression is specifically driven by a MEF2A-regulated enhancer in endocrine-resistant and triple-negative breast cancer (TNBC). High levels of BDNF-AS in breast cancer tissues not only feature endocrine resistance in hormone receptor (HR)-positive patients but also correlate with poor outcomes in both HR-positive and TNBC patients. Mechanistically, BDNF-AS acts as a molecular scaffold to promote RNH1 protein degradation via TRIM21-mediated ubiquitination of RNH1 at K225. Subsequently, BDNF-AS abolishes RNH1-regulated and RISC-mediated mTOR mRNA decay, therefore sustaining the activation of mTOR signaling. Importantly, mTOR inhibitor, but not PI3K inhibitor, could reverse tamoxifen resistance induced by the overexpression of BDNF-AS. These results point toward a master regulatory role of an enhancer-activated cascade of BDNF-AS/RNH1/TRIM21/mTOR in endocrine resistance and malignant progression of breast cancer.
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Affiliation(s)
- Xiaorong Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China; Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China; Diagnosis and Treatment Center of Breast Diseases, Shantou Affiliated Hospital, Sun Yat-sen University, Shantou 515031, People's Republic of China
| | - Xiaoxiao Dinglin
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China
| | - Siting Cao
- Department of Endocrinology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510030, People's Republic of China
| | - Senyou Zheng
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China
| | - Cheng Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510663, People's Republic of China
| | - Wenying Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China; Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China
| | - Qingjian Li
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China
| | - Qian Hu
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China
| | - Fang Zheng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China
| | - Zhiyong Wu
- Diagnosis and Treatment Center of Breast Diseases, Shantou Affiliated Hospital, Sun Yat-sen University, Shantou 515031, People's Republic of China
| | - De-Chen Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China
| | - Yandan Yao
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China
| | - Xiaoding Xu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510663, People's Republic of China
| | - Qiang Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China; Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China
| | - Herui Yao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China; Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China.
| | - Hai Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China; Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China.
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11
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Angiogenin (ANG)-Ribonuclease Inhibitor (RNH1) System in Protein Synthesis and Disease. Int J Mol Sci 2021; 22:ijms22031287. [PMID: 33525475 PMCID: PMC7866052 DOI: 10.3390/ijms22031287] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 12/16/2022] Open
Abstract
Protein synthesis is a highly complex process executed by well-organized translation machinery. Ribosomes, tRNAs and mRNAs are the principal components of this machinery whereas RNA binding proteins and ribosome interacting partners act as accessory factors. Angiogenin (ANG)-Ribonuclease inhibitor (RNH1) system is one such accessory part of the translation machinery that came into focus afresh due to its unconventional role in the translation. ANG is conventionally known for its ability to induce blood vessel formation and RNH1 as a "sentry" to protect RNAs from extracellular RNases. However, recent studies suggest them to be important in translation regulation. During cell homeostasis, ANG in the nucleus promotes rRNA transcription. While under stress, ANG translocates to the cytosol and cleaves tRNA into fragments which inhibit ribosome biogenesis and protein synthesis. RNH1, which intimately interacts with ANG to inhibit its ribonucleolytic activity, can also bind to the 40S ribosomes and control translation by yet to be known mechanisms. Here, we review recent advancement in the knowledge of translation regulation by the ANG-RNH1 system. We also gather information about this system in cell homeostasis as well as in pathological conditions such as cancer and ribosomopathies. Additionally, we discuss the future research directions and therapeutic potential of this system.
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12
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Da Costa L, Leblanc T, Mohandas N. Diamond-Blackfan anemia. Blood 2020; 136:1262-1273. [PMID: 32702755 PMCID: PMC7483438 DOI: 10.1182/blood.2019000947] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/30/2019] [Indexed: 12/15/2022] Open
Abstract
Diamond-Blackfan anemia (DBA) was the first ribosomopathy described and is a constitutional inherited bone marrow failure syndrome. Erythroblastopenia is the major characteristic of the disease, which is a model for ribosomal diseases, related to a heterozygous allelic variation in 1 of the 20 ribosomal protein genes of either the small or large ribosomal subunit. The salient feature of classical DBA is a defect in ribosomal RNA maturation that generates nucleolar stress, leading to stabilization of p53 and activation of its targets, resulting in cell-cycle arrest and apoptosis. Although activation of p53 may not explain all aspects of DBA erythroid tropism, involvement of GATA1/HSP70 and globin/heme imbalance, with an excess of the toxic free heme leading to reactive oxygen species production, account for defective erythropoiesis in DBA. Despite significant progress in defining the molecular basis of DBA and increased understanding of the mechanistic basis for DBA pathophysiology, progress in developing new therapeutic options has been limited. However, recent advances in gene therapy, better outcomes with stem cell transplantation, and discoveries of putative new drugs through systematic drug screening using large chemical libraries provide hope for improvement.
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MESH Headings
- Abnormalities, Multiple/genetics
- Adenosine Deaminase/blood
- Adenosine Deaminase/genetics
- Anemia, Diamond-Blackfan/diagnosis
- Anemia, Diamond-Blackfan/genetics
- Anemia, Diamond-Blackfan/metabolism
- Anemia, Diamond-Blackfan/therapy
- Child, Preschool
- Congenital Abnormalities/genetics
- Diagnosis, Differential
- Disease Management
- Drug Resistance
- Erythrocytes/enzymology
- Fetal Growth Retardation/etiology
- GATA1 Transcription Factor/genetics
- GATA1 Transcription Factor/physiology
- Genetic Heterogeneity
- Genetic Therapy
- Glucocorticoids/therapeutic use
- HSP70 Heat-Shock Proteins/metabolism
- Hematopoietic Stem Cell Transplantation
- Humans
- Infant
- Infant, Newborn
- Intercellular Signaling Peptides and Proteins/blood
- Intercellular Signaling Peptides and Proteins/genetics
- Models, Biological
- Mutation
- Neoplastic Syndromes, Hereditary/genetics
- Ribosomal Proteins/genetics
- Ribosomal Proteins/physiology
- Tumor Suppressor Protein p53/physiology
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Affiliation(s)
- Lydie Da Costa
- Service d'Hématologie Biologique, Hôpital Robert-Debré, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- U1134, Université Paris, Paris, France
- Laboratoire d'Excellence GR-Ex, Paris, France
| | - Thierry Leblanc
- Service d'Immuno-Hématologie Pédiatrique, Hôpital Robert-Debré, AP-HP, Paris, France; and
| | - Narla Mohandas
- Laboratory of Red Cell Physiology, New York Blood Center, New York, NY
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13
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Cammayo PLT, Fernandez-Colorado CP, Flores RA, Roy A, Kim S, Lillehoj HS, Kim WH, Min W. IL-17A treatment influences murine susceptibility to experimental Riemerella anatipestifer infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 106:103633. [PMID: 31991165 DOI: 10.1016/j.dci.2020.103633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
Riemerella anatipestifer causes infectious disease and considerable economic loss in the duck industry worldwide. Our previous studies demonstrated an association between proinflammatory cytokine interleukin (IL)-17A and R. anatipestifer infection. Here, we provide evidence for IL-17A involvement in R. anatipestifer infection using a mouse model. Mice showed higher resistance to R. anatipestifer infection than ducks, with median lethal doses (LD50) of 3.5 × 1010 and 5 × 107 colony-forming units (CFU), respectively. Twenty-four hours after infection, mice with a sub-lethal dose (3.5 × 109 CFU) exhibited levels of IL-17A and IL-23 expression similar to uninfected mice. Thus, we hypothesized that exogenous IL-17A or IL-23 administration affects susceptibility of mice to R. anatipestifer. Mice pretreated with IL-17A or IL-23 prior to sub-lethal dose infection of R. anatipestifer exhibited increased bacterial burden and spleen weights compared to untreated infected mice, confirming the involvement of IL-17A in susceptibility to R. anatipestifer infection in vivo.
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Affiliation(s)
- Paula Leona T Cammayo
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Cherry P Fernandez-Colorado
- Department of Veterinary Paraclinical Sciences, College of Veterinary Medicine, University of the Philippines Los Banos, College, Laguna, 4031, Philippines
| | - Rochelle A Flores
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Anindita Roy
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Suk Kim
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Hyun S Lillehoj
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, 20705, USA
| | - Woo H Kim
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, 20705, USA
| | - Wongi Min
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju, 52828, Republic of Korea.
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14
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Gutiérrez L, Caballero N, Fernández-Calleja L, Karkoulia E, Strouboulis J. Regulation of GATA1 levels in erythropoiesis. IUBMB Life 2019; 72:89-105. [PMID: 31769197 DOI: 10.1002/iub.2192] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/14/2019] [Indexed: 12/15/2022]
Abstract
GATA1 is considered as the "master" transcription factor in erythropoiesis. It regulates at the transcriptional level all aspects of erythroid maturation and function, as revealed by gene knockout studies in mice and by genome-wide occupancies in erythroid cells. The GATA1 protein contains two zinc finger domains and an N-terminal transactivation domain. GATA1 translation results in the production of the full-length protein and of a shorter variant (GATA1s) lacking the N-terminal transactivation domain, which is functionally deficient in supporting erythropoiesis. GATA1 protein abundance is highly regulated in erythroid cells at different levels, including transcription, mRNA translation, posttranslational modifications, and protein degradation, in a differentiation-stage-specific manner. Maintaining high GATA1 protein levels is essential in the early stages of erythroid maturation, whereas downregulating GATA1 protein levels is a necessary step in terminal erythroid differentiation. The importance of maintaining proper GATA1 protein homeostasis in erythropoiesis is demonstrated by the fact that both GATA1 loss and its overexpression result in lethal anemia. Importantly, alterations in any of those GATA1 regulatory checkpoints have been recognized as an important cause of hematological disorders such as dyserythropoiesis (with or without thrombocytopenia), β-thalassemia, Diamond-Blackfan anemia, myelodysplasia, or leukemia. In this review, we provide an overview of the multilevel regulation of GATA1 protein homeostasis in erythropoiesis and of its deregulation in hematological disease.
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Affiliation(s)
- Laura Gutiérrez
- Platelet Research Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Department of Medicine, Universidad de Oviedo, Oviedo, Spain
| | - Noemí Caballero
- Platelet Research Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Luis Fernández-Calleja
- Platelet Research Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Elena Karkoulia
- Institute of Molecular Biology and Biotechnology, Foundation of Research & Technology Hellas, Heraklion, Crete, Greece
| | - John Strouboulis
- Cancer Comprehensive Center, School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
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15
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Ling T, Crispino JD. GATA1 mutations in red cell disorders. IUBMB Life 2019; 72:106-118. [PMID: 31652397 DOI: 10.1002/iub.2177] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 09/18/2019] [Indexed: 01/01/2023]
Abstract
GATA1 is an essential regulator of erythroid cell gene expression and maturation. In its absence, erythroid progenitors are arrested in differentiation and undergo apoptosis. Much has been learned about GATA1 function through animal models, which include genetic knockouts as well as ones with decreased levels of expression. However, even greater insights have come from the finding that a number of rare red cell disorders, including Diamond-Blackfan anemia, are associated with GATA1 mutations. These mutations affect the amino-terminal zinc finger (N-ZF) and the amino-terminus of the protein, and in both cases can alter the DNA-binding activity, which is primarily conferred by the third functional domain, the carboxyl-terminal zinc finger (C-ZF). Here we discuss the role of GATA1 in erythropoiesis with an emphasis on the mutations found in human patients with red cell disorders.
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Affiliation(s)
- Te Ling
- Division of Hematology/Oncology, Northwestern University, Chicago, Illinois
| | - John D Crispino
- Division of Hematology/Oncology, Northwestern University, Chicago, Illinois
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16
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Vatikioti A, Karkoulia E, Ioannou M, Strouboulis J. Translational regulation and deregulation in erythropoiesis. Exp Hematol 2019; 75:11-20. [PMID: 31154069 DOI: 10.1016/j.exphem.2019.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/23/2019] [Accepted: 05/25/2019] [Indexed: 02/02/2023]
Abstract
Translational regulation plays a critical role in erythropoiesis, as it reflects the translational needs of enucleated mature erythroid cells in the absence of transcription and the large translational demands of balanced globin chain synthesis during erythroid maturation. In addition, red blood cells need to respond quickly to changes in their environment and the demands of the organism. Translational regulation occurs at several levels in erythroid cells, including the differential utilization of upstream open reading frames during differentiation and in response to signaling and the employment of RNA-binding proteins in an erythroid cell-specific fashion. Translation initiation is a critical juncture for translational regulation in response to environmental signals such as heme and iron availability, whereas regulatory mechanisms for ribosome recycling are consistent with recent observations highlighting the importance of maintaining adequate ribosome levels in differentiating erythroid cells. Translational deregulation in erythroid cells leads to disease associated with ineffective erythropoiesis, further highlighting the pivotal role translational regulation in erythropoiesis plays in human physiology and homeostasis. Overall, erythropoiesis has served as a unique model that has provided invaluable insight into translational regulation.
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Affiliation(s)
- Alexandra Vatikioti
- Laboratory of Molecular Hematopoiesis, Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Crete, Greece; Graduate Program in Molecular Biology and Biomedicine, Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Elena Karkoulia
- Laboratory of Molecular Hematopoiesis, Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Crete, Greece
| | - Marina Ioannou
- Laboratory of Molecular Hematopoiesis, Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Crete, Greece
| | - John Strouboulis
- Laboratory of Molecular Hematopoiesis, Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Crete, Greece.
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17
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Tavernier Q, Bennana E, Poindessous V, Schaeffer C, Rampoldi L, Pietrancosta N, Pallet N. Regulation of IRE1 RNase activity by the Ribonuclease inhibitor 1 (RNH1). Cell Cycle 2018; 17:1901-1916. [PMID: 30109813 DOI: 10.1080/15384101.2018.1506655] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Adaptation to endoplasmic reticulum (ER) stress depends on the activation of the sensor inositol-requiring enzyme 1α (IRE1), an endoribonuclease that splices the mRNA of the transcription factor XBP1 (X-box-binding protein 1). To better understand the protein network that regulates the activity of the IRE1 pathway, we systematically screened the proteins that interact with IRE1 and identified a ribonuclease inhibitor called ribonuclease/angiogenin inhibitor 1 (RNH1). RNH1 is a leucine-rich repeat domains-containing protein that binds to and inhibits ribonucleases. Immunoprecipitation experiments confirmed this interaction. Docking experiments indicated that RNH1 physically interacts with IRE1 through its cytosolic RNase domain. Upon ER stress, the interaction of RNH1 with IRE1 in the ER increased at the expense of the nuclear pool of RNH1. Inhibition of RNH1 expression using siRNA mediated RNA interference upon ER stress led to an increased splicing activity of XBP1. Modulation of IRE1 RNase activity by RNH1 was recapitulated in a cell-free system, suggesting direct regulation of IRE1 by RNH. We conclude that RNH1 attenuates the activity of IRE1 by interacting with its ribonuclease domain. These findings have implications for understanding the molecular mechanism by which IRE1 signaling is attenuated upon ER stress.
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Affiliation(s)
- Quentin Tavernier
- a Institut National de la Santé et de la Recherche Médicale (INSERM) U1147 , Paris , France.,b Paris Descartes University , Paris , France
| | - Evangeline Bennana
- b Paris Descartes University , Paris , France.,c 3P5 Proteomic facility, COMUE Sorbonne Paris Cité , Université Paris Descartes , Paris , France
| | - Virginie Poindessous
- a Institut National de la Santé et de la Recherche Médicale (INSERM) U1147 , Paris , France.,b Paris Descartes University , Paris , France
| | - Celine Schaeffer
- d Molecular Genetics of Renal Disorders Unit, Division of Genetics and Cell Biology , IRCCS San Raffaele Scientific Institute , Milan , Italy
| | - Luca Rampoldi
- d Molecular Genetics of Renal Disorders Unit, Division of Genetics and Cell Biology , IRCCS San Raffaele Scientific Institute , Milan , Italy
| | - Nicolas Pietrancosta
- b Paris Descartes University , Paris , France.,e Centre National pour la Recherche Scientifique (CNRS) U8601 , Paris , France.,f Team Chemistry and Biology, Modeling & Immunology for Therapy , CBMIT, 2MI Platform , Paris , France
| | - Nicolas Pallet
- a Institut National de la Santé et de la Recherche Médicale (INSERM) U1147 , Paris , France.,b Paris Descartes University , Paris , France.,g Clinical Chemistry Department , Hôpital Européen Gorges Pompidou, APHP , Paris , France.,h Plate-forme Proteomique 3P5 , Universite Paris Descartes, Sorbonne Paris Cite , Paris , France
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18
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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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19
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Khajuria RK, Munschauer M, Ulirsch JC, Fiorini C, Ludwig LS, McFarland SK, Abdulhay NJ, Specht H, Keshishian H, Mani DR, Jovanovic M, Ellis SR, Fulco CP, Engreitz JM, Schütz S, Lian J, Gripp KW, Weinberg OK, Pinkus GS, Gehrke L, Regev A, Lander ES, Gazda HT, Lee WY, Panse VG, Carr SA, Sankaran VG. Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis. Cell 2018; 173:90-103.e19. [PMID: 29551269 DOI: 10.1016/j.cell.2018.02.036] [Citation(s) in RCA: 246] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/28/2017] [Accepted: 02/15/2018] [Indexed: 01/17/2023]
Abstract
Blood cell formation is classically thought to occur through a hierarchical differentiation process, although recent studies have shown that lineage commitment may occur earlier in hematopoietic stem and progenitor cells (HSPCs). The relevance to human blood diseases and the underlying regulation of these refined models remain poorly understood. By studying a genetic blood disorder, Diamond-Blackfan anemia (DBA), where the majority of mutations affect ribosomal proteins and the erythroid lineage is selectively perturbed, we are able to gain mechanistic insight into how lineage commitment is programmed normally and disrupted in disease. We show that in DBA, the pool of available ribosomes is limited, while ribosome composition remains constant. Surprisingly, this global reduction in ribosome levels more profoundly alters translation of a select subset of transcripts. We show how the reduced translation of select transcripts in HSPCs can impair erythroid lineage commitment, illuminating a regulatory role for ribosome levels in cellular differentiation.
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Affiliation(s)
- Rajiv K Khajuria
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Berlin-Brandenburg School for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin 13353, Germany
| | | | - Jacob C Ulirsch
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Claudia Fiorini
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Leif S Ludwig
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sean K McFarland
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nour J Abdulhay
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Harrison Specht
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - D R Mani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marko Jovanovic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven R Ellis
- Department of Biochemistry and Molecular Biology, University of Louisville, Louisville, KY 40202, USA
| | - Charles P Fulco
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Sabina Schütz
- Institute of Medical Microbiology, Department of Medicine, University of Zurich, 8006 Zurich, Switzerland
| | - John Lian
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Karen W Gripp
- Division of Medical Genetics, A. I. duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Olga K Weinberg
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Geraldine S Pinkus
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Lee Gehrke
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hanna 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
| | - Winston Y Lee
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Vikram G Panse
- Institute of Medical Microbiology, Department of Medicine, University of Zurich, 8006 Zurich, Switzerland
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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