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Zuo Z, Cheng X, Ferdous S, Shao J, Li J, Bao Y, Li J, Lu J, Jacobo Lopez A, Wohlschlegel J, Prieve A, Thomas MG, Reh TA, Li Y, Moshiri A, Chen R. Single cell dual-omic atlas of the human developing retina. Nat Commun 2024; 15:6792. [PMID: 39117640 PMCID: PMC11310509 DOI: 10.1038/s41467-024-50853-5] [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: 10/06/2023] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
The development of the retina is under tight temporal and spatial control. To gain insights into the molecular basis of this process, we generate a single-nuclei dual-omic atlas of the human developing retina with approximately 220,000 nuclei from 14 human embryos and fetuses aged between 8 and 23-weeks post-conception with matched macular and peripheral tissues. This atlas captures all major cell classes in the retina, along with a large proportion of progenitors and cell-type-specific precursors. Cell trajectory analysis reveals a transition from continuous progression in early progenitors to a hierarchical development during the later stages of cell type specification. Both known and unrecorded candidate transcription factors, along with gene regulatory networks that drive the transitions of various cell fates, are identified. Comparisons between the macular and peripheral retinae indicate a largely consistent yet distinct developmental pattern. This atlas offers unparalleled resolution into the transcriptional and chromatin accessibility landscapes during development, providing an invaluable resource for deeper insights into retinal development and associated diseases.
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Affiliation(s)
- Zhen Zuo
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
| | - Xuesen Cheng
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
| | - Salma Ferdous
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
| | - Jianming Shao
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
| | - Jin Li
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
| | - Yourong Bao
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
| | - Jean Li
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
| | - Jiaxiong Lu
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
| | - Antonio Jacobo Lopez
- Department of Ophthalmology & Vision Science, UC Davis School of Medicine, 4860 Y St, Sacramento, CA, USA
| | - Juliette Wohlschlegel
- Department of Biological Structure, University of Washington, 1410 NE Campus Pkwy, Seattle, WA, USA
| | - Aric Prieve
- Department of Biological Structure, University of Washington, 1410 NE Campus Pkwy, Seattle, WA, USA
| | - Mervyn G Thomas
- Ulverscroft Eye Unit, School of Psychology and Vision Sciences, The University of Leicester, Leicester, UK
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, 1410 NE Campus Pkwy, Seattle, WA, USA
| | - Yumei Li
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA
| | - Ala Moshiri
- Department of Ophthalmology & Vision Science, UC Davis School of Medicine, 4860 Y St, Sacramento, CA, USA
| | - Rui Chen
- HGSC, Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA.
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA.
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, USA.
- Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California Irvine School of Medicine, Irvine, USA.
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2
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Zhou YJ, Yang ML, He X, Gu HY, Ren JH, Cheng ST, Fu Z, Zhang ZZ, Chen J. RNA-binding protein RPS7 promotes hepatocellular carcinoma progression via LOXL2-dependent activation of ITGB1/FAK/SRC signaling. J Exp Clin Cancer Res 2024; 43:45. [PMID: 38326908 PMCID: PMC10851485 DOI: 10.1186/s13046-023-02929-1] [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: 07/19/2023] [Accepted: 12/07/2023] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Metastasis is one of the leading cause contributes to treatment failure and poor prognosis of hepatocellular carcinoma (HCC) patients. The underlying mechanism of HCC metastasis remains to be determined. Although several RNA binding proteins (RBPs) have been found to participate in tumorigenesis and progression of liver cancer, the role of RBPs in HCC patients with extrahepatic metastases is poorly understood. METHODS By performing RNA-seq of primary HCC tissues (including HCC with extrahepatic metastasis and those did not develop metastasis), we identified a set of HCC metastasis-associated RBPs candidates. Among which, ribosomal protein S7 (RPS7) was found to be remarkably increased in HCC tissues and be strongly related to HCC poor survival. Overexpression or CRISPR-Cas9-mediated knockout were applied to investigate the role of RPS7 on the metastasis-associated phenotypes of HCC cells. RNA sequencing, RIP, RNA-pull down, dual luciferase reporter assay, nascent RNA capture assay, and RNA decay and so on, were applied to reveal the underlying mechanism of RPS7 induced HCC metastasis. RESULTS Gain- and loss- of function analyses revealed that RPS7 promoted HCC cells adhesion, migration and invasion capabilities, as well as lung metastasis. Mechanistically, we uncovered that lysyl oxidase-like 2 (LOXL2) was a critical downstream target of RPS7. RPS7 could stabilize LOXL2 mRNA by binding to AUUUA motifs in the 3155-3375 region of the 3'UTR of LOXL2 mRNA, thus increased LOXL2 expression via elevating LOXL2 mRNA abundance. Further research revealed that LOXL2 could accelerate focal adhesion formation through maintaining the protein stability of ITGB1 and activating ITGB1-mediated FAK/SRC signaling pathway, and thereby contribute to the pro-metastasis effect of RPS7. CONCLUSIONS Taken together, our data reveal a novel function of RPS7 in HCC metastasis, also reveal the critical roles of the RPS7/LOXL2/ITGB1 axis in HCC metastasis and shed new light on the exploration of molecular drugs against HCC.
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Affiliation(s)
- Yu-Jiao Zhou
- Department of Infectious Disease, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, No.20 Jinyu Road, Yubei District, Chongqing, 401122, China
| | - Min-Li Yang
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xin He
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Hui-Ying Gu
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Ji-Hua Ren
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Sheng-Tao Cheng
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Zhou Fu
- Stem Cell Biology and Therapy Laboratory, Ministry of Education Key Laboratory of Child Development and Disorders, and the Department of Respiratory Diseases, The Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Zhen-Zhen Zhang
- Department of Infectious Disease, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, No.20 Jinyu Road, Yubei District, Chongqing, 401122, China.
| | - Juan Chen
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China.
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, China.
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3
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Folgado-Marco V, Ames K, Chuen J, Gritsman K, Baker NE. Haploinsufficiency of the essential gene Rps12 causes defects in erythropoiesis and hematopoietic stem cell maintenance. eLife 2023; 12:e69322. [PMID: 37272618 PMCID: PMC10287158 DOI: 10.7554/elife.69322] [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: 04/12/2021] [Accepted: 04/26/2023] [Indexed: 06/06/2023] Open
Abstract
Ribosomal protein (Rp) gene haploinsufficiency can result in Diamond-Blackfan Anemia (DBA), characterized by defective erythropoiesis and skeletal defects. Some mouse Rp mutations recapitulate DBA phenotypes, although others lack erythropoietic or skeletal defects. We generated a conditional knockout mouse to partially delete Rps12. Homozygous Rps12 deletion resulted in embryonic lethality. Mice inheriting the Rps12KO/+ genotype had growth and morphological defects, pancytopenia, and impaired erythropoiesis. A striking reduction in hematopoietic stem cells (HSCs) and progenitors in the bone marrow (BM) was associated with decreased ability to repopulate the blood system after competitive and non-competitive BM transplantation. Rps12KO/+ lost HSC quiescence, experienced ERK and MTOR activation, and increased global translation in HSC and progenitors. Post-natal heterozygous deletion of Rps12 in hematopoietic cells using Tal1-Cre-ERT also resulted in pancytopenia with decreased HSC numbers. However, post-natal Cre-ERT induction led to reduced translation in HSCs and progenitors, suggesting that this is the most direct consequence of Rps12 haploinsufficiency in hematopoietic cells. Thus, RpS12 has a strong requirement in HSC function, in addition to erythropoiesis.
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Affiliation(s)
| | - Kristina Ames
- Department of Medical Oncology, Albert Einstein College of MedicineBronxUnited States
- Department of Cell Biology, Albert Einstein College of MedicineBronxUnited States
| | - Jacky Chuen
- Department of Genetics, Albert Einstein College of MedicineBronxUnited States
| | - Kira Gritsman
- Department of Medical Oncology, Albert Einstein College of MedicineBronxUnited States
- Department of Cell Biology, Albert Einstein College of MedicineBronxUnited States
| | - Nicholas E Baker
- Department of Genetics, Albert Einstein College of MedicineBronxUnited States
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4
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Schreiner C, Kernl B, Dietmann P, Riegger RJ, Kühl M, Kühl SJ. The Ribosomal Protein L5 Functions During Xenopus Anterior Development Through Apoptotic Pathways. Front Cell Dev Biol 2022; 10:777121. [PMID: 35281111 PMCID: PMC8905602 DOI: 10.3389/fcell.2022.777121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 02/08/2022] [Indexed: 01/24/2023] Open
Abstract
Ribosomal biogenesis is a fundamental process necessary for cell growth and division. Ribosomal protein L5 (Rpl5) is part of the large ribosomal subunit. Mutations in this protein have been associated with the congenital disease Diamond Blackfan anemia (DBA), a so called ribosomopathy. Despite of the ubiquitous need of ribosomes, clinical manifestations of DBA include tissue-specific symptoms, e.g., craniofacial malformations, eye abnormalities, skin pigmentation failure, cardiac defects or liver cirrhosis. Here, we made use of the vertebrate model organism Xenopus laevis and showed a specific expression of rpl5 in the developing anterior tissue correlating with tissues affected in ribosomopathies. Upon Rpl5 knockdown using an antisense-based morpholino oligonucleotide approach, we showed different phenotypes affecting anterior tissue, i.e., defective cranial cartilage, malformed eyes, and microcephaly. Hence, the observed phenotypes in Xenopus laevis resemble the clinical manifestations of DBA. Analyses of the underlying molecular basis revealed that the expression of several marker genes of neural crest, eye, and brain are decreased during induction and differentiation of the respective tissue. Furthermore, Rpl5 knockdown led to decreased cell proliferation and increased cell apoptosis during early embryogenesis. Investigating the molecular mechanisms underlying Rpl5 function revealed a more than additive effect between either loss of function of Rpl5 and loss of function of c-Myc or loss of function of Rpl5 and gain of function of Tp53, suggesting a common signaling pathway of these proteins. The co-injection of the apoptosis blocking molecule Bcl2 resulted in a partial rescue of the eye phenotype, supporting the hypothesis that apoptosis is one main reason for the phenotypes occurring upon Rpl5 knockdown. With this study, we are able to shed more light on the still poorly understood molecular background of ribosomopathies.
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Affiliation(s)
- Corinna Schreiner
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany.,International Graduate School in Molecular Medicine Ulm, Ulm, Germany
| | - Bianka Kernl
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany.,International Graduate School in Molecular Medicine Ulm, Ulm, Germany
| | - Petra Dietmann
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Ricarda J Riegger
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Michael Kühl
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Susanne J Kühl
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
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5
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Chern T, Achilleos A, Tong X, Hill MC, Saltzman AB, Reineke LC, Chaudhury A, Dasgupta SK, Redhead Y, Watkins D, Neilson JR, Thiagarajan P, Green JBA, Malovannaya A, Martin JF, Rosenblatt DS, Poché RA. Mutations in Hcfc1 and Ronin result in an inborn error of cobalamin metabolism and ribosomopathy. Nat Commun 2022; 13:134. [PMID: 35013307 PMCID: PMC8748873 DOI: 10.1038/s41467-021-27759-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 12/13/2021] [Indexed: 12/26/2022] Open
Abstract
Combined methylmalonic acidemia and homocystinuria (cblC) is the most common inborn error of intracellular cobalamin metabolism and due to mutations in Methylmalonic Aciduria type C and Homocystinuria (MMACHC). Recently, mutations in the transcriptional regulators HCFC1 and RONIN (THAP11) were shown to result in cellular phenocopies of cblC. Since HCFC1/RONIN jointly regulate MMACHC, patients with mutations in these factors suffer from reduced MMACHC expression and exhibit a cblC-like disease. However, additional de-regulated genes and the resulting pathophysiology is unknown. Therefore, we have generated mouse models of this disease. In addition to exhibiting loss of Mmachc, metabolic perturbations, and developmental defects previously observed in cblC, we uncovered reduced expression of target genes that encode ribosome protein subunits. We also identified specific phenotypes that we ascribe to deregulation of ribosome biogenesis impacting normal translation during development. These findings identify HCFC1/RONIN as transcriptional regulators of ribosome biogenesis during development and their mutation results in complex syndromes exhibiting aspects of both cblC and ribosomopathies. Combined methylmalonic acidemia (MMA) and hyperhomocysteinemias are inborn errors of vitamin B12 metabolism, and mutations in the transcriptional regulators HCFC1 and RONIN (THAP11) underlie some forms of these disorders. Here the authors generated mouse models of a human syndrome due to mutations in RONIN (THAP11) and HCFC1, and show that this syndrome is both an inborn error of vitamin B12 metabolism and displays some features of ribosomopathy.
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Affiliation(s)
- Tiffany Chern
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Graduate Program in Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Annita Achilleos
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Basic and Clinical Sciences, University of Nicosia Medical School, Nicosia, Cyprus.
| | - Xuefei Tong
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Matthew C Hill
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alexander B Saltzman
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lucas C Reineke
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arindam Chaudhury
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Swapan K Dasgupta
- Department of Pathology, Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, 77030, USA
| | - Yushi Redhead
- The Francis Crick Institute, London, NW1 1AT, UK.,Centre for Craniofacial Biology and Regeneration, King's College London, London, SE1 9RT, UK
| | - David Watkins
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Montreal, QC, Canada.,Division of Medical Biochemistry, Department of Specialized Medicine, McGill University Health Centre, Montreal, QC, Canada
| | - Joel R Neilson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Graduate Program in Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Development, Disease Models and Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Perumal Thiagarajan
- Department of Pathology, Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jeremy B A Green
- Centre for Craniofacial Biology and Regeneration, King's College London, London, SE1 9RT, UK
| | - Anna Malovannaya
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James F Martin
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Graduate Program in Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Development, Disease Models and Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Heart Institute, Houston, TX, 77030, USA
| | - David S Rosenblatt
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Montreal, QC, Canada.,Division of Medical Biochemistry, Department of Specialized Medicine, McGill University Health Centre, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Ross A Poché
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Graduate Program in Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Development, Disease Models and Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA.
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6
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A new murine Rpl5 (uL18) mutation provides a unique model of variably penetrant Diamond-Blackfan anemia. Blood Adv 2021; 5:4167-4178. [PMID: 34464976 PMCID: PMC8945612 DOI: 10.1182/bloodadvances.2021004658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/04/2021] [Indexed: 01/28/2023] Open
Abstract
Ribosome dysfunction is implicated in multiple abnormal developmental and disease states in humans. Heterozygous germline mutations in genes encoding ribosomal proteins are found in most individuals with Diamond-Blackfan anemia (DBA), whereas somatic mutations have been implicated in a variety of cancers and other disorders. Ribosomal protein-deficient animal models show variable phenotypes and penetrance, similar to human patients with DBA. In this study, we characterized a novel ENU mouse mutant (Skax23m1Jus) with growth and skeletal defects, cardiac malformations, and increased mortality. After genetic mapping and whole-exome sequencing, we identified an intronic Rpl5 mutation, which segregated with all affected mice. This mutation was associated with decreased ribosome generation, consistent with Rpl5 haploinsufficiency. Rpl5Skax23-Jus/+ animals had a profound delay in erythroid maturation and increased mortality at embryonic day (E) 12.5, which improved by E14.5. Surviving mutant animals had macrocytic anemia at birth, as well as evidence of ventricular septal defect (VSD). Surviving adult and aged mice exhibited no hematopoietic defect or VSD. We propose that this novel Rpl5Skax23-Jus/+ mutant mouse will be useful in studying the factors influencing the variable penetrance that is observed in DBA.
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7
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Taylor AM, Macari ER, Chan IT, Blair MC, Doulatov S, Vo LT, Raiser DM, Siva K, Basak A, Pirouz M, Shah AN, McGrath K, Humphries JM, Stillman E, Alter BP, Calo E, Gregory RI, Sankaran VG, Flygare J, Ebert BL, Zhou Y, Daley GQ, Zon LI. Calmodulin inhibitors improve erythropoiesis in Diamond-Blackfan anemia. Sci Transl Med 2021; 12:12/566/eabb5831. [PMID: 33087503 DOI: 10.1126/scitranslmed.abb5831] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022]
Abstract
Diamond-Blackfan anemia (DBA) is a rare hematopoietic disease characterized by a block in red cell differentiation. Most DBA cases are caused by mutations in ribosomal proteins and characterized by higher than normal activity of the tumor suppressor p53. Higher p53 activity is thought to contribute to DBA phenotypes by inducing apoptosis during red blood cell differentiation. Currently, there are few therapies available for patients with DBA. We performed a chemical screen using zebrafish ribosomal small subunit protein 29 (rps29) mutant embryos that have a p53-dependent anemia and identified calmodulin inhibitors that rescued the phenotype. Our studies demonstrated that calmodulin inhibitors attenuated p53 protein amount and activity. Treatment with calmodulin inhibitors led to decreased p53 translation and accumulation but does not affect p53 stability. A U.S. Food and Drug Administration-approved calmodulin inhibitor, trifluoperazine, rescued hematopoietic phenotypes of DBA models in vivo in zebrafish and mouse models. In addition, trifluoperazine rescued these phenotypes in human CD34+ hematopoietic stem and progenitor cells. Erythroid differentiation was also improved in CD34+ cells isolated from a patient with DBA. This work uncovers a potential avenue of therapeutic development for patients with DBA.
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Affiliation(s)
- Alison M Taylor
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth R Macari
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Iris T Chan
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - Megan C Blair
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - Sergei Doulatov
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Linda T Vo
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - David M Raiser
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Division of Hematology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kavitha Siva
- Stem Cell Center, Lund University, Lund 22184, Sweden
| | - Anindita Basak
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Mehdi Pirouz
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Arish N Shah
- MIT Department of Biology and David H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Katherine McGrath
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - Jessica M Humphries
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - Emma Stillman
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - Blanche P Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD 20850, USA
| | - Eliezer Calo
- MIT Department of Biology and David H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Richard I Gregory
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Johan Flygare
- Stem Cell Center, Lund University, Lund 22184, Sweden
| | - Benjamin L Ebert
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Yi Zhou
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - George Q Daley
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Leonard I Zon
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA. .,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Boston, MA 02115, USA.,Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA 02115, USA
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8
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Hassan FM, Alsultan A, Alzehrani F, Albuali W, Bubshait D, Abass E, Elbasheer M, Alkhanbashi A. Genetic Variants of RPL5 and RPL9 Genes among Saudi Patients Diagnosed with Thrombosis. Med Arch 2021; 75:188-193. [PMID: 34483448 PMCID: PMC8385736 DOI: 10.5455/medarh.2021.75.188-193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/20/2021] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Thrombosis directly affects the quality of life with increased mortality. The RPL5 (L5) gene on intron 6 on chromosome 1p22, rs6604026 is associated with multiple sclerosis risk, whereas RPL9 (L9) on 8 exons on chromosome 4p14 has been documented so far as being an essential involvement in the proliferation of protein synthesized cells mostly by gene products. OBJECTIVE The aim of this work was to assess genetic variants of RPL5 and RPL9 and thrombosis to characterize their role in the diagnosis of thrombosis among the Saudi population. METHODS The cross-sectional study involved 100 Saudi patients diagnosed with thrombosis (arterial or venous) in 50 healthy individuals as controls in the same age and sex groups. Primers were designed RPL5 and RPL9 for molecular analysis. The Sanger System ABI-3730xL (Hong Kong) automatic sequencing was used for DNA sequencing. Statistical analysis was performed using the Prism 5 and SPSS version-21 programs. RESULTS The male / female age ratio was 66.7 / 57.4, and the mean age was 61.2 years. Most of the patients were self-identifiable and without a previous history of thrombosis (61.0%). Most of the patients had just been diagnosed, that is, in the last five years (74.0%), about 43% of the patients underwent treatment using combination therapy (Aspirin and oral anticoagulants). New gene variants of RPL5 (5 SNPs) and RPL9 (9 SNPs) were detected in Saudi thrombotic patients. CONCLUSION Mutations in RPL5 and RPL9 were reported in all thrombotic patients, represented by a new variant of the ribosomal protein gene and correlated with thrombosis in the Saudi population. These results may reflect an association between the ribosomal protein SNP gene and the incidence and progression of thrombosis in the Saudi population.
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Affiliation(s)
- Fathelrahman Mahdi Hassan
- Department of Clinical Laboratory Sciences, College of Applied Medical Science. Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Afnan Alsultan
- Department of Clinical Laboratory Sciences, College of Applied Medical Science. Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Faisal Alzehrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Science. Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Waleed Albuali
- Department of Pediatrics, College of Medicine. Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Dalal Bubshait
- Department of Pediatrics, College of Medicine. Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Elfadil Abass
- Department of Clinical Laboratory Sciences, College of Applied Medical Science. Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Mudathir Elbasheer
- Department of Clinical Laboratory Sciences, College of Applied Medical Science. Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Abdulmohsen Alkhanbashi
- Department of Clinical Laboratory Sciences, College of Applied Medical Science. Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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9
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Lidgerwood GE, Senabouth A, Smith-Anttila CJA, Gnanasambandapillai V, Kaczorowski DC, Amann-Zalcenstein D, Fletcher EL, Naik SH, Hewitt AW, Powell JE, Pébay A. Transcriptomic Profiling of Human Pluripotent Stem Cell-derived Retinal Pigment Epithelium over Time. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 19:223-242. [PMID: 33307245 PMCID: PMC8602392 DOI: 10.1016/j.gpb.2020.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 07/04/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022]
Abstract
Human pluripotent stem cell (hPSC)-derived progenies are immature versions of cells, presenting a potential limitation to the accurate modelling of diseases associated with maturity or age. Hence, it is important to characterise how closely cells used in culture resemble their native counterparts. In order to select appropriate time points of retinal pigment epithelium (RPE) cultures that reflect native counterparts, we characterised the transcriptomic profiles of the hPSC-derived RPE cells from 1- and 12-month cultures. We differentiated the human embryonic stem cell line H9 into RPE cells, performed single-cell RNA-sequencing of a total of 16,576 cells to assess the molecular changes of the RPE cells across these two culture time points. Our results indicate the stability of the RPE transcriptomic signature, with no evidence of an epithelial–mesenchymal transition, and with the maturing populations of the RPE observed with time in culture. Assessment of Gene Ontology pathways revealed that as the cultures age, RPE cells upregulate expression of genes involved in metal binding and antioxidant functions. This might reflect an increased ability to handle oxidative stress as cells mature. Comparison with native human RPE data confirms a maturing transcriptional profile of RPE cells in culture. These results suggest that long-term in vitro culture of RPE cells allows the modelling of specific phenotypes observed in native mature tissues. Our work highlights the transcriptional landscape of hPSC-derived RPE cells as they age in culture, which provides a reference for native and patient samples to be benchmarked against.
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Affiliation(s)
- Grace E Lidgerwood
- Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia.
| | - Anne Senabouth
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Casey J A Smith-Anttila
- Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Vikkitharan Gnanasambandapillai
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Dominik C Kaczorowski
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Daniela Amann-Zalcenstein
- Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Erica L Fletcher
- Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Shalin H Naik
- Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Alex W Hewitt
- Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia; School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7005, Australia
| | - Joseph E Powell
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia; UNSW Cellular Genomics Futures Institute, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Alice Pébay
- Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia.
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10
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Kumari B, Mandal M, Dholaniya PS. Analysis of multiple transcriptome data to determine age-associated genes for the progression of Parkinson's disease. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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11
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Akram T, Fatima A, Klar J, Hoeber J, Zakaria M, Tariq M, Baig SM, Schuster J, Dahl N. Aberrant splicing due to a novel RPS7 variant causes Diamond-Blackfan Anemia associated with spontaneous remission and meningocele. Int J Hematol 2020; 112:894-899. [PMID: 32772263 DOI: 10.1007/s12185-020-02950-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 06/30/2020] [Accepted: 07/14/2020] [Indexed: 10/23/2022]
Abstract
Diamond-Blackfan Anemia (DBA) is a congenital pure red cell aplasia caused by heterozygous variants in ribosomal protein genes. The hematological features associated with DBA are highly variable and non-hematological abnormalities are common. We report herein on an affected mother and her daughter presenting with transfusion-dependent anemia. The mother showed mild physical abnormalities and entered spontaneous remission at age 13 years. Her daughter was born with occipital meningocele. Exome sequencing of DNA from the mother revealed a heterozygous novel splice site variant (NM_001011.4:c.508-3T > G) in the Ribosomal Protein S7 gene (RPS7) inherited by the daughter. Functional analysis of the RPS7 variant expressed from a mini-gene construct revealed that the exon 7 acceptor splice site was replaced by a cryptic splice resulting in a transcript missing 64 bp of exon 7 (p.Val170Serfs*8). Our study confirms a pathogenic effect of a novel RPS7 variant in DBA associated with spontaneous remission in the mother and meningocele in her daughter, thus adding to the genotype-phenotype correlations in DBA.
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Affiliation(s)
- Talia Akram
- Human Molecular Genetics Laboratory, National Institute for Biotechnology and Genetic Engineering (NIBGE-C)-PIEAS, Faisalabad, Pakistan.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, BMC Box 815, Uppsala, Sweden
| | - Ambrin Fatima
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, BMC Box 815, Uppsala, Sweden
| | - Joakim Klar
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, BMC Box 815, Uppsala, Sweden
| | - Jan Hoeber
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, BMC Box 815, Uppsala, Sweden
| | - Muhammad Zakaria
- Center for Human Genetics, Hazara University, Mansehra, Pakistan
| | - Muhammad Tariq
- Human Molecular Genetics Laboratory, National Institute for Biotechnology and Genetic Engineering (NIBGE-C)-PIEAS, Faisalabad, Pakistan
| | - Shahid M Baig
- Human Molecular Genetics Laboratory, National Institute for Biotechnology and Genetic Engineering (NIBGE-C)-PIEAS, Faisalabad, Pakistan
| | - Jens Schuster
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, BMC Box 815, Uppsala, Sweden
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, BMC Box 815, Uppsala, Sweden.
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12
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Aurora kinase B inhibitor barasertib (AZD1152) inhibits glucose metabolism in gastric cancer cells. Anticancer Drugs 2020; 30:19-26. [PMID: 30540594 DOI: 10.1097/cad.0000000000000684] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Barasertib is a highly selective Aurora kinase B (AURKB) inhibitor and has been widely applied in a variety of cancer cells to investigate the regulatory function of AURKB. However, the effect of barasertib on glucose metabolism in gastric cancer (GC) remains illustrated. Here, barasertib was identified to effectively reduce glucose uptake and lactate production in GC cells in a dose-dependent and time-dependent manner. The expression levels of GLUT1, LDHA and HK2 were decreased by barasertib treatment of GC cells. Furthermore, we found that barasertib induced the expression of ribosomal protein S7 (RPS7), as a tumor suppressor, to regulate glucose metabolism. Silencing of RPS7 rescued the effects of barasertib on glucose metabolism in GC cells. Overexpression of RPS7 suppressed the promoter activity of C-Myc, which has been identified as an important regulator of glucose metabolism in cancer cells. The clinical data showed that the expression level of AURKB in GC patients' sera and tissues were positively correlated with those of C-Myc, GLUT1 and LDHA, but negatively with that of RPS7. Therefore, these findings provide new evidence that barasertib regulates GC cell glucose metabolism by inducing the RPS7/C-Myc signal pathway, and have important implications for the development of therapeutic approaches using AURKB as a target protein to prevent tumor recurrence.
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13
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Beauchamp MC, Alam SS, Kumar S, Jerome-Majewska LA. Spliceosomopathies and neurocristopathies: Two sides of the same coin? Dev Dyn 2020; 249:924-945. [PMID: 32315467 DOI: 10.1002/dvdy.183] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/26/2020] [Accepted: 04/15/2020] [Indexed: 12/14/2022] Open
Abstract
Mutations in core components of the spliceosome are responsible for a group of syndromes collectively known as spliceosomopathies. Patients exhibit microcephaly, micrognathia, malar hypoplasia, external ear anomalies, eye anomalies, psychomotor delay, intellectual disability, limb, and heart defects. Craniofacial malformations in these patients are predominantly found in neural crest cells-derived structures of the face and head. Mutations in eight genes SNRPB, RNU4ATAC, SF3B4, PUF60, EFTUD2, TXNL4, EIF4A3, and CWC27 are associated with craniofacial spliceosomopathies. In this review, we provide a brief description of the normal development of the head and the face and an overview of mutations identified in genes associated with craniofacial spliceosomopathies. We also describe a model to explain how and when these mutations are most likely to impact neural crest cells. We speculate that mutations in a subset of core splicing factors lead to disrupted splicing in neural crest cells because these cells have increased sensitivity to inefficient splicing. Hence, disruption in splicing likely activates a cellular stress response that includes increased skipping of regulatory exons in genes such as MDM2 and MDM4, key regulators of P53. This would result in P53-associated death of neural crest cells and consequently craniofacial malformations associated with spliceosomopathies.
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Affiliation(s)
- Marie-Claude Beauchamp
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada.,McGill University Health Centre at Glen Site, Montreal, Quebec, Canada
| | - Sabrina Shameen Alam
- McGill University Health Centre at Glen Site, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Shruti Kumar
- McGill University Health Centre at Glen Site, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Loydie Anne Jerome-Majewska
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada.,McGill University Health Centre at Glen Site, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
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14
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Cataloguing and Selection of mRNAs Localized to Dendrites in Neurons and Regulated by RNA-Binding Proteins in RNA Granules. Biomolecules 2020; 10:biom10020167. [PMID: 31978946 PMCID: PMC7072219 DOI: 10.3390/biom10020167] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 12/15/2022] Open
Abstract
Spatiotemporal translational regulation plays a key role in determining cell fate and function. Specifically, in neurons, local translation in dendrites is essential for synaptic plasticity and long-term memory formation. To achieve local translation, RNA-binding proteins in RNA granules regulate target mRNA stability, localization, and translation. To date, mRNAs localized to dendrites have been identified by comprehensive analyses. In addition, mRNAs associated with and regulated by RNA-binding proteins have been identified using various methods in many studies. However, the results obtained from these numerous studies have not been compiled together. In this review, we have catalogued mRNAs that are localized to dendrites and are associated with and regulated by the RNA-binding proteins fragile X mental retardation protein (FMRP), RNA granule protein 105 (RNG105, also known as Caprin1), Ras-GAP SH3 domain binding protein (G3BP), cytoplasmic polyadenylation element binding protein 1 (CPEB1), and staufen double-stranded RNA binding proteins 1 and 2 (Stau1 and Stau2) in RNA granules. This review provides comprehensive information on dendritic mRNAs, the neuronal functions of mRNA-encoded proteins, the association of dendritic mRNAs with RNA-binding proteins in RNA granules, and the effects of RNA-binding proteins on mRNA regulation. These findings provide insights into the mechanistic basis of protein-synthesis-dependent synaptic plasticity and memory formation and contribute to future efforts to understand the physiological implications of local regulation of dendritic mRNAs in neurons.
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15
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Genuth NR, Barna M. Heterogeneity and specialized functions of translation machinery: from genes to organisms. Nat Rev Genet 2019; 19:431-452. [PMID: 29725087 DOI: 10.1038/s41576-018-0008-z] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Regulation of mRNA translation offers the opportunity to diversify the expression and abundance of proteins made from individual gene products in cells, tissues and organisms. Emerging evidence has highlighted variation in the composition and activity of several large, highly conserved translation complexes as a means to differentially control gene expression. Heterogeneity and specialized functions of individual components of the ribosome and of the translation initiation factor complexes eIF3 and eIF4F, which are required for recruitment of the ribosome to the mRNA 5' untranslated region, have been identified. In this Review, we summarize the evidence for selective mRNA translation by components of these macromolecular complexes as a means to dynamically control the translation of the proteome in time and space. We further discuss the implications of this form of gene expression regulation for a growing number of human genetic disorders associated with mutations in the translation machinery.
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Affiliation(s)
- Naomi R Genuth
- Departments of Genetics and Developmental Biology, Stanford University, Stanford, CA, USA.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Maria Barna
- Departments of Genetics and Developmental Biology, Stanford University, Stanford, CA, USA.
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16
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Bowen ME, Attardi LD. The role of p53 in developmental syndromes. J Mol Cell Biol 2019; 11:200-211. [PMID: 30624728 PMCID: PMC6478128 DOI: 10.1093/jmcb/mjy087] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/22/2018] [Accepted: 01/06/2019] [Indexed: 12/17/2022] Open
Abstract
While it is well appreciated that loss of the p53 tumor suppressor protein promotes cancer, growing evidence indicates that increased p53 activity underlies the developmental defects in a wide range of genetic syndromes. The inherited or de novo mutations that cause these syndromes affect diverse cellular processes, such as ribosome biogenesis, DNA repair, and centriole duplication, and analysis of human patient samples and mouse models demonstrates that disrupting these cellular processes can activate the p53 pathway. Importantly, many of the developmental defects in mouse models of these syndromes can be rescued by loss of p53, indicating that inappropriate p53 activation directly contributes to their pathogenesis. A role for p53 in driving developmental defects is further supported by the observation that mouse strains with broad p53 hyperactivation, due to mutations affecting p53 pathway components, display a host of tissue-specific developmental defects, including hematopoietic, neuronal, craniofacial, cardiovascular, and pigmentation defects. Furthermore, germline activating mutations in TP53 were recently identified in two human patients exhibiting bone marrow failure and other developmental defects. Studies in mice suggest that p53 drives developmental defects by inducing apoptosis, restraining proliferation, or modulating other developmental programs in a cell type-dependent manner. Here, we review the growing body of evidence from mouse models that implicates p53 as a driver of tissue-specific developmental defects in diverse genetic syndromes.
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Affiliation(s)
- Margot E Bowen
- Division of Radiation and Cancer Biology in the Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura D Attardi
- Division of Radiation and Cancer Biology in the Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
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17
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Abstract
Diamond-Blackfan anaemia (DBA) is a rare inherited marrow failure disorder, characterized by hypoplastic anaemia, congenital anomalies and a predisposition to cancer as a result of ribosomal dysfunction. Historically, treatment is based on glucocorticoids and/or blood transfusions, which is accompanied by significant toxicity and long-term sequelae. Currently, stem cell transplantation is the only curative option for the haematological DBA phenotype. Whereas this procedure has been quite successful in the last decade in selected patients, novel therapies and biological insights are still warranted to improve clinical care for all DBA patients. In addition to paediatric haematologists, other physicians (e.g. endocrinologist, gynaecologist) should ideally be involved in the care of this chronic condition from an early age, to improve lifelong management of haematological and non-haematological symptoms, and screen for DBA-associated malignancies. Here we provide an overview of current knowledge and recommendations for the day-to-day care of DBA patients.
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Affiliation(s)
- Marije Bartels
- Paediatric Haematology DepartmentWilhelmina Children's HospitalUniversity Medical Centre Utrecht Utrechtthe Netherlands
| | - Marc Bierings
- Department of Stem cell transplantationPrincess Maxima Centre for Paediatric OncologyWilhelmina Children's HospitalUniversity Medical Centre UtrechtUtrechtthe Netherlands
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18
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Oyarbide U, Topczewski J, Corey SJ. Peering through zebrafish to understand inherited bone marrow failure syndromes. Haematologica 2018; 104:13-24. [PMID: 30573510 PMCID: PMC6312012 DOI: 10.3324/haematol.2018.196105] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/14/2018] [Indexed: 12/22/2022] Open
Abstract
Inherited bone marrow failure syndromes are experiments of nature characterized by impaired hematopoiesis with cancer and leukemia predisposition. The mutations associated with inherited bone marrow failure syndromes affect fundamental cellular pathways, such as DNA repair, telomere maintenance, or proteostasis. How these disturbed pathways fail to produce sufficient blood cells and lead to leukemogenesis are not understood. The rarity of inherited cytopenias, the paucity of affected primary human hematopoietic cells, and the sometime inadequacy of murine or induced pluripotential stem cell models mean it is difficult to acquire a greater understanding of them. Zebrafish offer a model organism to study gene functions. As vertebrates, zebrafish share with humans many orthologous genes involved in blood disorders. As a model organism, zebrafish provide advantages that include rapid development of transparent embryos, high fecundity (providing large numbers of mutant and normal siblings), and a large collection of mutant and transgenic lines useful for investigating the blood system and other tissues during development. Importantly, recent advances in genomic editing in zebrafish can speedily validate the new genes or novel variants discovered in clinical investigation as causes for marrow failure. Here we review zebrafish as a model organism that phenocopies Fanconi anemia, Diamond-Blackfan anemia, dyskeratosis congenita, Shwachman-Diamond syndrome, congenital amegakaryocytic thrombocytopenia, and severe congenital neutropenia. Two important insights, provided by modeling inherited cytopenias in zebrafish, widen understanding of ribosome biogenesis and TP53 in mediating marrow failure and non-hematologic defects. They suggest that TP53-independent pathways contribute to marrow failure. In addition, zebrafish provide an attractive model organism for drug development.
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Affiliation(s)
- Usua Oyarbide
- Department of Pediatrics, Children's Hospital of Richmond and Massey Cancer Center at Virginia Commonwealth University, Richmond, VA, USA
| | - Jacek Topczewski
- Department of Pediatrics, Stanley Manne Children's Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, Medical University of Lublin, Poland
| | - Seth J Corey
- Department of Pediatrics, Children's Hospital of Richmond and Massey Cancer Center at Virginia Commonwealth University, Richmond, VA, USA .,Department of Microbiology/Immunology, Virginia Commonwealth University, USA.,Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, USA
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19
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Ayodele BA, Mirams M, Pagel CN, Mackie EJ. The vacuolar H + ATPase V 0 subunit d 2 is associated with chondrocyte hypertrophy and supports chondrocyte differentiation. Bone Rep 2017; 7:98-107. [PMID: 29062863 PMCID: PMC5647522 DOI: 10.1016/j.bonr.2017.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/21/2017] [Accepted: 08/17/2017] [Indexed: 11/20/2022] Open
Abstract
Chondrocyte hypertrophy makes important contributions to bone development and growth. We have investigated a number of novel cartilage genes identified in a recent transcriptomic study to determine whether they are differentially expressed between different zones of equine foetal growth cartilage. Twelve genes (ATP6V0D2, BAK1, DDX5, GNB1, PIP4K2A, RAP1B, RPS7, SRSF3, SUB1, TMSB4, TPI1 and WSB2) were found to be more highly expressed in the zone of hypertrophic chondrocytes than in the reserve or proliferative zones, whereas FOXA3 and SERPINA1 were expressed at lower levels in the hypertrophic zone than in the reserve zone. ATP6V0D2, which encodes vacuolar H+ ATPase (V-ATPase) V0 subunit d2 (ATP6V0D2), was selected for further study. Immunohistochemical analysis of ATP6V0D2 in growth cartilage showed stronger staining in hypertrophic than in reserve zone or proliferative chondrocytes. Expression of ATP6V0D2 mRNA and protein was up-regulated in the mouse chondrocytic ATDC5 cell line by conditions inducing expression of hypertrophy-associated genes including Col10a1 and Mmp13 (differentiation medium). In ATDC5 cells cultured in control medium, knockdown of Atp6v0d2 or inhibition of V-ATPase activity using bafilomycin A1 caused a decrease in Col2a1 expression, and in cells cultured in differentiation medium the two treatments caused a decrease in nuclear area. Inhibition of V-ATPase, but not Atp6v0d2 knockdown, prevented the upregulation of Col10a1, Mmp13 and Vegf by differentiation medium, while Atp6v0d2 knockdown, but not inhibition of V-ATPase, caused an increase in the number of ATDC5 cells cultured in differentiation medium. These observations identify ATP6V0D2 as a novel chondrocyte hypertrophy-associated gene. The results are consistent with roles for V-ATPase, both ATP6V0D2-dependent and -independent, in supporting chondrocyte differentiation and hypertrophy.
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Key Words
- ABH, alcian blue/haematoxylin/eosin/acid fuchsin stain
- ATP6V0D2
- ATP6V0D2, vacuolar H+ ATPase V0 subunit d2
- Chondrocyte
- DAPI, 4′,6-diamidino-2-phenylindole
- DMEM, Dulbecco's modified Eagle's medium
- Endochondral ossification
- FCS, foetal calf serum
- Hypertrophy
- MMP-13, matrix metalloproteinase-13
- MNE, mean normalised expression
- PBS, phosphate-buffered saline
- V-ATPase, vacuolar H+ ATPase
- Vacuolar H+-ATPase
- qPCR, quantitative polymerase chain reaction
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20
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Takafuji T, Kayama K, Sugimoto N, Fujita M. GRWD1, a new player among oncogenesis-related ribosomal/nucleolar proteins. Cell Cycle 2017; 16:1397-1403. [PMID: 28722511 DOI: 10.1080/15384101.2017.1338987] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Increasing attention has been paid to certain ribosomal or ribosome biosynthesis-related proteins involved in oncogenesis. Members of one group are classified as "tumor suppressive factors" represented by RPL5 and RPL11; loss of their functions leads to cancer predisposition. RPL5 and RPL11 prevent tumorigenesis by binding to and inhibiting the MDM2 ubiquitin ligase and thereby up-regulating p53. Many other candidate tumor suppressive ribosomal/nucleolar proteins have been suggested. However, it remains to be experimentally clarified whether many of these factors can actually prevent tumorigenesis and if so, how they do so. Conversely, some ribosomal/nucleolar proteins promote tumorigenesis. For example, PICT1 binds to and anchors RPL11 in nucleoli, down-regulating p53 and promoting tumorigenesis. GRWD1 was recently identified as another such factor. When overexpressed, GRWD1 suppresses p53 and transforms normal human cells, probably by binding to RPL11 and sequestrating it from MDM2. However, other pathways may also be involved.
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Affiliation(s)
- Takuya Takafuji
- a Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences , Kyushu University , Higashi-ku, Fukuoka , Japan
| | - Kota Kayama
- a Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences , Kyushu University , Higashi-ku, Fukuoka , Japan
| | - Nozomi Sugimoto
- a Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences , Kyushu University , Higashi-ku, Fukuoka , Japan
| | - Masatoshi Fujita
- a Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences , Kyushu University , Higashi-ku, Fukuoka , Japan
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21
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Adam S, Melguizo Sanchis D, El-Kamah G, Samarasinghe S, Alharthi S, Armstrong L, Lako M. Concise Review: Getting to the Core of Inherited Bone Marrow Failures. Stem Cells 2016; 35:284-298. [PMID: 27870251 PMCID: PMC5299470 DOI: 10.1002/stem.2543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/15/2016] [Accepted: 10/28/2016] [Indexed: 12/20/2022]
Abstract
Bone marrow failure syndromes (BMFS) are a group of disorders with complex pathophysiology characterized by a common phenotype of peripheral cytopenia and/or hypoplastic bone marrow. Understanding genetic factors contributing to the pathophysiology of BMFS has enabled the identification of causative genes and development of diagnostic tests. To date more than 40 mutations in genes involved in maintenance of genomic stability, DNA repair, ribosome and telomere biology have been identified. In addition, pathophysiological studies have provided insights into several biological pathways leading to the characterization of genotype/phenotype correlations as well as the development of diagnostic approaches and management strategies. Recent developments in bone marrow transplant techniques and the choice of conditioning regimens have helped improve transplant outcomes. However, current morbidity and mortality remain unacceptable underlining the need for further research in this area. Studies in mice have largely been unable to mimic disease phenotype in humans due to difficulties in fully replicating the human mutations and the differences between mouse and human cells with regard to telomere length regulation, processing of reactive oxygen species and lifespan. Recent advances in induced pluripotency have provided novel insights into disease pathogenesis and have generated excellent platforms for identifying signaling pathways and functional mapping of haplo‐insufficient genes involved in large‐scale chromosomal deletions–associated disorders. In this review, we have summarized the current state of knowledge in the field of BMFS with specific focus on modeling the inherited forms and how to best utilize these models for the development of targeted therapies. Stem Cells2017;35:284–298
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Affiliation(s)
- Soheir Adam
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA.,Hematology Department, Medical School, King Abdulaziz University, Jeddah, KSA
| | | | - Ghada El-Kamah
- Division of Human Genetics & Genome Research, National Research Center, Cairo, Egypt
| | - Sujith Samarasinghe
- Department of Hematology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Sameer Alharthi
- Princess Al Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, KSA
| | - Lyle Armstrong
- Institute of Genetic Medicine, Newcastle University, United Kingdom
| | - Majlinda Lako
- Institute of Genetic Medicine, Newcastle University, United Kingdom
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22
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Mikhaleva A, Kannan M, Wagner C, Yalcin B. Histomorphological Phenotyping of the Adult Mouse Brain. ACTA ACUST UNITED AC 2016; 6:307-332. [PMID: 27584555 DOI: 10.1002/cpmo.12] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
This article describes a series of standard operating procedures for morphological phenotyping of the mouse brain using basic histology. Many histological studies of the mouse brain use qualitative approaches based on what the human eye can detect. Consequently, some phenotypic information may be missed. Here we describe a quantitative approach for the assessment of brain morphology that is simple and robust. A total of 78 measurements are made throughout the brain at specific and well-defined regions, including the cortex, the hippocampus, and the cerebellum. Experimental design and timeline considerations, including strain background effects, the importance of sectioning quality, measurement variability, and efforts to correct human errors are discussed. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Anna Mikhaleva
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Meghna Kannan
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Institute of Genetics and Molecular and Cellular Biology, Illkirch, France.,National Centre for Scientific Research, UMR7104, Illkirch, France.,National Institute of Health and Medical Research, U964, Illkirch, France.,University of Strasbourg, Illkirch, France
| | - Christel Wagner
- Institute of Genetics and Molecular and Cellular Biology, Illkirch, France.,National Centre for Scientific Research, UMR7104, Illkirch, France.,National Institute of Health and Medical Research, U964, Illkirch, France.,University of Strasbourg, Illkirch, France
| | - Binnaz Yalcin
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Institute of Genetics and Molecular and Cellular Biology, Illkirch, France.,National Centre for Scientific Research, UMR7104, Illkirch, France.,National Institute of Health and Medical Research, U964, Illkirch, France.,University of Strasbourg, Illkirch, France
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23
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Danilova N, Gazda HT. Ribosomopathies: how a common root can cause a tree of pathologies. Dis Model Mech 2016; 8:1013-26. [PMID: 26398160 PMCID: PMC4582105 DOI: 10.1242/dmm.020529] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Defects in ribosome biogenesis are associated with a group of diseases called the ribosomopathies, of which Diamond-Blackfan anemia (DBA) is the most studied. Ribosomes are composed of ribosomal proteins (RPs) and ribosomal RNA (rRNA). RPs and multiple other factors are necessary for the processing of pre-rRNA, the assembly of ribosomal subunits, their export to the cytoplasm and for the final assembly of subunits into a ribosome. Haploinsufficiency of certain RPs causes DBA, whereas mutations in other factors cause various other ribosomopathies. Despite the general nature of their underlying defects, the clinical manifestations of ribosomopathies differ. In DBA, for example, red blood cell pathology is especially evident. In addition, individuals with DBA often have malformations of limbs, the face and various organs, and also have an increased risk of cancer. Common features shared among human DBA and animal models have emerged, such as small body size, eye defects, duplication or overgrowth of ectoderm-derived structures, and hematopoietic defects. Phenotypes of ribosomopathies are mediated both by p53-dependent and -independent pathways. The current challenge is to identify differences in response to ribosomal stress that lead to specific tissue defects in various ribosomopathies. Here, we review recent findings in this field, with a particular focus on animal models, and discuss how, in some cases, the different phenotypes of ribosomopathies might arise from differences in the spatiotemporal expression of the affected genes. Summary: This paper reviews recent data on Diamond Blackfan anemia and discusses them in connection with other ribosomopathies.
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Affiliation(s)
- Nadia Danilova
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Hanna T Gazda
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA Broad Institute, Cambridge, MA 02142, USA
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24
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Liu Y, Deisenroth C, Zhang Y. RP-MDM2-p53 Pathway: Linking Ribosomal Biogenesis and Tumor Surveillance. Trends Cancer 2016; 2:191-204. [PMID: 28741571 DOI: 10.1016/j.trecan.2016.03.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/03/2016] [Accepted: 03/04/2016] [Indexed: 12/18/2022]
Abstract
Ribosomal biogenesis is tightly associated with cellular activities, such as growth, proliferation, and cell cycle progression. Perturbations in ribosomal biogenesis can initiate so-called nucleolar stress. The process through which ribosomal proteins (RPs) transduce nucleolar stress signals via MDM2 to p53 has been described as a crucial tumor-suppression mechanism. In this review we focus on recent progress pertaining to the function and mechanism of RPs in association with the MDM2-p53 tumor-suppression network, and the potential implications this surveillance network has for cancer development.
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Affiliation(s)
- Yong Liu
- Department of Radiation Oncology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chad Deisenroth
- The Hamner Institutes for Health Sciences, Institute for Chemical Safety Sciences, 6 Davis Drive, PO Box 12137, Research Triangle Park, NC 27709, USA
| | - Yanping Zhang
- Department of Radiation Oncology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical College, Xuzhou, Jiangsu 221002, China.
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25
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Reconciling diverse mammalian pigmentation patterns with a fundamental mathematical model. Nat Commun 2016; 7:10288. [PMID: 26732977 PMCID: PMC4729835 DOI: 10.1038/ncomms10288] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 11/26/2015] [Indexed: 12/18/2022] Open
Abstract
Bands of colour extending laterally from the dorsal to ventral trunk are a common feature of mouse chimeras. These stripes were originally taken as evidence of the directed dorsoventral migration of melanoblasts (the embryonic precursors of melanocytes) as they colonize the developing skin. Depigmented ‘belly spots' in mice with mutations in the receptor tyrosine kinase Kit are thought to represent a failure of this colonization, either due to impaired migration or proliferation. Tracing of single melanoblast clones, however, has revealed a diffuse distribution with high levels of axial mixing—hard to reconcile with directed migration. Here we construct an agent-based stochastic model calibrated by experimental measurements to investigate the formation of diffuse clones, chimeric stripes and belly spots. Our observations indicate that melanoblast colonization likely proceeds through a process of undirected migration, proliferation and tissue expansion, and that reduced proliferation is the cause of the belly spots in Kit mutants. How embryonic melanoblast behaviour influences adult pigmentation patterns and causes patterning defects is unclear. Here, Mort et al. construct a stochastic model parameterised experimentally to show that melanoblast migration is undirected and that reduced proliferation causes patterning defects.
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26
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Shi Z, Barna M. Translating the genome in time and space: specialized ribosomes, RNA regulons, and RNA-binding proteins. Annu Rev Cell Dev Biol 2015; 31:31-54. [PMID: 26443190 DOI: 10.1146/annurev-cellbio-100814-125346] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A central question in cell and developmental biology is how the information encoded in the genome is differentially interpreted to generate a diverse array of cell types. A growing body of research on posttranscriptional gene regulation is revealing that both global protein synthesis rates and the translation of specific mRNAs are highly specialized in different cell types. How this exquisite translational regulation is achieved is the focus of this review. Two levels of regulation are discussed: the translation machinery and cis-acting elements within mRNAs. Recent evidence shows that the ribosome itself directs how the genome is translated in time and space and reveals surprising functional specificity in individual components of the core translation machinery. We are also just beginning to appreciate the rich regulatory information embedded in the untranslated regions of mRNAs, which direct the selective translation of transcripts. These hidden RNA regulons may interface with a myriad of RNA-binding proteins and specialized translation machinery to provide an additional layer of regulation to how transcripts are spatiotemporally expressed. Understanding this largely unexplored world of translational codes hardwired in the core translation machinery is an exciting new research frontier fundamental to our understanding of gene regulation, organismal development, and evolution.
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Affiliation(s)
- Zhen Shi
- Department of Developmental Biology and Department of Genetics, Stanford University, Stanford, California 94305;
| | - Maria Barna
- Department of Developmental Biology and Department of Genetics, Stanford University, Stanford, California 94305;
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27
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Tourlakis ME, Zhang S, Ball HL, Gandhi R, Liu H, Zhong J, Yuan JS, Guidos CJ, Durie PR, Rommens JM. In Vivo Senescence in the Sbds-Deficient Murine Pancreas: Cell-Type Specific Consequences of Translation Insufficiency. PLoS Genet 2015; 11:e1005288. [PMID: 26057580 PMCID: PMC4461263 DOI: 10.1371/journal.pgen.1005288] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 05/18/2015] [Indexed: 01/01/2023] Open
Abstract
Genetic models of ribosome dysfunction show selective organ failure, highlighting a gap in our understanding of cell-type specific responses to translation insufficiency. Translation defects underlie a growing list of inherited and acquired cancer-predisposition syndromes referred to as ribosomopathies. We sought to identify molecular mechanisms underlying organ failure in a recessive ribosomopathy, with particular emphasis on the pancreas, an organ with a high and reiterative requirement for protein synthesis. Biallelic loss of function mutations in SBDS are associated with the ribosomopathy Shwachman-Diamond syndrome, which is typified by pancreatic dysfunction, bone marrow failure, skeletal abnormalities and neurological phenotypes. Targeted disruption of Sbds in the murine pancreas resulted in p53 stabilization early in the postnatal period, specifically in acinar cells. Decreased Myc expression was observed and atrophy of the adult SDS pancreas could be explained by the senescence of acinar cells, characterized by induction of Tgfβ, p15Ink4b and components of the senescence-associated secretory program. This is the first report of senescence, a tumour suppression mechanism, in association with SDS or in response to a ribosomopathy. Genetic ablation of p53 largely resolved digestive enzyme synthesis and acinar compartment hypoplasia, but resulted in decreased cell size, a hallmark of decreased translation capacity. Moreover, p53 ablation resulted in expression of acinar dedifferentiation markers and extensive apoptosis. Our findings indicate a protective role for p53 and senescence in response to Sbds ablation in the pancreas. In contrast to the pancreas, the Tgfβ molecular signature was not detected in fetal bone marrow, liver or brain of mouse models with constitutive Sbds ablation. Nevertheless, as observed with the adult pancreas phenotype, disease phenotypes of embryonic tissues, including marked neuronal cell death due to apoptosis, were determined to be p53-dependent. Our findings therefore point to cell/tissue-specific responses to p53-activation that include distinction between apoptosis and senescence pathways, in the context of translation disruption. Growth of all living things relies on protein synthesis. Failure of components of the complex protein synthesis machinery underlies a growing list of inherited and acquired multi—organ syndromes referred to as ribosomopathies. While ribosomes, the critical working components of the protein synthesis machinery, are required in all cell types to translate the genetic code, only certain organs manifest clinical symptoms in ribosomopathies, indicating specific cell-type features of protein synthesis control. Further, many of these diseases result in cancer despite an inherent deficit in growth. Here we report a range of consequences of protein synthesis insufficiency with loss of a broadly expressed ribosome factor, leading to growth impairment and cell cycle arrest at different stages. Apparent induction of p53-dependent cell death and arrest pathways included apoptosis in the fetal brain and senescence in the mature exocrine pancreas. The senescence, considered a tumour suppression mechanism, was accompanied by the expression of biomarkers associated with early stages of malignant transformation. These findings inform how cancer may initiate when growth is compromised and provide new insights into cell-type specific consequences of protein synthesis insufficiency.
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Affiliation(s)
- Marina E. Tourlakis
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Siyi Zhang
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Heather L. Ball
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
| | - Rikesh Gandhi
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
| | - Hongrui Liu
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Jian Zhong
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
| | - Julie S. Yuan
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Department of Immunology, University of Toronto, Toronto, Canada
| | - Cynthia J. Guidos
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Department of Immunology, University of Toronto, Toronto, Canada
| | - Peter R. Durie
- Program in Physiology & Experimental Medicine, Research Institute, Division of Gastroenterology & Nutrition, The Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, Canada
| | - Johanna M. Rommens
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- * E-mail:
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28
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Zhou X, Liao WJ, Liao JM, Liao P, Lu H. Ribosomal proteins: functions beyond the ribosome. J Mol Cell Biol 2015; 7:92-104. [PMID: 25735597 DOI: 10.1093/jmcb/mjv014] [Citation(s) in RCA: 427] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 12/05/2014] [Indexed: 01/05/2023] Open
Abstract
Although ribosomal proteins are known for playing an essential role in ribosome assembly and protein translation, their ribosome-independent functions have also been greatly appreciated. Over the past decade, more than a dozen of ribosomal proteins have been found to activate the tumor suppressor p53 pathway in response to ribosomal stress. In addition, these ribosomal proteins are involved in various physiological and pathological processes. This review is composed to overview the current understanding of how ribosomal stress provokes the accumulation of ribosome-free ribosomal proteins, as well as the ribosome-independent functions of ribosomal proteins in tumorigenesis, immune signaling, and development. We also propose the potential of applying these pieces of knowledge to the development of ribosomal stress-based cancer therapeutics.
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Affiliation(s)
- Xiang Zhou
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Wen-Juan Liao
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jun-Ming Liao
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Peng Liao
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Hua Lu
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
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29
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Armistead J, Patel N, Wu X, Hemming R, Chowdhury B, Basra GS, Del Bigio MR, Ding H, Triggs-Raine B. Growth arrest in the ribosomopathy, Bowen-Conradi syndrome, is due to dramatically reduced cell proliferation and a defect in mitotic progression. Biochim Biophys Acta Mol Basis Dis 2015; 1852:1029-37. [PMID: 25708872 DOI: 10.1016/j.bbadis.2015.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/10/2015] [Accepted: 02/14/2015] [Indexed: 02/05/2023]
Abstract
Bowen-Conradi syndrome (BCS) is a ribosomopathy characterized by severe developmental delay and growth failure that typically leads to death by one year of age. It is caused by a c.257A>G, p.D86G substitution in the ribosomal biogenesis protein, Essential for Mitotic Growth 1 (EMG1). We generated a knock-in of the D86G substitution in mice to characterize the effects of EMG1 deficiency, particularly in the brain, where EMG1 expression is high. Embryos homozygous for the mutation in Emg1 were small for gestational age with neural tube defects, and died between embryonic days 8.5 and 12.5. These embryos exhibited dramatically reduced cell proliferation, which we also detected in autopsy brain tissue and bone marrow of BCS patients, consistent with a requirement for high levels of EMG1 in tissues with rapid cell proliferation. In fibroblasts derived from the BCS mouse embryos, we detected a high proportion of binucleated cells, indicating that a mitotic defect underlies the growth arrest in BCS. These studies add to growing evidence of a link between ribosome biogenesis, mitotic progression, and brain development that is currently unexplored.
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Affiliation(s)
- Joy Armistead
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada; Manitoba Institute of Child Health, Winnipeg, MB, Canada; Institute of Developmental Biology, University of Cologne, Cologne, Germany.
| | - Nehal Patel
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada.
| | - Xiaoli Wu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada.
| | - Richard Hemming
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada.
| | - Biswajit Chowdhury
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada; Manitoba Institute of Child Health, Winnipeg, MB, Canada.
| | - Gagandeep Singh Basra
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada.
| | - Marc R Del Bigio
- Department of Pathology, University of Manitoba, Winnipeg, MB, Canada; Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada; Manitoba Institute of Child Health, Winnipeg, MB, Canada.
| | - Hao Ding
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada.
| | - Barbara Triggs-Raine
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada; Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada; Manitoba Institute of Child Health, Winnipeg, MB, Canada.
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30
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Gamalinda M, Woolford JL. Deletion of L4 domains reveals insights into the importance of ribosomal protein extensions in eukaryotic ribosome assembly. RNA (NEW YORK, N.Y.) 2014; 20:1725-31. [PMID: 25246649 PMCID: PMC4201825 DOI: 10.1261/rna.046649.114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Numerous ribosomal proteins have a striking bipartite architecture: a globular body positioned on the ribosomal exterior and an internal loop buried deep into the rRNA core. In eukaryotes, a significant number of conserved r-proteins have evolved extra amino- or carboxy-terminal tail sequences, which thread across the solvent-exposed surface. The biological importance of these extended domains remains to be established. In this study, we have investigated the universally conserved internal loop and the eukaryote-specific extensions of yeast L4. We show that in contrast to findings with bacterial L4, deleting the internal loop of yeast L4 causes severely impaired growth and reduced levels of large ribosomal subunits. We further report that while depleting the entire L4 protein blocks early assembly steps in yeast, deletion of only its extended internal loop affects later steps in assembly, revealing a second role for L4 during ribosome biogenesis. Surprisingly, deletion of the entire eukaryote-specific carboxy-terminal tail of L4 has no effect on viability, production of 60S subunits, or translation. These unexpected observations provide impetus to further investigate the functions of ribosomal protein extensions, especially eukaryote-specific examples, in ribosome assembly and function.
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Affiliation(s)
- Michael Gamalinda
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - John L Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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31
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Wang W, Nag S, Zhang X, Wang MH, Wang H, Zhou J, Zhang R. Ribosomal proteins and human diseases: pathogenesis, molecular mechanisms, and therapeutic implications. Med Res Rev 2014; 35:225-85. [PMID: 25164622 DOI: 10.1002/med.21327] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ribosomes are essential components of the protein synthesis machinery. The process of ribosome biogenesis is well organized and tightly regulated. Recent studies have shown that ribosomal proteins (RPs) have extraribosomal functions that are involved in cell proliferation, differentiation, apoptosis, DNA repair, and other cellular processes. The dysfunction of RPs has been linked to the development and progression of hematological, metabolic, and cardiovascular diseases and cancer. Perturbation of ribosome biogenesis results in ribosomal stress, which triggers activation of the p53 signaling pathway through RPs-MDM2 interactions, resulting in p53-dependent cell cycle arrest and apoptosis. RPs also regulate cellular functions through p53-independent mechanisms. We herein review the recent advances in several forefronts of RP research, including the understanding of their biological features and roles in regulating cellular functions, maintaining cell homeostasis, and their involvement in the pathogenesis of human diseases. We also highlight the translational potential of this research for the identification of molecular biomarkers, and in the discovery and development of novel treatments for human diseases.
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Affiliation(s)
- Wei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas, 79106; Cancer Biology Center, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas, 79106
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32
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Zsögön A, Szakonyi D, Shi X, Byrne ME. Ribosomal Protein RPL27a Promotes Female Gametophyte Development in a Dose-Dependent Manner. PLANT PHYSIOLOGY 2014; 165:1133-1143. [PMID: 24872379 PMCID: PMC4081327 DOI: 10.1104/pp.114.241778] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Ribosomal protein mutations in Arabidopsis (Arabidopsis thaliana) result in a range of specific developmental phenotypes. Why ribosomal protein mutants have specific phenotypes is not fully known, but such defects potentially result from ribosome insufficiency, ribosome heterogeneity, or extraribosomal functions of ribosomal proteins. Here, we report that ovule development is sensitive to the level of Ribosomal Protein L27a (RPL27a) and is disrupted by mutations in the two paralogs RPL27aC and RPL27aB. Mutations in RPL27aC result in high levels of female sterility, whereas mutations in RPL27aB have a significant but lesser effect on fertility. Progressive reduction in RPL27a function results in increasing sterility, indicating a dose-dependent relationship between RPL27a and female fertility. RPL27a levels in both the sporophyte and gametophyte affect female gametogenesis, with different developmental outcomes determined by the dose of RPL27a. These results demonstrate that RPL27aC and RPL27aB act redundantly and reveal a function for RPL27a in coordinating complex interactions between sporophyte and gametophyte during ovule development.
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Affiliation(s)
- Agustin Zsögön
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Dóra Szakonyi
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Xiuling Shi
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Mary E Byrne
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
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33
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Beck-Cormier S, Escande M, Souilhol C, Vandormael-Pournin S, Sourice S, Pilet P, Babinet C, Cohen-Tannoudji M. Notchless is required for axial skeleton formation in mice. PLoS One 2014; 9:e98507. [PMID: 24875805 PMCID: PMC4038589 DOI: 10.1371/journal.pone.0098507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 05/03/2014] [Indexed: 01/19/2023] Open
Abstract
Maintenance of cell survival is essential for proper embryonic development. In the mouse, Notchless homolog 1 (Drosophila) (Nle1) is instrumental for survival of cells of the inner cell mass upon implantation. Here, we analyze the function of Nle1 after implantation using the Meox2tm1(cre)Sor mouse that expresses the Cre recombinase specifically in the epiblast at E5.5. First, we find that NLE1 function is required in epiblast cells, as Nle1-deficient cells are rapidly eliminated. In this report, we also show that the Meox2Cre transgene is active in specific tissues during organogenesis. In particular, we detect high Cre expression in the vertebral column, ribs, limbs and tailbud. We took advantage of this dynamic expression profile to analyze the effects of inducing mosaic deletion of Nle1 in the embryo. We show that Nle1 deletion in this context, results in severe developmental anomalies leading to lethality at birth. Mutant embryos display multiple developmental defects in particular during axial skeletal formation. We also provide evidence that axial defects are due to an increase in apoptotic cell death in the somite at E9.5. These data demonstrate an essential role for Nle1 during organogenesis and in particular during axial development.
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Affiliation(s)
- Sarah Beck-Cormier
- Mouse Functional Genetics, Department of Developmental & Stem Cell Biology, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique, URA 2578, Institut Pasteur, Paris, France
- * E-mail:
| | - Marie Escande
- Mouse Functional Genetics, Department of Developmental & Stem Cell Biology, Institut Pasteur, Paris, France
| | - Céline Souilhol
- Mouse Functional Genetics, Department of Developmental & Stem Cell Biology, Institut Pasteur, Paris, France
| | - Sandrine Vandormael-Pournin
- Mouse Functional Genetics, Department of Developmental & Stem Cell Biology, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique, URA 2578, Institut Pasteur, Paris, France
| | - Sophie Sourice
- Institut National de la Santé et de la recherche Médicale, U791, LIOAD, STEP group “Skeletal Tissue Engineering and Physiopathology”, Nantes, France
| | - Paul Pilet
- Institut National de la Santé et de la recherche Médicale, U791, LIOAD, STEP group “Skeletal Tissue Engineering and Physiopathology”, Nantes, France
| | - Charles Babinet
- Mouse Functional Genetics, Department of Developmental & Stem Cell Biology, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique, URA 2578, Institut Pasteur, Paris, France
| | - Michel Cohen-Tannoudji
- Mouse Functional Genetics, Department of Developmental & Stem Cell Biology, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique, URA 2578, Institut Pasteur, Paris, France
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Uslu VV, Petretich M, Ruf S, Langenfeld K, Fonseca NA, Marioni JC, Spitz F. Long-range enhancers regulating Myc expression are required for normal facial morphogenesis. Nat Genet 2014; 46:753-8. [DOI: 10.1038/ng.2971] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 04/08/2014] [Indexed: 12/12/2022]
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Armistead J, Triggs-Raine B. Diverse diseases from a ubiquitous process: the ribosomopathy paradox. FEBS Lett 2014; 588:1491-500. [PMID: 24657617 DOI: 10.1016/j.febslet.2014.03.024] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/08/2014] [Accepted: 03/12/2014] [Indexed: 01/03/2023]
Abstract
Collectively, the ribosomopathies are caused by defects in ribosome biogenesis. Although these disorders encompass deficiencies in a ubiquitous and fundamental process, the clinical manifestations are extremely variable and typically display tissue specificity. Research into this paradox has offered fascinating new insights into the role of the ribosome in the regulation of mRNA translation, cell cycle control, and signaling pathways involving TP53, MYC and mTOR. Several common features of ribosomopathies such as small stature, cancer predisposition, and hematological defects, point to how these diverse diseases may be related at a molecular level.
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Affiliation(s)
- Joy Armistead
- Department of Biochemistry and Medical Genetics, The University of Manitoba, 745 Bannatyne Ave., Winnipeg, MB R3E 0J9, Canada
| | - Barbara Triggs-Raine
- Department of Biochemistry and Medical Genetics, The University of Manitoba, 745 Bannatyne Ave., Winnipeg, MB R3E 0J9, Canada; The Manitoba Institute of Child Health, 715 McDermot Ave., Winnipeg, MB R3E 3P4, Canada.
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Yadav GV, Chakraborty A, Uechi T, Kenmochi N. Ribosomal protein deficiency causes Tp53-independent erythropoiesis failure in zebrafish. Int J Biochem Cell Biol 2014; 49:1-7. [PMID: 24417973 DOI: 10.1016/j.biocel.2014.01.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 11/17/2013] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
Abstract
Diamond-Blackfan anemia is an inherited genetic disease caused by mutations in ribosomal protein genes. The disease is characterized by bone marrow failure, congenital anomalies, and a severe erythroid defect. The activation of the TP53 pathway has been suggested to be critical for the pathophysiology of Diamond-Blackfan anemia. While this pathway plays a role in the morphological defects that associate with ribosomal protein loss-of-function in animal models, its role in the erythroid defects has not been clearly established. To understand the specificity of erythroid defects in Diamond-Blackfan anemia, we knocked down five RP genes (two Diamond-Blackfan anemia-associated and three non-Diamond-Blackfan anemia-associated) in zebrafish and analyzed the effects on the developmental and erythroid phenotypes in the presence and absence of Tp53. The co-inhibition of Tp53 activity rescued the morphological deformities but did not alleviate the erythroid aplasia indicating that ribosomal protein deficiency causes erythroid failure in a Tp53-independent manner. Interestingly, treatment with L-Leucine or L-Arginine, amino acids that augment mRNA translation via mTOR pathway, rescued the morphological defects and resulted in a substantial recovery of erythroid cells. Our results suggest that altered translation because of impaired ribosome function could be responsible for the morphological and erythroid defects in ribosomal protein-deficient zebrafish.
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Affiliation(s)
- Gnaneshwar V Yadav
- Frontier Science Research Center, University of Miyazaki, Kiyotake, Miyazaki, Japan
| | - Anirban Chakraborty
- Frontier Science Research Center, University of Miyazaki, Kiyotake, Miyazaki, Japan
| | - Tamayo Uechi
- Frontier Science Research Center, University of Miyazaki, Kiyotake, Miyazaki, Japan
| | - Naoya Kenmochi
- Frontier Science Research Center, University of Miyazaki, Kiyotake, Miyazaki, Japan.
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Bursac S, Brdovcak MC, Donati G, Volarevic S. Activation of the tumor suppressor p53 upon impairment of ribosome biogenesis. Biochim Biophys Acta Mol Basis Dis 2013; 1842:817-30. [PMID: 24514102 DOI: 10.1016/j.bbadis.2013.08.014] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 08/27/2013] [Indexed: 12/31/2022]
Abstract
Errors in ribosome biogenesis can result in quantitative or qualitative defects in protein synthesis and consequently lead to improper execution of the genetic program and the development of specific diseases. Evidence has accumulated over the last decade suggesting that perturbation of ribosome biogenesis triggers a p53-activating checkpoint signaling pathway, often referred to as the ribosome biogenesis stress checkpoint pathway. Although it was originally suggested that p53 has a prominent role in preventing diseases by monitoring the fidelity of ribosome biogenesis, recent work has demonstrated that p53 activation upon impairment of ribosome biogenesis also mediates pathological manifestations in humans. Perturbations of ribosome biogenesis can trigger a p53-dependent checkpoint signaling pathway independent of DNA damage and the tumor suppressor ARF through inhibitory interactions of specific ribosomal components with the p53 negative regulator, Mdm2. Here we review the recent advances made toward understanding of this newly-recognized checkpoint signaling pathway, its role in health and disease, and discuss possible future directions in this exciting research field. This article is part of a Special Issue entitled: Role of the Nucleolus in Human Disease.
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Affiliation(s)
- Sladana Bursac
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Braće Branchetta 20, 51000 Rijeka, Croatia
| | - Maja Cokaric Brdovcak
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Braće Branchetta 20, 51000 Rijeka, Croatia
| | - Giulio Donati
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, Institut d'Investigacio' Biome'dica de Bellvitge (IDIBELL), 08908 Hospitalet de Llobregat, Barcelona, Spain
| | - Sinisa Volarevic
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Braće Branchetta 20, 51000 Rijeka, Croatia.
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Affiliation(s)
- Tamara Terzian
- University of Colorado Denver, Dermatology Department and Center for Regenerative and Medicine and Stem Cell Biology, Aurora, Colorado, United States of America
- * E-mail: (TT); (NB)
| | - Neil Box
- University of Colorado Denver, Dermatology Department and Center for Regenerative and Medicine and Stem Cell Biology, Aurora, Colorado, United States of America
- * E-mail: (TT); (NB)
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