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Samanta P, Ghosh R, Pakhira S, Mondal M, Biswas S, Sarkar R, Bhowmik A, Saha P, Hajra S. Ribosome biogenesis and ribosomal proteins in cancer stem cells: a new therapeutic prospect. Mol Biol Rep 2024; 51:1016. [PMID: 39325314 DOI: 10.1007/s11033-024-09963-y] [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: 08/13/2024] [Accepted: 09/20/2024] [Indexed: 09/27/2024]
Abstract
Ribosome has been considered as the fundamental macromolecular machine involved in protein synthesis in both prokaryotic and eukaryotic cells. This protein synthesis machinery consists of several rRNAs and numerous proteins. All of these factors are synthesized, translocated and assembled in a tightly regulated process known as ribosome biogenesis. Any impairment in this process causes development of several diseases like cancer. According to growing evidences, cancer cells display alteration of several ribosomal proteins. Besides, most of them are considered as key molecules involved in ribosome biogenesis, suggesting a correlation between those proteins and formation of ribosomes. Albeit, defective ribosome biogenesis in several cancers has gained prime importance, regulation of this process in cancer stem cells (CSCs) are still unrecognized. In this article, we aim to summarize the alteration of ribosome biogenesis and ribosomal proteins in CSCs. Moreover, we want to highlight the relation of ribosome biogenesis with hypoxia and drug resistance in CSCs based on the existing evidences. Lastly, this review wants to pay attention about the promising anti-cancer drugs which have potential to inhibit ribosome biogenesis in cancer cells as well as CSCs.
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Affiliation(s)
- Priya Samanta
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Rituparna Ghosh
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Shampa Pakhira
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Mrinmoyee Mondal
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Souradeep Biswas
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Rupali Sarkar
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Arijit Bhowmik
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Prosenjit Saha
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Subhadip Hajra
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India.
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Hwang SP, Denicourt C. The impact of ribosome biogenesis in cancer: from proliferation to metastasis. NAR Cancer 2024; 6:zcae017. [PMID: 38633862 PMCID: PMC11023387 DOI: 10.1093/narcan/zcae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/23/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
The dysregulation of ribosome biogenesis is a hallmark of cancer, facilitating the adaptation to altered translational demands essential for various aspects of tumor progression. This review explores the intricate interplay between ribosome biogenesis and cancer development, highlighting dynamic regulation orchestrated by key oncogenic signaling pathways. Recent studies reveal the multifaceted roles of ribosomes, extending beyond protein factories to include regulatory functions in mRNA translation. Dysregulated ribosome biogenesis not only hampers precise control of global protein production and proliferation but also influences processes such as the maintenance of stem cell-like properties and epithelial-mesenchymal transition, contributing to cancer progression. Interference with ribosome biogenesis, notably through RNA Pol I inhibition, elicits a stress response marked by nucleolar integrity loss, and subsequent G1-cell cycle arrest or cell death. These findings suggest that cancer cells may rely on heightened RNA Pol I transcription, rendering ribosomal RNA synthesis a potential therapeutic vulnerability. The review further explores targeting ribosome biogenesis vulnerabilities as a promising strategy to disrupt global ribosome production, presenting therapeutic opportunities for cancer treatment.
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Affiliation(s)
- Sseu-Pei Hwang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Catherine Denicourt
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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3
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Sullivan DK, Deutzmann A, Yarbrough J, Krishnan MS, Gouw AM, Bellovin DI, Adam SJ, Liefwalker DF, Dhanasekaran R, Felsher DW. MYC oncogene elicits tumorigenesis associated with embryonic, ribosomal biogenesis, and tissue-lineage dedifferentiation gene expression changes. Oncogene 2022; 41:4960-4970. [PMID: 36207533 PMCID: PMC10257951 DOI: 10.1038/s41388-022-02458-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 11/09/2022]
Abstract
MYC is a transcription factor frequently overexpressed in cancer. To determine how MYC drives the neoplastic phenotype, we performed transcriptomic analysis using a panel of MYC-driven autochthonous transgenic mouse models. We found that MYC elicited gene expression changes mostly in a tissue- and lineage-specific manner across B-cell lymphoma, T-cell acute lymphoblastic lymphoma, hepatocellular carcinoma, renal cell carcinoma, and lung adenocarcinoma. However, despite these gene expression changes being mostly tissue-specific, we uncovered a convergence on a common pattern of upregulation of embryonic stem cell gene programs and downregulation of tissue-of-origin gene programs across MYC-driven cancers. These changes are representative of lineage dedifferentiation, that may be facilitated by epigenetic alterations that occur during tumorigenesis. Moreover, while several cellular processes are represented among embryonic stem cell genes, ribosome biogenesis is most specifically associated with MYC expression in human primary cancers. Altogether, MYC's capability to drive tumorigenesis in diverse tissue types appears to be related to its ability to both drive a core signature of embryonic genes that includes ribosomal biogenesis genes as well as promote tissue and lineage specific dedifferentiation.
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Affiliation(s)
- Delaney K Sullivan
- Division of Oncology, Departments of Medicine and Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Anja Deutzmann
- Division of Oncology, Departments of Medicine and Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Josiah Yarbrough
- Division of Oncology, Departments of Medicine and Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Maya S Krishnan
- Division of Oncology, Departments of Medicine and Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Arvin M Gouw
- Division of Oncology, Departments of Medicine and Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - David I Bellovin
- Division of Oncology, Departments of Medicine and Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Stacey J Adam
- Division of Oncology, Departments of Medicine and Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Daniel F Liefwalker
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Renumathy Dhanasekaran
- Division of Oncology, Departments of Medicine and Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Dean W Felsher
- Division of Oncology, Departments of Medicine and Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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Antony C, George SS, Blum J, Somers P, Thorsheim CL, Wu-Corts DJ, Ai Y, Gao L, Lv K, Tremblay MG, Moss T, Tan K, Wilusz JE, Ganley ARD, Pimkin M, Paralkar VR. Control of ribosomal RNA synthesis by hematopoietic transcription factors. Mol Cell 2022; 82:3826-3839.e9. [PMID: 36113481 PMCID: PMC9588704 DOI: 10.1016/j.molcel.2022.08.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/23/2022] [Accepted: 08/23/2022] [Indexed: 11/19/2022]
Abstract
Ribosomal RNAs (rRNAs) are the most abundant cellular RNAs, and their synthesis from rDNA repeats by RNA polymerase I accounts for the bulk of all transcription. Despite substantial variation in rRNA transcription rates across cell types, little is known about cell-type-specific factors that bind rDNA and regulate rRNA transcription to meet tissue-specific needs. Using hematopoiesis as a model system, we mapped about 2,200 ChIP-seq datasets for 250 transcription factors (TFs) and chromatin proteins to human and mouse rDNA and identified robust binding of multiple TF families to canonical TF motifs on rDNA. Using a 47S-FISH-Flow assay developed for nascent rRNA quantification, we demonstrated that targeted degradation of C/EBP alpha (CEBPA), a critical hematopoietic TF with conserved rDNA binding, caused rapid reduction in rRNA transcription due to reduced RNA Pol I occupancy. Our work identifies numerous potential rRNA regulators and provides a template for dissection of TF roles in rRNA transcription.
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Affiliation(s)
- Charles Antony
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Subin S George
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Justin Blum
- The College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Patrick Somers
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Chelsea L Thorsheim
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Dexter J Wu-Corts
- The College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuxi Ai
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Long Gao
- Beijing Advanced Innovation Center for Genomics (ICG) & Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Kaosheng Lv
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Michel G Tremblay
- Laboratory of Growth and Development, St Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre (CRCHU de Québec-Université Laval), Québec, QC G1R 3S3, Canada
| | - Tom Moss
- Laboratory of Growth and Development, St Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre (CRCHU de Québec-Université Laval), Québec, QC G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Québec, QC G1V 0A6, Canada
| | - Kai Tan
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Austen R D Ganley
- School of Biological Sciences, University of Auckland, Auckland 0623, New Zealand; Digital Life Institute, University of Auckland, Auckland 0632, New Zealand
| | - Maxim Pimkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Vikram R Paralkar
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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5
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Nucleolus and Nucleolar Stress: From Cell Fate Decision to Disease Development. Cells 2022; 11:cells11193017. [PMID: 36230979 PMCID: PMC9563748 DOI: 10.3390/cells11193017] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 11/30/2022] Open
Abstract
Besides the canonical function in ribosome biogenesis, there have been significant recent advances towards the fascinating roles of the nucleolus in stress response, cell destiny decision and disease progression. Nucleolar stress, an emerging concept describing aberrant nucleolar structure and function as a result of impaired rRNA synthesis and ribosome biogenesis under stress conditions, has been linked to a variety of signaling transductions, including but not limited to Mdm2-p53, NF-κB and HIF-1α pathways. Studies have uncovered that nucleolus is a stress sensor and signaling hub when cells encounter various stress conditions, such as nutrient deprivation, DNA damage and oxidative and thermal stress. Consequently, nucleolar stress plays a pivotal role in the determination of cell fate, such as apoptosis, senescence, autophagy and differentiation, in response to stress-induced damage. Nucleolar homeostasis has been involved in the pathogenesis of various chronic diseases, particularly tumorigenesis, neurodegenerative diseases and metabolic disorders. Mechanistic insights have revealed the indispensable role of nucleolus-initiated signaling in the progression of these diseases. Accordingly, the intervention of nucleolar stress may pave the path for developing novel therapies against these diseases. In this review, we systemically summarize recent findings linking the nucleolus to stress responses, signaling transduction and cell-fate decision, set the spotlight on the mechanisms by which nucleolar stress drives disease progression, and highlight the merit of the intervening nucleolus in disease treatment.
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Zhong L, Yao L, Holdreith N, Yu W, Gui T, Miao Z, Elkaim Y, Li M, Gong Y, Pacifici M, Maity A, Busch TM, Joeng KS, Cengel K, Seale P, Tong W, Qin L. Transient expansion and myofibroblast conversion of adipogenic lineage precursors mediate bone marrow repair after radiation. JCI Insight 2022; 7:150323. [PMID: 35393948 PMCID: PMC9057603 DOI: 10.1172/jci.insight.150323] [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: 04/08/2021] [Accepted: 02/23/2022] [Indexed: 11/19/2022] Open
Abstract
Radiation causes a collapse of bone marrow cells and elimination of microvasculature. To understand how bone marrow recovers after radiation, we focused on mesenchymal lineage cells that provide a supportive microenvironment for hematopoiesis and angiogenesis in bone. We recently discovered a nonproliferative subpopulation of marrow adipogenic lineage precursors (MALPs) that express adipogenic markers with no lipid accumulation. Single-cell transcriptomic analysis revealed that MALPs acquire proliferation and myofibroblast features shortly after radiation. Using an adipocyte-specific Adipoq-Cre, we validated that MALPs rapidly and transiently expanded at day 3 after radiation, coinciding with marrow vessel dilation and diminished marrow cellularity. Concurrently, MALPs lost most of their cell processes, became more elongated, and highly expressed myofibroblast-related genes. Radiation activated mTOR signaling in MALPs that is essential for their myofibroblast conversion and subsequent bone marrow recovery at day 14. Ablation of MALPs blocked the recovery of bone marrow vasculature and cellularity, including hematopoietic stem and progenitors. Moreover, VEGFa deficiency in MALPs delayed bone marrow recovery after radiation. Taken together, our research demonstrates a critical role of MALPs in mediating bone marrow repair after radiation injury and sheds light on a cellular target for treating marrow suppression after radiotherapy.
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Affiliation(s)
- Leilei Zhong
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lutian Yao
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Translational Research Program in Pediatric Orthopaedics, Division of Orthopaedic Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Orthopaedics, The First Hospital of China Medical University, Shenyang, China
| | - Nicholas Holdreith
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Wei Yu
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Gui
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Zhen Miao
- Department of Biostatistics, Epidemiology and Informatics
| | - Yehuda Elkaim
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics
| | - Yanqing Gong
- Division of Translational Medicine and Human Genetics
| | - Maurizio Pacifici
- Translational Research Program in Pediatric Orthopaedics, Division of Orthopaedic Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | - Kyu Sang Joeng
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Patrick Seale
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Wei Tong
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ling Qin
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Lao M, Hurtado A, de Castro AC, Burgos M, Jiménez R, Barrionuevo FJ. Sox9 is required for nail bed differentiation and digit tip regeneration. J Invest Dermatol 2022; 142:2613-2622.e6. [DOI: 10.1016/j.jid.2022.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/15/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
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Brombin A, Simpson DJ, Travnickova J, Brunsdon H, Zeng Z, Lu Y, Young AIJ, Chandra T, Patton EE. Tfap2b specifies an embryonic melanocyte stem cell that retains adult multifate potential. Cell Rep 2022; 38:110234. [PMID: 35021087 PMCID: PMC8764619 DOI: 10.1016/j.celrep.2021.110234] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/26/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022] Open
Abstract
Melanocytes, the pigment-producing cells, are replenished from multiple stem cell niches in adult tissue. Although pigmentation traits are known risk factors for melanoma, we know little about melanocyte stem cell (McSC) populations other than hair follicle McSCs and lack key lineage markers with which to identify McSCs and study their function. Here we find that Tfap2b and a select set of target genes specify an McSC population at the dorsal root ganglia in zebrafish. Functionally, Tfap2b is required for only a few late-stage embryonic melanocytes, and is essential for McSC-dependent melanocyte regeneration. Fate mapping data reveal that tfap2b+ McSCs have multifate potential, and are the cells of origin for large patches of adult melanocytes, two other pigment cell types (iridophores and xanthophores), and nerve-associated cells. Hence, Tfap2b confers McSC identity in early development, distinguishing McSCs from other neural crest and pigment cell lineages, and retains multifate potential in the adult zebrafish.
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Affiliation(s)
- Alessandro Brombin
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Daniel J Simpson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jana Travnickova
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Hannah Brunsdon
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Zhiqiang Zeng
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Yuting Lu
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Adelaide I J Young
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Tamir Chandra
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK.
| | - E Elizabeth Patton
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK.
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Analysis of the early response to spinal cord injury identified a key role for mTORC1 signaling in the activation of neural stem progenitor cells. NPJ Regen Med 2021; 6:68. [PMID: 34686684 PMCID: PMC8536777 DOI: 10.1038/s41536-021-00179-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 09/30/2021] [Indexed: 02/07/2023] Open
Abstract
Xenopus laevis are able to regenerate the spinal cord during larvae stages through the activation of neural stem progenitor cells (NSPCs). Here we use high-resolution expression profiling to characterize the early transcriptome changes induced after spinal cord injury, aiming to identify the signals that trigger NSPC proliferation. The analysis delineates a pathway that starts with a rapid and transitory activation of immediate early genes, followed by migration processes and immune response genes, the pervasive increase of NSPC-specific ribosome biogenesis factors, and genes involved in stem cell proliferation. Western blot and immunofluorescence analysis showed that mTORC1 is rapidly and transiently activated after SCI, and its pharmacological inhibition impairs spinal cord regeneration and proliferation of NSPC through the downregulation of genes involved in the G1/S transition of cell cycle, with a strong effect on PCNA. We propose that the mTOR signaling pathway is a key player in the activation of NPSCs during the early steps of spinal cord regeneration.
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10
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Drosophila to Explore Nucleolar Stress. Int J Mol Sci 2021; 22:ijms22136759. [PMID: 34201772 PMCID: PMC8267670 DOI: 10.3390/ijms22136759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 01/29/2023] Open
Abstract
Nucleolar stress occurs when ribosome production or function declines. Nucleolar stress in stem cells or progenitor cells often leads to disease states called ribosomopathies. Drosophila offers a robust system to explore how nucleolar stress causes cell cycle arrest, apoptosis, or autophagy depending on the cell type. We provide an overview of nucleolar stress in Drosophila by depleting nucleolar phosphoprotein of 140 kDa (Nopp140), a ribosome biogenesis factor (RBF) in nucleoli and Cajal bodies (CBs). The depletion of Nopp140 in eye imaginal disc cells generates eye deformities reminiscent of craniofacial deformities associated with the Treacher Collins syndrome (TCS), a human ribosomopathy. We show the activation of c-Jun N-terminal Kinase (JNK) in Drosophila larvae homozygous for a Nopp140 gene deletion. JNK is known to induce the expression of the pro-apoptotic Hid protein and autophagy factors Atg1, Atg18.1, and Atg8a; thus, JNK is a central regulator in Drosophila nucleolar stress. Ribosome abundance declines upon Nopp140 loss, but unusual cytoplasmic granules accumulate that resemble Processing (P) bodies based on marker proteins, Decapping Protein 1 (DCP1) and Maternal expression at 31B (Me31B). Wild type brain neuroblasts (NBs) express copious amounts of endogenous coilin, but coilin levels decline upon nucleolar stress in most NB types relative to the Mushroom body (MB) NBs. MB NBs exhibit resilience against nucleolar stress as they maintain normal coilin, Deadpan, and EdU labeling levels.
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11
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Ho CMK, Bringmann M, Oshima Y, Mitsuda N, Bergmann DC. Transcriptional profiling reveals signatures of latent developmental potential in Arabidopsis stomatal lineage ground cells. Proc Natl Acad Sci U S A 2021; 118:e2021682118. [PMID: 33875598 PMCID: PMC8092560 DOI: 10.1073/pnas.2021682118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In many developmental contexts, cell lineages have variable or flexible potency to self-renew. What drives a cell to exit from a proliferative state and begin differentiation, or to retain the capacity to divide days or years later is not clear. Here we exploit the mixed potential of the stomatal lineage ground cell (SLGC) in the Arabidopsis leaf epidermis as a model to explore how cells might balance potential to differentiate with a reentry into proliferation. By generating transcriptomes of fluorescence-activated cell sorting-isolated populations that combinatorically define SLGCs and integrating these data with other stomatal lineage datasets, we find that SLGCs appear poised between proliferation and endoreduplication. Furthermore, we found the RNA polymerase II-related mediator complex interactor DEK and the transcription factor MYB16 accumulate differentially in the stomatal lineage and influence the extent of cell proliferation during leaf development. These findings suggest that SLGC latent potential is maintained by poising of the cell cycle machinery, as well as general and site-specific gene-expression regulators.
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Affiliation(s)
- Chin-Min Kimmy Ho
- Department of Biology, Stanford University, Stanford, CA 94305-5020;
| | - Martin Bringmann
- Department of Biology, Stanford University, Stanford, CA 94305-5020
| | - Yoshimi Oshima
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 305-8562 Tsukuba, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 305-8562 Tsukuba, Japan
| | - Dominique C Bergmann
- Department of Biology, Stanford University, Stanford, CA 94305-5020;
- HHMI, Stanford University, Stanford, CA 94305
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Wang M, Chen X, Wu Y, Zheng Q, Chen W, Yan Y, Luan X, Shen C, Fang J, Zheng B, Yu J. RpS13 controls the homeostasis of germline stem cell niche through Rho1-mediated signals in the Drosophila testis. Cell Prolif 2020; 53:e12899. [PMID: 32896929 PMCID: PMC7574871 DOI: 10.1111/cpr.12899] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/15/2020] [Accepted: 08/18/2020] [Indexed: 12/20/2022] Open
Abstract
Objectives Stem cell niche regulated the renewal and differentiation of germline stem cells (GSCs) in Drosophila. Previously, we and others identified a series of genes encoding ribosomal proteins that may contribute to the self‐renewal and differentiation of GSCs. However, the mechanisms that maintain and differentiate GSCs in their niches were not well understood. Materials and Methods Flies were used to generate tissue‐specific gene knockdown. Small interfering RNAs were used to knockdown genes in S2 cells. qRT‐PCR was used to examine the relative mRNA expression level. TUNEL staining or flow cytometry assays were used to detect cell survival. Immunofluorescence was used to determine protein localization and expression pattern. Results Herein, using a genetic manipulation approach, we investigated the role of ribosomal protein S13 (RpS13) in testes and S2 cells. We reported that RpS13 was required for the self‐renewal and differentiation of GSCs. We also demonstrated that RpS13 regulated cell proliferation and apoptosis. Mechanistically, we showed that RpS13 regulated the expression of ribosome subunits and could moderate the expression of the Rho1, DE‐cad and Arm proteins. Notably, Rho1 imitated the phenotype of RpS13 in both Drosophila testes and S2 cells, and recruited cell adhesions, which was mediated by the DE‐cad and Arm proteins. Conclusion These findings uncover a novel mechanism of RpS13 that mediates Rho1 signals in the stem cell niche of the Drosophila testis.
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Affiliation(s)
- Min Wang
- Department of Gynecology, the Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Xia Chen
- Department of Gynecology, the Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Yibo Wu
- Human Reproductive and Genetic Center, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Qianwen Zheng
- Department of Gynecology, the Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Wanyin Chen
- Department of Gynecology, the Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Yidan Yan
- Department of Gynecology, the Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Xiaojin Luan
- Department of Gynecology, the Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Cong Shen
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Jie Fang
- Department of Gynecology, the Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Bo Zheng
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Jun Yu
- Department of Gynecology, the Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
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13
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Ribosomes: An Exciting Avenue in Stem Cell Research. Stem Cells Int 2020; 2020:8863539. [PMID: 32695182 PMCID: PMC7362291 DOI: 10.1155/2020/8863539] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 02/07/2023] Open
Abstract
Stem cell research has focused on genomic studies. However, recent evidence has indicated the involvement of epigenetic regulation in determining the fate of stem cells. Ribosomes play a crucial role in epigenetic regulation, and thus, we focused on the role of ribosomes in stem cells. Majority of living organisms possess ribosomes that are involved in the translation of mRNA into proteins and promote cellular proliferation and differentiation. Ribosomes are stable molecular machines that play a role with changes in the levels of RNA during translation. Recent research suggests that specific ribosomes actively regulate gene expression in multiple cell types, such as stem cells. Stem cells have the potential for self-renewal and differentiation into multiple lineages and, thus, require high efficiency of translation. Ribosomes induce cellular transdifferentiation and reprogramming, and disrupted ribosome synthesis affects translation efficiency, thereby hindering stem cell function leading to cell death and differentiation. Stem cell function is regulated by ribosome-mediated control of stem cell-specific gene expression. In this review, we have presented a detailed discourse on the characteristics of ribosomes in stem cells. Understanding ribosome biology in stem cells will provide insights into the regulation of stem cell function and cellular reprogramming.
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14
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Lu CJ, Fan XY, Guo YF, Cheng ZC, Dong J, Chen JZ, Li LY, Wang MW, Wu ZK, Wang F, Tong XJ, Luo LF, Tang FC, Zhu ZY, Zhang B. Single-cell analyses identify distinct and intermediate states of zebrafish pancreatic islet development. J Mol Cell Biol 2020; 11:435-447. [PMID: 30407522 PMCID: PMC6604604 DOI: 10.1093/jmcb/mjy064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 10/31/2018] [Accepted: 11/08/2018] [Indexed: 12/13/2022] Open
Abstract
Pancreatic endocrine islets are vital for glucose homeostasis. However, the islet developmental trajectory and its regulatory network are not well understood. To define the features of these specification and differentiation processes, we isolated individual islet cells from TgBAC(neurod1:EGFP) transgenic zebrafish and analyzed islet developmental dynamics across four different embryonic stages using a single-cell RNA-seq strategy. We identified proliferative endocrine progenitors, which could be further categorized by different cell cycle phases with the G1/S subpopulation displaying a distinct differentiation potential. We identified endocrine precursors, a heterogeneous intermediate-state population consisting of lineage-primed alpha, beta and delta cells that were characterized by the expression of lineage-specific transcription factors and relatively low expression of terminally differentiation markers. The terminally differentiated alpha, beta, and delta cells displayed stage-dependent differentiation states, which were related to their functional maturation. Our data unveiled distinct states, events and molecular features during the islet developmental transition, and provided resources to comprehensively understand the lineage hierarchy of islet development at the single-cell level.
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Affiliation(s)
- Chong-Jian Lu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Xiao-Ying Fan
- Beijing Advanced Innovation Center for Genomics (ICG), College of Life Sciences, Peking University, Beijing, China
| | - Yue-Feng Guo
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Zhen-Chao Cheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Ji Dong
- Beijing Advanced Innovation Center for Genomics (ICG), College of Life Sciences, Peking University, Beijing, China
| | - Jin-Zi Chen
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing, China
| | - Lian-Yan Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Mei-Wen Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Ze-Kai Wu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Fei Wang
- National Center for Protein Sciences, Peking University, Beijing, China
| | - Xiang-Jun Tong
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Ling-Fei Luo
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing, China
| | - Fu-Chou Tang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), College of Life Sciences, Peking University, Beijing, China
| | - Zuo-Yan Zhu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Bo Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
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15
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Sharifi S, da Costa HFR, Bierhoff H. The circuitry between ribosome biogenesis and translation in stem cell function and ageing. Mech Ageing Dev 2020; 189:111282. [PMID: 32531294 DOI: 10.1016/j.mad.2020.111282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/11/2020] [Accepted: 06/01/2020] [Indexed: 12/13/2022]
Abstract
Ribosome biogenesis takes place mainly in the nucleolus, a nuclear, non-membrane bound organelle forming around the gene arrays encoding ribosomal RNA (rRNA). Nucleolar activity comprises synthesis, processing and maturation of rRNAs, followed by their assembly with ribosomal proteins into pre-ribosomal particles. The final formation of translation-competent ribosomes in the cytoplasm is the prerequisite for protein synthesis, which is the most energy-consuming cellular process. In adult stem cells, ribosome biogenesis and protein synthesis determine the switch between the quiescent and the activated state, but also decide whether activated stem cells self-renew or differentiate. Given this major impact on cellular function, it seems likely that perturbations of the circuitry between nucleolar activity and translation lead to ageing-related stem cell deterioration. This review provides an overview of how ribosome biogenesis and translation govern stem cell function and discusses the resultant implication in stem cell ageing.
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Affiliation(s)
- Samim Sharifi
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany; Leibniz-Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Hugo Filipe Rangel da Costa
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany
| | - Holger Bierhoff
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany; Leibniz-Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany.
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16
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Liao C, Pang N, Liu Z, Lei L. Transient inhibition of rDNA transcription in donor cells improves ribosome biogenesis and preimplantation development of embryos derived from somatic cell nuclear transfer. FASEB J 2020; 34:8283-8295. [PMID: 32323360 DOI: 10.1096/fj.202000025rr] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 11/11/2022]
Abstract
Ribosomal DNA (rDNA) transcription is a limiting step in ribosome biogenesis, crucial for protein synthesis and cell growth-especially at the early stages of embryonic development-and is regulated in a mammalian target of rapamycin (mTOR)-dependent manner. Our previous report demonstrated that treatment with mTOR inhibitors during artificial embryonic activation improved the development of embryos derived from somatic cell nuclear transfer (SCNT). We hypothesize that inhibition of ribosome biogenesis in somatic cells facilitates reactivation of embryonic nucleolar establishment and ribosome biogenesis in SCNT embryos. Herein, we show that mTOR inhibitors suppressed ribosome biogenesis in somatic cells, and more importantly, improved development potential of SCNT embryos (blastocyst rate, 34% vs 24%). SCNT embryos derived from drug-treated somatic cells exhibited higher levels of 47S, 18S, and 5S rRNAs, upstream binding factor (UBF) mRNA, ribosomal protein S6; they also improved the rebuilding of the nucleolar ultrastructure. In addition, treatment of donor cells with the RNA polymerase I (Pol I) inhibitor cx5461 caused similar effects on SCNT embryos. These results indicated that transient inhibition of rDNA transcription in donor cells facilitated the establishment of functional nucleoli and improved preimplantation development of SCNT embryos.
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Affiliation(s)
- Chen Liao
- Department of Histology and Embryology, Harbin Medical University, Harbin, China
| | - Nan Pang
- Department of Histology and Embryology, Harbin Medical University, Harbin, China
| | - Zhaojun Liu
- Department of Histology and Embryology, Harbin Medical University, Harbin, China
| | - Lei Lei
- Department of Histology and Embryology, Harbin Medical University, Harbin, China
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17
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Baral SS, Lieux ME, DiMario PJ. Nucleolar stress in Drosophila neuroblasts, a model for human ribosomopathies. Biol Open 2020; 9:bio046565. [PMID: 32184230 PMCID: PMC7197718 DOI: 10.1242/bio.046565] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 03/03/2020] [Indexed: 12/11/2022] Open
Abstract
Different stem cells or progenitor cells display variable threshold requirements for functional ribosomes. This is particularly true for several human ribosomopathies in which select embryonic neural crest cells or adult bone marrow stem cells, but not others, show lethality due to failures in ribosome biogenesis or function (now known as nucleolar stress). To determine if various Drosophila neuroblasts display differential sensitivities to nucleolar stress, we used CRISPR-Cas9 to disrupt the Nopp140 gene that encodes two splice variant ribosome biogenesis factors (RBFs). Disruption of Nopp140 induced nucleolar stress that arrested larvae in the second instar stage. While the majority of larval neuroblasts arrested development, the mushroom body (MB) neuroblasts continued to proliferate as shown by their maintenance of deadpan, a neuroblast-specific transcription factor, and by their continued EdU incorporation. MB neuroblasts in wild-type larvae appeared to contain more fibrillarin and Nopp140 in their nucleoli as compared to other neuroblasts, indicating that MB neuroblasts stockpile RBFs as they proliferate in late embryogenesis while other neuroblasts normally enter quiescence. A greater abundance of Nopp140 encoded by maternal transcripts in Nopp140-/- MB neuroblasts of 1----2-day-old larvae likely rendered these cells more resilient to nucleolar stress.
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Affiliation(s)
- Sonu Shrestha Baral
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Molly E Lieux
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Patrick J DiMario
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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18
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Teixeira FK, Lehmann R. Translational Control during Developmental Transitions. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032987. [PMID: 30082467 DOI: 10.1101/cshperspect.a032987] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The many steps of gene expression, from the transcription of a gene to the production of its protein product, are well understood. Yet, transcriptional regulation has been the focal point for the study of gene expression during development. However, quantitative studies reveal that messenger RNA (mRNA) levels are not necessarily good predictors of the respective proteins' levels in a cell. This discrepancy is, at least in part, the result of developmentally regulated, translational mechanisms that control the spatiotemporal regulation of gene expression. In this review, we focus on translational regulatory mechanisms mediating global transitions in gene expression: the shift from the maternal to the embryonic developmental program in the early embryo and the switch from the self-renewal of stem cells to differentiation in the adult.
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Affiliation(s)
| | - Ruth Lehmann
- Howard Hughes Medical Institute (HHMI) and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, New York 10016
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19
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Prakash V, Carson BB, Feenstra JM, Dass RA, Sekyrova P, Hoshino A, Petersen J, Guo Y, Parks MM, Kurylo CM, Batchelder JE, Haller K, Hashimoto A, Rundqivst H, Condeelis JS, Allis CD, Drygin D, Nieto MA, Andäng M, Percipalle P, Bergh J, Adameyko I, Farrants AKÖ, Hartman J, Lyden D, Pietras K, Blanchard SC, Vincent CT. Ribosome biogenesis during cell cycle arrest fuels EMT in development and disease. Nat Commun 2019; 10:2110. [PMID: 31068593 PMCID: PMC6506521 DOI: 10.1038/s41467-019-10100-8] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 04/16/2019] [Indexed: 12/15/2022] Open
Abstract
Ribosome biogenesis is a canonical hallmark of cell growth and proliferation. Here we show that execution of Epithelial-to-Mesenchymal Transition (EMT), a migratory cellular program associated with development and tumor metastasis, is fueled by upregulation of ribosome biogenesis during G1/S arrest. This unexpected EMT feature is independent of species and initiating signal, and is accompanied by release of the repressive nucleolar chromatin remodeling complex (NoRC) from rDNA, together with recruitment of the EMT-driving transcription factor Snai1 (Snail1), RNA Polymerase I (Pol I) and the Upstream Binding Factor (UBF). EMT-associated ribosome biogenesis is also coincident with increased nucleolar recruitment of Rictor, an essential component of the EMT-promoting mammalian target of rapamycin complex 2 (mTORC2). Inhibition of rRNA synthesis in vivo differentiates primary tumors to a benign, Estrogen Receptor-alpha (ERα) positive, Rictor-negative phenotype and reduces metastasis. These findings implicate the EMT-associated ribosome biogenesis program with cellular plasticity, de-differentiation, cancer progression and metastatic disease.
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Affiliation(s)
- Varsha Prakash
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Brittany B Carson
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Jennifer M Feenstra
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Randall A Dass
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Petra Sekyrova
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Ayuko Hoshino
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Pediatrics and Cell and Developmental Biology, Weill Cornell Medicine College, New York, NY, 10065, USA
| | - Julian Petersen
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden
- Department for Brain Research, Medical University of Vienna, 1090, Vienna, Austria
| | - Yuan Guo
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691, Stockholm, Sweden
| | - Matthew M Parks
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Chad M Kurylo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Jake E Batchelder
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kristian Haller
- Department of Laboratory Medicine, Center for Molecular Pathology, Lund University, Lund, SE-223 81, Sweden
| | - Ayako Hashimoto
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Pediatrics and Cell and Developmental Biology, Weill Cornell Medicine College, New York, NY, 10065, USA
| | - Helene Rundqivst
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, SE-171 77, Sweden
| | - John S Condeelis
- Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
- Department of Pathology, Montefiore Medical Center, Bronx, 10461, NY, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Denis Drygin
- Pimera, Inc, 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - M Angela Nieto
- Instituto de Neurociencias, CSIC-UMH, Alicante, 03550, Spain
| | - Michael Andäng
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Piergiorgio Percipalle
- Science Division, Biology Program, New York University Abu Dhabi, Abu Dhabi, 129188, UAE
| | - Jonas Bergh
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, S-171 76, Solna, Sweden
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden
- Department for Brain Research, Medical University of Vienna, 1090, Vienna, Austria
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691, Stockholm, Sweden
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, S-171 76, Solna, Sweden
| | - David Lyden
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Pediatrics and Cell and Developmental Biology, Weill Cornell Medicine College, New York, NY, 10065, USA
| | - Kristian Pietras
- Department of Laboratory Medicine, Center for Molecular Pathology, Lund University, Lund, SE-223 81, Sweden
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA.
- Tri-Institutional Training Program in Chemical Biology, Weill Cornell Medicine, New York, NY, 10065, USA.
| | - C Theresa Vincent
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden.
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA.
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Mohammad K, Dakik P, Medkour Y, Mitrofanova D, Titorenko VI. Quiescence Entry, Maintenance, and Exit in Adult Stem Cells. Int J Mol Sci 2019; 20:ijms20092158. [PMID: 31052375 PMCID: PMC6539837 DOI: 10.3390/ijms20092158] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/24/2019] [Accepted: 04/28/2019] [Indexed: 12/13/2022] Open
Abstract
Cells of unicellular and multicellular eukaryotes can respond to certain environmental cues by arresting the cell cycle and entering a reversible state of quiescence. Quiescent cells do not divide, but can re-enter the cell cycle and resume proliferation if exposed to some signals from the environment. Quiescent cells in mammals and humans include adult stem cells. These cells exhibit improved stress resistance and enhanced survival ability. In response to certain extrinsic signals, adult stem cells can self-renew by dividing asymmetrically. Such asymmetric divisions not only allow the maintenance of a population of quiescent cells, but also yield daughter progenitor cells. A multistep process of the controlled proliferation of these progenitor cells leads to the formation of one or more types of fully differentiated cells. An age-related decline in the ability of adult stem cells to balance quiescence maintenance and regulated proliferation has been implicated in many aging-associated diseases. In this review, we describe many traits shared by different types of quiescent adult stem cells. We discuss how these traits contribute to the quiescence, self-renewal, and proliferation of adult stem cells. We examine the cell-intrinsic mechanisms that allow establishing and sustaining the characteristic traits of adult stem cells, thereby regulating quiescence entry, maintenance, and exit.
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Affiliation(s)
- Karamat Mohammad
- Department of Biology, Concordia University, 7141 Sherbrooke Street, West, SP Building, Room 501-13, Montreal, QC H4B 1R6, Canada.
| | - Paméla Dakik
- Department of Biology, Concordia University, 7141 Sherbrooke Street, West, SP Building, Room 501-13, Montreal, QC H4B 1R6, Canada.
| | - Younes Medkour
- Department of Biology, Concordia University, 7141 Sherbrooke Street, West, SP Building, Room 501-13, Montreal, QC H4B 1R6, Canada.
| | - Darya Mitrofanova
- Department of Biology, Concordia University, 7141 Sherbrooke Street, West, SP Building, Room 501-13, Montreal, QC H4B 1R6, Canada.
| | - Vladimir I Titorenko
- Department of Biology, Concordia University, 7141 Sherbrooke Street, West, SP Building, Room 501-13, Montreal, QC H4B 1R6, Canada.
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Abstract
The mechanisms responsible for maintaining ribosomal component stoichiometry, which is critical during cell fate transitions, are currently not well understood. In this issue of Cell Stem Cell, Corsini et al. (2018) demonstrate that the transcription and splicing-associated factor HTATSF1 controls stem cell fate by coordinately regulating ribosomal protein and RNA production.
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Affiliation(s)
- Eesha Sharma
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada.
| | - Benjamin J Blencowe
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada.
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Emerging Role of Eukaryote Ribosomes in Translational Control. Int J Mol Sci 2019; 20:ijms20051226. [PMID: 30862090 PMCID: PMC6429320 DOI: 10.3390/ijms20051226] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/06/2019] [Accepted: 03/08/2019] [Indexed: 12/15/2022] Open
Abstract
Translation is one of the final steps that regulate gene expression. The ribosome is the effector of translation through to its role in mRNA decoding and protein synthesis. Many mechanisms have been extensively described accounting for translational regulation. However it emerged only recently that ribosomes themselves could contribute to this regulation. Indeed, though it is well-known that the translational efficiency of the cell is linked to ribosome abundance, studies recently demonstrated that the composition of the ribosome could alter translation of specific mRNAs. Evidences suggest that according to the status, environment, development, or pathological conditions, cells produce different populations of ribosomes which differ in their ribosomal protein and/or RNA composition. Those observations gave rise to the concept of "specialized ribosomes", which proposes that a unique ribosome composition determines the translational activity of this ribosome. The current review will present how technological advances have participated in the emergence of this concept, and to which extent the literature sustains this concept today.
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McGrath J, Panzica L, Ransom R, Withers HG, Gelman IH. Identification of Genes Regulating Breast Cancer Dormancy in 3D Bone Endosteal Niche Cultures. Mol Cancer Res 2019; 17:860-869. [PMID: 30651373 DOI: 10.1158/1541-7786.mcr-18-0956] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/17/2018] [Accepted: 01/07/2019] [Indexed: 01/25/2023]
Abstract
Tumor cell dormancy is a significant clinical problem in breast cancer. We used a three-dimensional (3D) in vitro model of the endosteal bone niche (EN), consisting of endothelial, bone marrow stromal cells, and fetal osteoblasts in a 3D collagen matrix (GELFOAM), to identify genes required for dormancy. Human triple-negative MDA-MB-231 breast cancer cells, but not the bone-tropic metastatic variant, BoM1833, established dormancy in 3D-EN cultures in a p38-MAPK-dependent manner, whereas both cell types proliferated on two-dimensional (2D) plastic or in 3D collagen alone. "Dormancy-reactivation suppressor genes" (DRSG) were identified using a genomic short hairpin RNA (shRNA) screen in MDA-MB-231 cells for gene knockdowns that induced proliferation in the 3D-EN. DRSG candidates enriched for genes controlling stem cell biology, neurogenesis, MYC targets, ribosomal structure, and translational control. Several potential DRSG were confirmed using independent shRNAs, including BHLHE41, HBP1, and WNT3. Overexpression of the WNT3/a antagonists secreted frizzled-related protein 2 or 4 (SFRP2/4) and induced MDA-MB-231 proliferation in the EN. In contrast, overexpression of SFRP3, known not to antagonize WNT3/a, did not induce proliferation. Decreased WNT3 or BHLHE41 expression was found in clinical breast cancer metastases compared with primary-site lesions, and the loss of WNT3 or BHLHE41 or gain of SFRP1, 2, and 4 in the context of TP53 loss/mutation correlated with decreased progression-free and overall survival. IMPLICATIONS: These data describe several novel, potentially targetable pathways controlling breast cancer dormancy in the EN.
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Affiliation(s)
- Julie McGrath
- Department of Cancer Biology, University of Arizona, Tucson, Arizona
| | - Louis Panzica
- University at Buffalo School of Law, Buffalo, New York
| | | | - Henry G Withers
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Irwin H Gelman
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York.
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24
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Agrawal S, Ganley ARD. The conservation landscape of the human ribosomal RNA gene repeats. PLoS One 2018; 13:e0207531. [PMID: 30517151 PMCID: PMC6281188 DOI: 10.1371/journal.pone.0207531] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 11/01/2018] [Indexed: 01/27/2023] Open
Abstract
Ribosomal RNA gene repeats (rDNA) encode ribosomal RNA, a major component of ribosomes. Ribosome biogenesis is central to cellular metabolic regulation, and several diseases are associated with rDNA dysfunction, notably cancer, However, its highly repetitive nature has severely limited characterization of the elements responsible for rDNA function. Here we make use of phylogenetic footprinting to provide a comprehensive list of novel, potentially functional elements in the human rDNA. Complete rDNA sequences for six non-human primate species were constructed using de novo whole genome assemblies. These new sequences were used to determine the conservation profile of the human rDNA, revealing 49 conserved regions in the rDNA intergenic spacer (IGS). To provide insights into the potential roles of these conserved regions, the conservation profile was integrated with functional genomics datasets. We find two major zones that contain conserved elements characterised by enrichment of transcription-associated chromatin factors, and transcription. Conservation of some IGS transcripts in the apes underpins the potential functional significance of these transcripts and the elements controlling their expression. Our results characterize the conservation landscape of the human IGS and suggest that noncoding transcription and chromatin elements are conserved and important features of this unique genomic region.
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Affiliation(s)
- Saumya Agrawal
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Austen R. D. Ganley
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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25
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Jarzebowski L, Le Bouteiller M, Coqueran S, Raveux A, Vandormael-Pournin S, David A, Cumano A, Cohen-Tannoudji M. Mouse adult hematopoietic stem cells actively synthesize ribosomal RNA. RNA (NEW YORK, N.Y.) 2018; 24:1803-1812. [PMID: 30242063 PMCID: PMC6239186 DOI: 10.1261/rna.067843.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/14/2018] [Indexed: 06/08/2023]
Abstract
The contribution of basal cellular processes to the regulation of tissue homeostasis has just started to be appreciated. However, our knowledge of the modulation of ribosome biogenesis activity in situ within specific lineages remains very limited. This is largely due to the lack of assays that enable quantitation of ribosome biogenesis in small numbers of cells in vivo. We used a technique, named Flow-FISH, combining cell surface antibody staining and flow cytometry with intracellular ribosomal RNA (rRNA) FISH, to measure the levels of pre-rRNAs of hematopoietic cells in vivo. Here, we show that Flow-FISH reports and quantifies ribosome biogenesis activity in hematopoietic cell populations, thereby providing original data on this fundamental process notably in rare populations such as hematopoietic stem and progenitor cells. We unravel variations in pre-rRNA levels between different hematopoietic progenitor compartments and during erythroid differentiation. In particular, our data indicate that, contrary to what may be anticipated from their quiescent state, hematopoietic stem cells have significant ribosome biogenesis activity. Moreover, variations in pre-rRNA levels do not correlate with proliferation rates, suggesting that cell type-specific mechanisms might regulate ribosome biogenesis in hematopoietic stem cells and progenitors. Our study contributes to a better understanding of the cellular physiology of the hematopoietic system in vivo in unperturbed situations.
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Affiliation(s)
- Léonard Jarzebowski
- Early Mammalian Development and Stem Cell Biology, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris 75015, France
- CNRS UMR 3738, Institut Pasteur, Paris 75015, France
| | - Marie Le Bouteiller
- Early Mammalian Development and Stem Cell Biology, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris 75015, France
- CNRS UMR 3738, Institut Pasteur, Paris 75015, France
| | - Sabrina Coqueran
- Early Mammalian Development and Stem Cell Biology, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris 75015, France
- CNRS UMR 3738, Institut Pasteur, Paris 75015, France
| | - Aurélien Raveux
- Early Mammalian Development and Stem Cell Biology, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris 75015, France
- CNRS UMR 3738, Institut Pasteur, Paris 75015, France
| | - Sandrine Vandormael-Pournin
- Early Mammalian Development and Stem Cell Biology, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris 75015, France
- CNRS UMR 3738, Institut Pasteur, Paris 75015, France
| | - Alexandre David
- Team "Signaling and Cancer," Institut de Génomique Fonctionnelle, Montpellier 34094, France
| | - Ana Cumano
- Lymphocyte Development Unit, Institut Pasteur, Paris 75015, France
| | - Michel Cohen-Tannoudji
- Early Mammalian Development and Stem Cell Biology, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris 75015, France
- CNRS UMR 3738, Institut Pasteur, Paris 75015, France
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26
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Bouffard S, Dambroise E, Brombin A, Lempereur S, Hatin I, Simion M, Corre R, Bourrat F, Joly JS, Jamen F. Fibrillarin is essential for S-phase progression and neuronal differentiation in zebrafish dorsal midbrain and retina. Dev Biol 2018; 437:1-16. [PMID: 29477341 DOI: 10.1016/j.ydbio.2018.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 01/11/2018] [Accepted: 02/13/2018] [Indexed: 10/18/2022]
Abstract
Fibrillarin (Fbl) is a highly conserved protein that plays an essential role in ribosome biogenesis and more particularly in the methylation of ribosomal RNAs and rDNA histones. In cellular models, FBL was shown to play an important role in tumorigenesis and stem cell differentiation. We used the zebrafish as an in vivo model to study Fbl function during embryonic development. We show here that the optic tectum and the eye are severely affected by Fbl depletion whereas ventral regions of the brain are less impacted. The morphogenesis defects are associated with impaired neural differentiation and massive apoptosis. Polysome gradient experiments show that fbl mutant larvae display defects in ribosome biogenesis and activity. Strikingly, flow cytometry analyses revealed different S-phase profiles between wild-type and mutant cells, suggesting a defect in S-phase progression.
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Affiliation(s)
- Stéphanie Bouffard
- INRA CASBAH Group, Neurosciences Paris-Saclay Institute, CNRS, Université Paris-Saclay, Université Paris-Sud, Gif-sur-Yvette, France
| | - Emilie Dambroise
- INRA CASBAH Group, Neurosciences Paris-Saclay Institute, CNRS, Université Paris-Saclay, Université Paris-Sud, Gif-sur-Yvette, France
| | - Alessandro Brombin
- INRA CASBAH Group, Neurosciences Paris-Saclay Institute, CNRS, Université Paris-Saclay, Université Paris-Sud, Gif-sur-Yvette, France
| | - Sylvain Lempereur
- Tefor Core Facility, TEFOR Infrastructure, NeuroPSI, CNRS, Gif-sur-Yvette, France; Université Paris-Est, LIGM, ESIEE, Noisy-le-Grand, France
| | - Isabelle Hatin
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Bâtiment 400, 91400 Orsay, France
| | - Matthieu Simion
- INRA CASBAH Group, Neurosciences Paris-Saclay Institute, CNRS, Université Paris-Saclay, Université Paris-Sud, Gif-sur-Yvette, France
| | - Raphaël Corre
- INRA CASBAH Group, Neurosciences Paris-Saclay Institute, CNRS, Université Paris-Saclay, Université Paris-Sud, Gif-sur-Yvette, France
| | - Franck Bourrat
- INRA CASBAH Group, Neurosciences Paris-Saclay Institute, CNRS, Université Paris-Saclay, Université Paris-Sud, Gif-sur-Yvette, France
| | - Jean-Stéphane Joly
- INRA CASBAH Group, Neurosciences Paris-Saclay Institute, CNRS, Université Paris-Saclay, Université Paris-Sud, Gif-sur-Yvette, France; Tefor Core Facility, TEFOR Infrastructure, NeuroPSI, CNRS, Gif-sur-Yvette, France
| | - Françoise Jamen
- INRA CASBAH Group, Neurosciences Paris-Saclay Institute, CNRS, Université Paris-Saclay, Université Paris-Sud, Gif-sur-Yvette, France.
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27
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Athanasiadis EI, Botthof JG, Andres H, Ferreira L, Lio P, Cvejic A. Single-cell RNA-sequencing uncovers transcriptional states and fate decisions in haematopoiesis. Nat Commun 2017; 8:2045. [PMID: 29229905 PMCID: PMC5725498 DOI: 10.1038/s41467-017-02305-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 11/17/2017] [Indexed: 12/23/2022] Open
Abstract
The success of marker-based approaches for dissecting haematopoiesis in mouse and human is reliant on the presence of well-defined cell surface markers specific for diverse progenitor populations. An inherent problem with this approach is that the presence of specific cell surface markers does not directly reflect the transcriptional state of a cell. Here, we used a marker-free approach to computationally reconstruct the blood lineage tree in zebrafish and order cells along their differentiation trajectory, based on their global transcriptional differences. Within the population of transcriptionally similar stem and progenitor cells, our analysis reveals considerable cell-to-cell differences in their probability to transition to another committed state. Once fate decision is executed, the suppression of transcription of ribosomal genes and upregulation of lineage-specific factors coordinately controls lineage differentiation. Evolutionary analysis further demonstrates that this haematopoietic programme is highly conserved between zebrafish and higher vertebrates.
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Affiliation(s)
- Emmanouil I Athanasiadis
- Department of Haematology, University of Cambridge, Cambridge, CB2 0XY, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, CB2 1QR, UK
| | - Jan G Botthof
- Department of Haematology, University of Cambridge, Cambridge, CB2 0XY, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, CB2 1QR, UK
| | - Helena Andres
- Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD, UK
| | - Lauren Ferreira
- Department of Haematology, University of Cambridge, Cambridge, CB2 0XY, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, CB2 1QR, UK
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, 6139, South Africa
| | - Pietro Lio
- Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD, UK
| | - Ana Cvejic
- Department of Haematology, University of Cambridge, Cambridge, CB2 0XY, UK.
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK.
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, CB2 1QR, UK.
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28
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Hein N, Hannan KM, D'Rozario J, Hannan R. Inhibition of Pol I Transcription a New Chance in the Fight Against Cancer. Technol Cancer Res Treat 2017. [PMCID: PMC5762094 DOI: 10.1177/1533034617744955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
While new cancer treatments continue to improve patient outcomes, for some cancers there have been limited or no improvements for a long time. It is for these cases radically new approaches are required. Recent publications proposing ribosome biogenesis, in particular RNA polymerase I transcription, as a suitable target for cancer treatment has been gaining momentum. For example, we demonstrated that CX-5461, a specific RNA polymerase I transcription inhibitor, is effective in treating an aggressive subtype of acute myeloid leukemia, regardless of p53 status. Notably, CX-5461 reduces the leukemia initiating/stem cells, the cell population believed to be responsible for chemotherapy resistance and disease relapse in numerous cancers. Targeting ribosome biogenesis, once considered merely a “housekeeping process,” is showing promise in a continuously growing list of cancers including lymphoma, prostate, and now acute myeloid leukemia. Evidence suggests the therapeutic efficacy of RNA polymerase I therapy in preclinical models is mediated through a variety of mechanisms including nucleolar stress activation of p53, DNA damage-like activation of ataxia-telangiectasia mutated/ataxia-telangiectasia and Rad3 related, and cellular differentiation. Overall, the available data suggests the potential for targeting ribosome biogenesis to be effective in a broad spectrum of cancers. The outcomes of 2 phase 1/2 trials of CX-5461 in hematological malignancies and breast cancer are eagerly awaited.
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Affiliation(s)
- Nadine Hein
- Australian Cancer Research Foundation Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, ANU, 131 Garran Road, Canberra, ACT, Australia
| | - Kathrine M. Hannan
- Australian Cancer Research Foundation Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, ANU, 131 Garran Road, Canberra, ACT, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - James D'Rozario
- Clinical Haematology Unit, The Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - Ross Hannan
- Australian Cancer Research Foundation Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, ANU, 131 Garran Road, Canberra, ACT, Australia
- Division of Cancer Research, Peter MacCallum Cancer Centre, St. Andrews Place, East Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
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29
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Hu WY, Hu DP, Xie L, Li Y, Majumdar S, Nonn L, Hu H, Shioda T, Prins GS. Isolation and functional interrogation of adult human prostate epithelial stem cells at single cell resolution. Stem Cell Res 2017. [PMID: 28651114 DOI: 10.1016/j.scr.2017.06.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Using primary cultures of normal human prostate epithelial cells, we developed a novel prostasphere-based, label-retention assay that permits identification and isolation of stem cells at a single cell level. Their bona fide stem cell nature was corroborated using in vitro and in vivo regenerative assays and documentation of symmetric/asymmetric division. Robust WNT10B and KRT13 levels without E-cadherin or KRT14 staining distinguished individual stem cells from daughter progenitors in spheroids. Following FACS to isolate label-retaining stem cells from label-free progenitors, RNA-seq identified unique gene signatures for the separate populations which may serve as useful biomarkers. Knockdown of KRT13 or PRAC1 reduced sphere formation and symmetric self-renewal highlighting their role in stem cell maintenance. Pathways analysis identified ribosome biogenesis and membrane estrogen-receptor signaling enriched in stem cells with NF-ĸB signaling enriched in progenitors; activities that were biologically confirmed. Further, bioassays identified heightened autophagy flux and reduced metabolism in stem cells relative to progenitors. These approaches similarly identified stem-like cells from prostate cancer specimens and prostate, breast and colon cancer cell lines suggesting wide applicability. Together, the present studies isolate and identify unique characteristics of normal human prostate stem cells and uncover processes that maintain stem cell homeostasis in the prostate gland.
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Affiliation(s)
- Wen-Yang Hu
- Department of Urology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Dan-Ping Hu
- Department of Urology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Lishi Xie
- Department of Urology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Ye Li
- Department of Urology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Shyama Majumdar
- Department of Urology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Larisa Nonn
- Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA; University of Illinois Cancer Center, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Hong Hu
- Research Resources Center, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Toshi Shioda
- Massachusetts General Hospital Center for Cancer Research and Harvard Medical School, Charlestown, MA 02129, USA
| | - Gail S Prins
- Department of Urology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA; Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA; University of Illinois Cancer Center, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA.
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30
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Drosophila dyskerin is required for somatic stem cell homeostasis. Sci Rep 2017; 7:347. [PMID: 28337032 PMCID: PMC5428438 DOI: 10.1038/s41598-017-00446-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 02/27/2017] [Indexed: 02/07/2023] Open
Abstract
Drosophila represents an excellent model to dissect the roles played by the evolutionary conserved family of eukaryotic dyskerins. These multifunctional proteins are involved in the formation of H/ACA snoRNP and telomerase complexes, both involved in essential cellular tasks. Since fly telomere integrity is guaranteed by a different mechanism, we used this organism to investigate the specific role played by dyskerin in somatic stem cell maintenance. To this aim, we focussed on Drosophila midgut, a hierarchically organized and well characterized model for stemness analysis. Surprisingly, the ubiquitous loss of the protein uniquely affects the formation of the larval stem cell niches, without altering other midgut cell types. The number of adult midgut precursor stem cells is dramatically reduced, and this effect is not caused by premature differentiation and is cell-autonomous. Moreover, a few dispersed precursors found in the depleted midguts can maintain stem identity and the ability to divide asymmetrically, nor show cell-growth defects or undergo apoptosis. Instead, their loss is mainly specifically dependent on defective amplification. These studies establish a strict link between dyskerin and somatic stem cell maintenance in a telomerase-lacking organism, indicating that loss of stemness can be regarded as a conserved, telomerase-independent effect of dyskerin dysfunction.
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31
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Kraushar ML, Popovitchenko T, Volk NL, Rasin MR. The frontier of RNA metamorphosis and ribosome signature in neocortical development. Int J Dev Neurosci 2016; 55:131-139. [PMID: 27241046 PMCID: PMC5124555 DOI: 10.1016/j.ijdevneu.2016.02.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/26/2016] [Accepted: 02/28/2016] [Indexed: 12/14/2022] Open
Abstract
More than a passive effector of gene expression, mRNA translation (protein synthesis) by the ribosome is a rapidly tunable and dynamic molecular mechanism. Neurodevelopmental disorders are associated with abnormalities in mRNA translation, protein synthesis, and neocortical development; yet, we know little about the molecular mechanisms underlying these abnormalities. Furthermore, our understanding of regulation of the ribosome and mRNA translation during normal brain development is only in its early stages. mRNA translation is emerging as a key driver of the rapid and timed regulation of spatiotemporal gene expression in the developing nervous system, including the neocortex. In this review, we focus on the regulatory role of the ribosome in neocortical development, and construct a current understanding of how ribosomal complex specificity may contribute to the development of the neocortex. We also present a microarray analysis of ribosomal protein-coding mRNAs across the neurogenic phase of neocortical development, in addition to the dynamic enrichment of these mRNAs in actively translating neocortical polysomal ribosomes. Understanding the multivariate control of mRNA translation by ribosomal complex specificity will be critical to reveal the intricate mechanisms of normal brain development and pathologies of neurodevelopmental disorders.
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Affiliation(s)
- Matthew L Kraushar
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Tatiana Popovitchenko
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Nicole L Volk
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Mladen-Roko Rasin
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA.
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32
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Mao H, McMahon JJ, Tsai YH, Wang Z, Silver DL. Haploinsufficiency for Core Exon Junction Complex Components Disrupts Embryonic Neurogenesis and Causes p53-Mediated Microcephaly. PLoS Genet 2016; 12:e1006282. [PMID: 27618312 PMCID: PMC5019403 DOI: 10.1371/journal.pgen.1006282] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 08/08/2016] [Indexed: 01/05/2023] Open
Abstract
The exon junction complex (EJC) is an RNA binding complex comprised of the core components Magoh, Rbm8a, and Eif4a3. Human mutations in EJC components cause neurodevelopmental pathologies. Further, mice heterozygous for either Magoh or Rbm8a exhibit aberrant neurogenesis and microcephaly. Yet despite the requirement of these genes for neurodevelopment, the pathogenic mechanisms linking EJC dysfunction to microcephaly remain poorly understood. Here we employ mouse genetics, transcriptomic and proteomic analyses to demonstrate that haploinsufficiency for each of the 3 core EJC components causes microcephaly via converging regulation of p53 signaling. Using a new conditional allele, we first show that Eif4a3 haploinsufficiency phenocopies aberrant neurogenesis and microcephaly of Magoh and Rbm8a mutant mice. Transcriptomic and proteomic analyses of embryonic brains at the onset of neurogenesis identifies common pathways altered in each of the 3 EJC mutants, including ribosome, proteasome, and p53 signaling components. We further demonstrate all 3 mutants exhibit defective splicing of RNA regulatory proteins, implying an EJC dependent RNA regulatory network that fine-tunes gene expression. Finally, we show that genetic ablation of one downstream pathway, p53, significantly rescues microcephaly of all 3 EJC mutants. This implicates p53 activation as a major node of neurodevelopmental pathogenesis following EJC impairment. Altogether our study reveals new mechanisms to help explain how EJC mutations influence neurogenesis and underlie neurodevelopmental disease.
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Affiliation(s)
- Hanqian Mao
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - John J. McMahon
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Yi-Hsuan Tsai
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Zefeng Wang
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Debra L. Silver
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Neurobiology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Institute for Brain Sciences, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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