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Li HY, Wang M, Jiang X, Jing Y, Wu Z, He Y, Yan K, Sun S, Ma S, Ji Z, Wang S, Belmonte JCI, Qu J, Zhang W, Wei T, Liu GH. CRISPR screening uncovers nucleolar RPL22 as a heterochromatin destabilizer and senescence driver. Nucleic Acids Res 2024:gkae740. [PMID: 39258545 DOI: 10.1093/nar/gkae740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 08/02/2024] [Accepted: 08/16/2024] [Indexed: 09/12/2024] Open
Abstract
Dysfunction of the ribosome manifests during cellular senescence and contributes to tissue aging, functional decline, and development of aging-related disorders in ways that have remained enigmatic. Here, we conducted a comprehensive CRISPR-based loss-of-function (LOF) screen of ribosome-associated genes (RAGs) in human mesenchymal progenitor cells (hMPCs). Through this approach, we identified ribosomal protein L22 (RPL22) as the foremost RAG whose deficiency mitigates the effects of cellular senescence. Consequently, absence of RPL22 delays hMPCs from becoming senescent, while an excess of RPL22 accelerates the senescence process. Mechanistically, we found in senescent hMPCs, RPL22 accumulates within the nucleolus. This accumulation triggers a cascade of events, including heterochromatin decompaction with concomitant degradation of key heterochromatin proteins, specifically heterochromatin protein 1γ (HP1γ) and heterochromatin protein KRAB-associated protein 1 (KAP1). Subsequently, RPL22-dependent breakdown of heterochromatin stimulates the transcription of ribosomal RNAs (rRNAs), triggering cellular senescence. In summary, our findings unveil a novel role for nucleolar RPL22 as a destabilizer of heterochromatin and a driver of cellular senescence, shedding new light on the intricate mechanisms underlying the aging process.
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Affiliation(s)
- Hong-Yu Li
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Xiaoyu Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaobin Jing
- International center for Aging and Cancer, Hainan Academy of Medical Sciences, Hainan Medical University, Haikou 571199, China
| | - Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yifang He
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Kaowen Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuhui Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Zhejun Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Aging Translational Medicine Center, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, China
- Aging Biomarker Consortium, Beijing 100101, China
| | | | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Weiqi Zhang
- CAS key laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Taotao Wei
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- International center for Aging and Cancer, Hainan Academy of Medical Sciences, Hainan Medical University, Haikou 571199, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Aging Translational Medicine Center, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, China
- Aging Biomarker Consortium, Beijing 100101, China
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2
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Jansen J, Bohnsack KE, Böhlken-Fascher S, Bohnsack MT, Dobbelstein M. The ribosomal protein L22 binds the MDM4 pre-mRNA and promotes exon skipping to activate p53 upon nucleolar stress. Cell Rep 2024; 43:114610. [PMID: 39116201 DOI: 10.1016/j.celrep.2024.114610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/09/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
The tumor suppressor p53 and its antagonists MDM2 and MDM4 integrate stress signaling. For instance, dysbalanced assembly of ribosomes in nucleoli induces p53. Here, we show that the ribosomal protein L22 (RPL22; eL22), under conditions of ribosomal and nucleolar stress, promotes the skipping of MDM4 exon 6. Upon L22 depletion, more full-length MDM4 is maintained, leading to diminished p53 activity and enhanced cellular proliferation. L22 binds to specific RNA elements within intron 6 of MDM4 that correspond to a stem-loop consensus, leading to exon 6 skipping. Targeted deletion of these intronic elements largely abolishes L22-mediated exon skipping and re-enables cell proliferation, despite nucleolar stress. L22 also governs alternative splicing of the L22L1 (RPL22L1) and UBAP2L mRNAs. Thus, L22 serves as a signaling intermediate that integrates different layers of gene expression. Defects in ribosome synthesis lead to specific alternative splicing, ultimately triggering p53-mediated transcription and arresting cell proliferation.
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Affiliation(s)
- Jennifer Jansen
- Department of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Susanne Böhlken-Fascher
- Department of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Matthias Dobbelstein
- Department of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
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Papadimitriou-Tsantarliotou A, Avgeros C, Konstantinidou M, Vizirianakis IS. Analyzing the role of ferroptosis in ribosome-related bone marrow failure disorders: From pathophysiology to potential pharmacological exploitation. IUBMB Life 2024. [PMID: 39052023 DOI: 10.1002/iub.2897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/04/2024] [Indexed: 07/27/2024]
Abstract
Within the last decade, the scientific community has witnessed the importance of ferroptosis as a novel cascade of molecular events leading to cellular decisions of death distinct from apoptosis and other known forms of cell death. Notably, such non- apoptotic and iron-dependent regulated cell death has been found to be intricately linked to several physiological processes as well as to the pathogenesis of various diseases. To this end, recent data support the notion that a potential molecular connection between ferroptosis and inherited bone marrow failure (IBMF) in individuals with ribosomopathies may exist. In this review, we suggest that in ribosome-related IBMFs the identified mutations in ribosomal proteins lead to changes in the ribosome composition of the hematopoietic progenitors, changes that seem to affect ribosomal function, thus enhancing the expression of some mRNAs subgroups while reducing the expression of others. These events lead to an imbalance inside the cell as some molecular pathways are promoted while others are inhibited. This disturbance is accompanied by ROS production and lipid peroxidation, while an additional finding in most of them is iron accumulation. Once lipid peroxidation and iron accumulation are the two main characteristics of ferroptosis, it is possible that this mechanism plays a key role in the manifestation of IBMF in this type of disease. If this molecular mechanism is further confirmed, new pharmacological targets such as ferroptosis inhibitors that are already exploited for the treatment of other diseases, could be utilized to improve the treatment of ribosomopathies.
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Affiliation(s)
| | - Chrysostomos Avgeros
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria Konstantinidou
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis S Vizirianakis
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Department of Health Sciences, School of Life and Health Sciences, University of Nicosia, Nicosia, Cyprus
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4
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Das AS, Basu A, Mukhopadhyay R. Ribosomal proteins: the missing piece in the inflammation puzzle? Mol Cell Biochem 2024:10.1007/s11010-024-05050-9. [PMID: 38951378 DOI: 10.1007/s11010-024-05050-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/09/2024] [Indexed: 07/03/2024]
Abstract
Ribosomal proteins (RPs) are constituents of macromolecular machinery, ribosome that translates genetic information into proteins. Besides ribosomal functions, RPs are now getting appreciated for their 'moonlighting'/extra-ribosomal functions modulating many cellular processes. Accumulating evidence suggests that a number of RPs are involved in inflammation. Though acute inflammation is a part of the innate immune response, uncontrolled inflammation is a driving factor for several chronic inflammatory diseases. An in-depth understanding of inflammation regulation has always been valued for the better management of associated diseases. Hence, this review first outlines the common livelihood of RPs and then provides a comprehensive account of five RPs that significantly contribute to the inflammation process. Finally, we discuss the possible therapeutic uses of RPs against chronic inflammatory diseases.
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Affiliation(s)
- Anindhya Sundar Das
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India.
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, 02912, USA.
| | - Anandita Basu
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India
- Division of Surgical Research, Department of Surgery, Rhode Island Hospital, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, 02903, USA
| | - Rupak Mukhopadhyay
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India.
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5
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Temaj G, Chichiarelli S, Telkoparan-Akillilar P, Saha S, Nuhii N, Hadziselimovic R, Saso L. Advances in molecular function of UPF1 in Cancer. Arch Biochem Biophys 2024; 756:109989. [PMID: 38621446 DOI: 10.1016/j.abb.2024.109989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/23/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
It is known that more than 10 % of genetic diseases are caused by a mutation in protein-coding mRNA (premature termination codon; PTC). mRNAs with an early stop codon are degraded by the cellular surveillance process known as nonsense-mediated mRNA decay (NMD), which prevents the synthesis of C-terminally truncated proteins. Up-frameshift-1 (UPF1) has been reported to be involved in the downregulation of various cancers, and low expression of UPF1 was shown to correlate with poor prognosis. It is known that UPF1 is a master regulator of nonsense-mediated mRNA decay (NMD). UPF1 may also function as an E3 ligase and degrade target proteins without using mRNA decay mechanisms. Increasing evidence indicates that UPF1 could serve as a good biomarker for cancer diagnosis and treatment for future therapeutic applications. Long non-coding RNAs (lncRNAs) have the ability to bind different proteins and regulate gene expression; this role in cancer cells has already been identified by different studies. This article provides an overview of the aberrant expression of UPF1, its functional properties, and molecular processes during cancer for clinical applications in cancer. We also discussed the interactions of lncRNA with UPF1 for cell growth during tumorigenesis.
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Affiliation(s)
- Gazmend Temaj
- Faculty of Pharmacy, College UBT, 10000, Prishtina, Republic of Kosovo.
| | - Silvia Chichiarelli
- Department of Biochemical Sciences "A. Rossi-Fanelli", Sapienza University of Rome, 00185, Rome, Italy.
| | | | - Sarmistha Saha
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh, India.
| | - Nexhibe Nuhii
- Department of Pharmacy, Faculty of Medical Sciences, State University of Tetovo, 1200, Tetovo, Macedonia.
| | - Rifat Hadziselimovic
- Faculty of Science, University of Sarajevo, 71000, Sarajevo, Bosnia and Herzegovina.
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", La Sapienza University, 00185, Rome, Italy.
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6
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Ng AYE, Chan SN, Pek JW. Genetic compensation between ribosomal protein paralogs mediated by a cognate circular RNA. Cell Rep 2024; 43:114228. [PMID: 38735045 DOI: 10.1016/j.celrep.2024.114228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
Inter-regulation between related genes, such as ribosomal protein (RP) paralogs, has been observed to be important for genetic compensation and paralog-specific functions. However, how paralogs communicate to modulate their expression levels is unknown. Here, we report a circular RNA involved in the inter-regulation between RP paralogs RpL22 and RpL22-like during Drosophila spermatogenesis. Both paralogs are mutually regulated by the circular stable intronic sequence RNA (sisRNA) circRpL22(NE,3S) produced from the RpL22 locus. RpL22 represses itself and RpL22-like. Interestingly, circRpL22 binds to RpL22 to repress RpL22-like, but not RpL22, suggesting that circRpL22 modulates RpL22's function. circRpL22 is in turn controlled by RpL22-like, which regulates RpL22 binding to circRpL22 to indirectly modulate RpL22. This circRpL22-centric inter-regulatory circuit enables the loss of RpL22-like to be genetically compensated by RpL22 upregulation to ensure robust male germline development. Thus, our study identifies sisRNA as a possible mechanism of genetic crosstalk between paralogous genes.
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Affiliation(s)
- Amanda Yunn Ee Ng
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive Singapore 117543, Singapore
| | - Seow Neng Chan
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive Singapore 117543, Singapore.
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7
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Islam RA, Rallis C. Ribosomal Biogenesis and Heterogeneity in Development, Disease, and Aging. EPIGENOMES 2023; 7:17. [PMID: 37606454 PMCID: PMC10443367 DOI: 10.3390/epigenomes7030017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/23/2023] Open
Abstract
Although reported in the literature, ribosome heterogeneity is a phenomenon whose extent and implications in cell and organismal biology is not fully appreciated. This has been the case due to the lack of the appropriate techniques and approaches. Heterogeneity can arise from alternative use and differential content of protein and RNA constituents, as well as from post-transcriptional and post-translational modifications. In the few examples we have, it is apparent that ribosomal heterogeneity offers an additional level and potential for gene expression regulation and might be a way towards tuning metabolism, stress, and growth programs to external and internal stimuli and needs. Here, we introduce ribosome biogenesis and discuss ribosomal heterogeneity in various reported occasions. We conclude that a systematic approach in multiple organisms will be needed to delineate this biological phenomenon and its contributions to growth, aging, and disease. Finally, we discuss ribosome mutations and their roles in disease.
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Affiliation(s)
- Rowshan Ara Islam
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK;
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Charalampos Rallis
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK;
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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8
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Harris B, Singh DK, Verma M, Fahl SP, Rhodes M, Sprinkle SR, Wang M, Zhang Y, Perrigoue J, Kessel R, Peri S, West J, Giricz O, Boultwood J, Pellagatti A, Ramesh KH, Montagna C, Pradhan K, Tyner JW, Kennedy BK, Holinstat M, Steidl U, Sykes S, Verma A, Wiest DL. Ribosomal protein control of hematopoietic stem cell transformation through direct, non-canonical regulation of metabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543132. [PMID: 37398007 PMCID: PMC10312568 DOI: 10.1101/2023.05.31.543132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
We report here that expression of the ribosomal protein, RPL22, is frequently reduced in human myelodysplastic syndrome (MDS) and acute myelogenous leukemia (AML); reduced RPL22 expression is associated with worse outcomes. Mice null for Rpl22 display characteristics of an MDS-like syndrome and develop leukemia at an accelerated rate. Rpl22-deficient mice also display enhanced hematopoietic stem cell (HSC) self-renewal and obstructed differentiation potential, which arises not from reduced protein synthesis but from increased expression of the Rpl22 target, ALOX12, an upstream regulator of fatty acid oxidation (FAO). The increased FAO mediated by Rpl22-deficiency also persists in leukemia cells and promotes their survival. Altogether, these findings reveal that Rpl22 insufficiency enhances the leukemia potential of HSC via non-canonical de-repression of its target, ALOX12, which enhances FAO, a process that may serve as a therapeutic vulnerability of Rpl22 low MDS and AML leukemia cells. Highlights RPL22 insufficiency is observed in MDS/AML and is associated with reduced survivalRpl22-deficiency produces an MDS-like syndrome and facilitates leukemogenesisRpl22-deficiency does not impair global protein synthesis by HSCRpl22 controls leukemia cell survival by non-canonical regulation of lipid oxidation eTOC: Rpl22 controls the function and transformation potential of hematopoietic stem cells through effects on ALOX12 expression, a regulator of fatty acid oxidation.
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9
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McGee JP, Armache JP, Lindner SE. Ribosome heterogeneity and specialization of Plasmodium parasites. PLoS Pathog 2023; 19:e1011267. [PMID: 37053161 PMCID: PMC10101515 DOI: 10.1371/journal.ppat.1011267] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Affiliation(s)
- James P McGee
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Pennsylvania, United States of America
- Huck Center for Malaria Research, Pennsylvania State University, Pennsylvania, United States of America
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Pennsylvania, United States of America
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, Pennsylvania, United States of America
| | - Scott E Lindner
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Pennsylvania, United States of America
- Huck Center for Malaria Research, Pennsylvania State University, Pennsylvania, United States of America
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, Pennsylvania, United States of America
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10
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Kochavi A, Lovecchio D, Faller WJ, Agami R. Proteome diversification by mRNA translation in cancer. Mol Cell 2023; 83:469-480. [PMID: 36521491 DOI: 10.1016/j.molcel.2022.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022]
Abstract
mRNA translation is a highly conserved and tightly controlled mechanism for protein synthesis and is well known to be altered by oncogenes to promote cancer development. This distorted mRNA translation is accompanied by the vulnerability of cancer to inhibitors of key mRNA translation components. Novel studies also suggest that these alternations could be utilized for immunotherapy. Ribosome heterogeneity and alternative responses to nutrient shortages, which aid cancer growth and spread, are proposed to elicit aberrant protein production but may also result in previously unidentified therapeutic targets, such as the presentation of cancer-specific peptides at the surface of cancer cells (neoepitopes). This review will assess the driving forces in tRNA and ribosome function that underlie proteome diversification due to alterations in mRNA translation in cancer cells.
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Affiliation(s)
- Adva Kochavi
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - Domenica Lovecchio
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - William James Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Reuven Agami
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands; Erasmus MC, Rotterdam University, Rotterdam, the Netherlands.
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11
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Sertori R, Zhang Y, Wiest DL. Zebrafish: A Tractable Model for Analysis of T Cell Development. Methods Mol Biol 2023; 2580:355-377. [PMID: 36374469 DOI: 10.1007/978-1-0716-2740-2_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
While the zebrafish has for some time been regarded as a powerful model organism with which to study early events in hematopoiesis, recent evidence suggests that it also ideal for unraveling the molecular requirements for T cell development in the thymus. Like mammals, zebrafish possess an adaptive immune system, comprising B lymphocytes as well as both the γδ and αβ lineages of T cells, which develop in the thymus. Moreover, the molecular processes underlying T cell development in zebrafish appear to be remarkably conserved. Thus, findings in the zebrafish model will be of high relevance to the equivalent processes in mammals. Finally, molecular processes can be interrogated in zebrafish far more rapidly than is possible in mammals because the zebrafish possesses many unique advantages. Here, we describe these unique attributes and the methods by which they can be exploited to investigate the role of novel genes in T cell development.
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Affiliation(s)
- Robert Sertori
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Yong Zhang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - David L Wiest
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA.
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12
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Lin S, Xian M, Ren T, Mo G, Zhang L, Zhang X. Mining of chicken muscle growth genes and the function of important candidate gene RPL3L in muscle development. Front Physiol 2022; 13:1033075. [PMID: 36407004 PMCID: PMC9669902 DOI: 10.3389/fphys.2022.1033075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/14/2022] [Indexed: 12/12/2023] Open
Abstract
The birth weight of chickens does not significantly affect the weight at slaughter, while the different growth rate after birth was one of the important reasons for the difference in slaughter weight. Also, the increase in chickens' postnatal skeletal muscle weight is the main cause of the slaughter weight gain, but which genes are involved in this biological process is still unclear. In this study, by integrating four transcriptome datasets containing chicken muscles at different developmental times or different chicken tissues in public databases, a total of nine candidate genes that may be related to postnatal muscle development in chickens were obtained, including RPL3L, FBP2, ASB4, ASB15, CKMT2, PGAM1, YIPF7, PFKM, and LDHA. One of these candidate genes is RPL3L, whose 42 bp insertion/deletion (indel) mutation significantly correlated with multiple carcass traits in the F2 resource population from Xinghua chickens crossing with White Recessive Rock (WRR) chickens, including live weight, carcass weight, half eviscerated weight, eviscerated weight, breast meat weight, wing weight, leg muscle shear force, and breast muscle shear force. Also, there was a very significant difference between different genotypes of the RPL3L 42 bp indel mutation in these trains. Further experiments showed that RPL3L was highly expressed in chicken skeletal muscle, and its overexpression could promote the proliferation and inhibit the differentiation of chicken myoblasts by regulating ASB4 and ASB15 expression. Our findings demonstrated that the RPL3L 42 bp indel may be one of the molecular markers of chicken weight-related traits.
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Affiliation(s)
- Shudai Lin
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Mingjian Xian
- Department of Animal Genetics Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Tuanhui Ren
- Department of Animal Genetics Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Guodong Mo
- Department of Animal Genetics Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Li Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Xiquan Zhang
- Department of Animal Genetics Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
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13
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Larionova TD, Bastola S, Aksinina TE, Anufrieva KS, Wang J, Shender VO, Andreev DE, Kovalenko TF, Arapidi GP, Shnaider PV, Kazakova AN, Latyshev YA, Tatarskiy VV, Shtil AA, Moreau P, Giraud F, Li C, Wang Y, Rubtsova MP, Dontsova OA, Condro M, Ellingson BM, Shakhparonov MI, Kornblum HI, Nakano I, Pavlyukov MS. Alternative RNA splicing modulates ribosomal composition and determines the spatial phenotype of glioblastoma cells. Nat Cell Biol 2022; 24:1541-1557. [PMID: 36192632 PMCID: PMC10026424 DOI: 10.1038/s41556-022-00994-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/15/2022] [Indexed: 02/08/2023]
Abstract
Glioblastoma (GBM) is characterized by exceptionally high intratumoral heterogeneity. However, the molecular mechanisms underlying the origin of different GBM cell populations remain unclear. Here, we found that the compositions of ribosomes of GBM cells in the tumour core and edge differ due to alternative RNA splicing. The acidic pH in the core switches before messenger RNA splicing of the ribosomal gene RPL22L1 towards the RPL22L1b isoform. This allows cells to survive acidosis, increases stemness and correlates with worse patient outcome. Mechanistically, RPL22L1b promotes RNA splicing by interacting with lncMALAT1 in the nucleus and inducing its degradation. Contrarily, in the tumour edge region, RPL22L1a interacts with ribosomes in the cytoplasm and upregulates the translation of multiple messenger RNAs including TP53. We found that the RPL22L1 isoform switch is regulated by SRSF4 and identified a compound that inhibits this process and decreases tumour growth. These findings demonstrate how distinct GBM cell populations arise during tumour growth. Targeting this mechanism may decrease GBM heterogeneity and facilitate therapy.
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Affiliation(s)
- Tatyana D Larionova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Soniya Bastola
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Tatiana E Aksinina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Ksenia S Anufrieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency, Moscow, Russian Federation
| | - Jia Wang
- Department of Neurosurgery, Centre of Brain Science, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Victoria O Shender
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency, Moscow, Russian Federation
| | - Dmitriy E Andreev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Tatiana F Kovalenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Georgij P Arapidi
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency, Moscow, Russian Federation
| | - Polina V Shnaider
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency, Moscow, Russian Federation
| | - Anastasia N Kazakova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency, Moscow, Russian Federation
| | - Yaroslav A Latyshev
- N.N. Burdenko National Medical Research Center of Neurosurgery, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - Victor V Tatarskiy
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander A Shtil
- Blokhin National Medical Research Center of Oncology, Moscow, Russian Federation
| | - Pascale Moreau
- Institute of Chemistry of Clermont-Ferrand, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Francis Giraud
- Institute of Chemistry of Clermont-Ferrand, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Chaoxi Li
- Department of Neurosurgery, School of Medicine and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yichan Wang
- Department of Neurosurgery, Centre of Brain Science, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Maria P Rubtsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Olga A Dontsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation
| | - Michael Condro
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Benjamin M Ellingson
- Brain Tumor Imaging Laboratory, Center for Computer Vision and Imaging Biomarkers, University of California Los Angeles, Los Angeles, CA, USA
- Department of Radiological Sciences, University of California Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry, University of California Los Angeles, Los Angeles, CA, USA
- Department of Neurosurgery, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Harley I Kornblum
- Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ichiro Nakano
- Department of Neurosurgery, Medical Institute of Hokuto, Hokkaido, Japan.
| | - Marat S Pavlyukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation.
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
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14
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Sertori R, Lin JX, Martinez E, Rana S, Sharo A, Kazemian M, Sunderam U, Andrake M, Shinton S, Truong B, Dunbrack RM, Liu C, Srinivasan R, Brenner SE, Seroogy CM, Puck JM, Leonard WJ, Wiest DL. Investigation of the causal etiology in a patient with T-B+NK+ immunodeficiency. Front Immunol 2022; 13:928252. [PMID: 35967429 PMCID: PMC9372720 DOI: 10.3389/fimmu.2022.928252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/27/2022] [Indexed: 11/24/2022] Open
Abstract
Newborn screening for severe combined immunodeficiency (SCID) has not only accelerated diagnosis and improved treatment for affected infants, but also led to identification of novel genes required for human T cell development. A male proband had SCID newborn screening showing very low T cell receptor excision circles (TRECs), a biomarker for thymic output of nascent T cells. He had persistent profound T lymphopenia, but normal numbers of B and natural killer (NK) cells. Despite an allogeneic hematopoietic stem cell transplant from his brother, he failed to develop normal T cells. Targeted resequencing excluded known SCID genes; however, whole exome sequencing (WES) of the proband and parents revealed a maternally inherited X-linked missense mutation in MED14 (MED14V763A), a component of the mediator complex. Morpholino (MO)-mediated loss of MED14 function attenuated T cell development in zebrafish. Moreover, this arrest was rescued by ectopic expression of cDNA encoding the wild type human MED14 ortholog, but not by MED14V763A , suggesting that the variant impaired MED14 function. Modeling of the equivalent mutation in mouse (Med14V769A) did not disrupt T cell development at baseline. However, repopulation of peripheral T cells upon competitive bone marrow transplantation was compromised, consistent with the incomplete T cell reconstitution experienced by the proband upon transplantation with bone marrow from his healthy male sibling, who was found to have the same MED14V763A variant. Suspecting that the variable phenotypic expression between the siblings was influenced by further mutation(s), we sought to identify genetic variants present only in the affected proband. Indeed, WES revealed a mutation in the L1 cell adhesion molecule (L1CAMQ498H); however, introducing that mutation in vivo in mice did not disrupt T cell development. Consequently, immunodeficiency in the proband may depend upon additional, unidentified gene variants.
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Affiliation(s)
- Robert Sertori
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Jian-Xin Lin
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Esteban Martinez
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Sadhna Rana
- Innovation Labs, Tata Consultancy Services, Hyderabad, India
| | - Andrew Sharo
- Center for Computational Biology, University of California, Berkeley, CA, United States
| | - Majid Kazemian
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, United States
| | - Uma Sunderam
- Innovation Labs, Tata Consultancy Services, Hyderabad, India
| | - Mark Andrake
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Susan Shinton
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Billy Truong
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Roland M. Dunbrack
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | | | - Steven E. Brenner
- Center for Computational Biology, University of California, Berkeley, CA, United States
| | - Christine M. Seroogy
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Jennifer M. Puck
- Department of Pediatrics, University of California San Francisco and UCSF Benioff Children’s Hospital, San Francisco, CA, United States
| | - Warren J. Leonard
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - David L. Wiest
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
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15
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Alkan F, Wilkins OG, Hernández-Pérez S, Ramalho S, Silva J, Ule J, Faller WJ. Identifying ribosome heterogeneity using ribosome profiling. Nucleic Acids Res 2022; 50:e95. [PMID: 35687114 PMCID: PMC9458444 DOI: 10.1093/nar/gkac484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 05/12/2022] [Accepted: 05/24/2022] [Indexed: 11/14/2022] Open
Abstract
Recent studies have revealed multiple mechanisms that can lead to heterogeneity in ribosomal composition. This heterogeneity can lead to preferential translation of specific panels of mRNAs, and is defined in large part by the ribosomal protein (RP) content, amongst other things. However, it is currently unknown to what extent ribosomal composition is heterogeneous across tissues, which is compounded by a lack of tools available to study it. Here we present dripARF, a method for detecting differential RP incorporation into the ribosome using Ribosome Profiling (Ribo-seq) data. We combine the 'waste' rRNA fragment data generated in Ribo-seq with the known 3D structure of the human ribosome to predict differences in the composition of ribosomes in the material being studied. We have validated this approach using publicly available data, and have revealed a potential role for eS25/RPS25 in development. Our results indicate that ribosome heterogeneity can be detected in Ribo-seq data, providing a new method to study this phenomenon. Furthermore, with dripARF, previously published Ribo-seq data provides a wealth of new information, allowing the identification of RPs of interest in many disease and normal contexts. dripARF is available as part of the ARF R package and can be accessed through https://github.com/fallerlab/ARF.
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Affiliation(s)
- Ferhat Alkan
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Oscar G Wilkins
- The Francis Crick Institute, London, UK.,UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | | | - Sofia Ramalho
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joana Silva
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jernej Ule
- The Francis Crick Institute, London, UK.,UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK.,UK Dementia Research Institute Centre, King's College London, London, UK
| | - William J Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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16
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Fahl SP, Sertori R, Zhang Y, Contreras AV, Harris B, Wang M, Perrigoue J, Balachandran S, Kennedy BK, Wiest DL. Loss of Ribosomal Protein Paralog Rpl22-like1 Blocks Lymphoid Development without Affecting Protein Synthesis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:870-880. [PMID: 35046107 PMCID: PMC8827804 DOI: 10.4049/jimmunol.2100668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/30/2021] [Indexed: 11/19/2022]
Abstract
Ribosomal proteins are thought to primarily facilitate biogenesis of the ribosome and its ability to synthesize protein. However, in this study, we show that Rpl22-like1 (Rpl22l1) regulates hematopoiesis without affecting ribosome biogenesis or bulk protein synthesis. Conditional loss of murine Rpl22l1 using stage or lineage-restricted Cre drivers impairs development of several hematopoietic lineages. Specifically, Tie2-Cre-mediated ablation of Rpl22l1 in hemogenic endothelium impairs the emergence of embryonic hematopoietic stem cells. Ablation of Rpl22l1 in late fetal liver progenitors impairs the development of B lineage progenitors at the pre-B stage and development of T cells at the CD44-CD25+ double-negative stage. In vivo labeling with O-propargyl-puromycin revealed that protein synthesis at the stages of arrest was not altered, indicating that the ribosome biogenesis and function were not generally compromised. The developmental arrest was associated with p53 activation, suggesting that the arrest may be p53-dependent. Indeed, development of both B and T lymphocytes was rescued by p53 deficiency. p53 induction was not accompanied by DNA damage as indicated by phospho-γH2AX induction or endoplasmic reticulum stress, as measured by phosphorylation of EIF2α, thereby excluding the known likely p53 inducers as causal. Finally, the developmental arrest of T cells was not rescued by elimination of the Rpl22l1 paralog, Rpl22, as we had previously found for the emergence of hematopoietic stem cells. This indicates that Rpl22 and Rpl22l1 play distinct and essential roles in supporting B and T cell development.
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Affiliation(s)
- Shawn P Fahl
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111; and
| | - Robert Sertori
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111; and
| | - Yong Zhang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111; and
| | - Alejandra V Contreras
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111; and
| | - Bryan Harris
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111; and
| | - Minshi Wang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111; and
| | - Jacqueline Perrigoue
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111; and
| | - Siddharth Balachandran
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111; and
| | - Brian K Kennedy
- Departments of Biochemistry and Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - David L Wiest
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111; and
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17
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Ottesen EW, Luo D, Singh NN, Singh RN. High Concentration of an ISS-N1-Targeting Antisense Oligonucleotide Causes Massive Perturbation of the Transcriptome. Int J Mol Sci 2021; 22:ijms22168378. [PMID: 34445083 PMCID: PMC8395096 DOI: 10.3390/ijms22168378] [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] [Received: 05/20/2021] [Revised: 07/14/2021] [Accepted: 07/31/2021] [Indexed: 12/17/2022] Open
Abstract
Intronic splicing silencer N1 (ISS-N1) located within Survival Motor Neuron 2 (SMN2) intron 7 is the target of a therapeutic antisense oligonucleotide (ASO), nusinersen (Spinraza), which is currently being used for the treatment of spinal muscular atrophy (SMA), a leading genetic disease associated with infant mortality. The discovery of ISS-N1 as a promising therapeutic target was enabled in part by Anti-N1, a 20-mer ASO that restored SMN2 exon 7 inclusion by annealing to ISS-N1. Here, we analyzed the transcriptome of SMA patient cells treated with 100 nM of Anti-N1 for 30 h. Such concentrations are routinely used to demonstrate the efficacy of an ASO. While 100 nM of Anti-N1 substantially stimulated SMN2 exon 7 inclusion, it also caused massive perturbations in the transcriptome and triggered widespread aberrant splicing, affecting expression of essential genes associated with multiple cellular processes such as transcription, splicing, translation, cell signaling, cell cycle, macromolecular trafficking, cytoskeletal dynamics, and innate immunity. We validated our findings with quantitative and semiquantitative PCR of 39 candidate genes associated with diverse pathways. We also showed a substantial reduction in off-target effects with shorter ISS-N1-targeting ASOs. Our findings are significant for implementing better ASO design and dosing regimens of ASO-based drugs.
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18
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Yuan J, Li Z, Li F, Lin Z, Yao S, Zhou H, Liu W, Yu H, Liu Y, Liu F, Li F, Ran H, Zhang J, Huang Y, Fu Q, Wang L, Liu J. Proteomics reveals the potential mechanism of Mrps35 controlling Listeria monocytogenes intracellular proliferation in macrophages. Proteomics 2021; 21:e2000262. [PMID: 33763969 DOI: 10.1002/pmic.202000262] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 11/10/2022]
Abstract
Macrophages are sentinels in the organism which can resist and destroy various bacteria through direct phagocytosis. Here, we reported that expression level of mitochondrial ribosomal protein S35 (Mrps35) continued to decrease over infection time after Listeria monocytogenes (L. monocytogenes) infected macrophages. Our results indicated that knockdown Mrps35 increased the load of L. monocytogenes in macrophages. This result supported that Mrps35 played the crucial roles in L. monocytogenes infection. Moreover, we performed the comprehensive proteomics to analyze the differentially expressed protein of wild type and Mrps35 Knockdown Raw264.7 cells by L. monocytogenes infection over 6 h. Based on the results of mass spectrometry, we presented a wide variety of hypotheses about the mechanism of Mrps35 controlling the L. monocytogenes intracellular proliferation. Among them, experiments confirmed that Mrps35 and 60S ribosomal protein L22-like 1 (Rpl22l1) were a functional correlation or potentially a compensatory mechanism during L. monocytogenes infection. This study provided new insights into understanding that L. monocytogenes infection changed the basic synthesis or metabolism-related proteins of host cells.
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Affiliation(s)
- Jiangbei Yuan
- Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Guangdong province, China
| | - Zhangfu Li
- Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Guangdong province, China
| | - Fang Li
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Zewei Lin
- Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Siyu Yao
- Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Hang Zhou
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Wenhu Liu
- School of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Haili Yu
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Yang Liu
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Fang Liu
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Fei Li
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Haiying Ran
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Junying Zhang
- School of Pharmaceutical Sciences and Innovative Drug Research Center, Chongqing University, Chongqing, China
| | - Yi Huang
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Qihuan Fu
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Liting Wang
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Jikui Liu
- Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
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19
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Ho JJD, Man JHS, Schatz JH, Marsden PA. Translational remodeling by RNA-binding proteins and noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1647. [PMID: 33694288 DOI: 10.1002/wrna.1647] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Responsible for generating the proteome that controls phenotype, translation is the ultimate convergence point for myriad upstream signals that influence gene expression. System-wide adaptive translational reprogramming has recently emerged as a pillar of cellular adaptation. As classic regulators of mRNA stability and translation efficiency, foundational studies established the concept of collaboration and competition between RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) on individual mRNAs. Fresh conceptual innovations now highlight stress-activated, evolutionarily conserved RBP networks and ncRNAs that increase the translation efficiency of populations of transcripts encoding proteins that participate in a common cellular process. The discovery of post-transcriptional functions for long noncoding RNAs (lncRNAs) was particularly intriguing given their cell-type-specificity and historical definition as nuclear-functioning epigenetic regulators. The convergence of RBPs, lncRNAs, and microRNAs on functionally related mRNAs to enable adaptive protein synthesis is a newer biological paradigm that highlights their role as "translatome (protein output) remodelers" and reinvigorates the paradigm of "RNA operons." Together, these concepts modernize our understanding of cellular stress adaptation and strategies for therapeutic development. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- J J David Ho
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Jeffrey H S Man
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Department of Respirology, University Health Network, Latner Thoracic Research Laboratories, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan H Schatz
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Philip A Marsden
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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20
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Bao B, An W, Lu Q, Wang Y, Lu Z, Tu J, Zhang H, Duan Y, Yuan W, Zhu X, Jia H. Sfxn1 is essential for erythrocyte maturation via facilitating hemoglobin production in zebrafish. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166096. [PMID: 33524530 DOI: 10.1016/j.bbadis.2021.166096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/19/2020] [Accepted: 01/26/2021] [Indexed: 12/31/2022]
Abstract
Previous reports revealed that mutation of mitochondrial inner-membrane located protein SFXN1 led to pleiotropic hematological and skeletal defects in mice, associated with the presence of hypochromic erythroid cell, iron overload in mitochondrion of erythroblast and the development of sideroblastic anemia (SA). However, the potential role of sfxn1 during erythrocyte differentiation and the development of anemia, especially the pathological molecular mechanism still remains elusive. In this study, the correlation between sfxn1 and erythroid cell development is explored through zebrafish in vivo coupled with human hematopoietic cells assay ex vivo. Both knockdown and knockout of sfxn1 result in hypochromic anemia phenotype in zebrafish. Further analyses demonstrate that the development of anemia attributes to the biosynthetic deficiency of hemoglobin, which is caused by the biosynthetic disorder of heme that associates with one‑carbon (1C) metabolism process of mitochondrial branch in erythrocyte. Sfxn1 is also involved in the differentiation and maturation of erythrocyte in inducible human umbilical cord blood stem cells. In addition, we found that functional disruption of sfxn1 causes hypochromic anemia that is distinct from SA. These findings reveal that sfxn1 is genetically conserved and essential for the maturation of erythrocyte via facilitating the production of hemoglobin, which may provide a possible guidance for the future clinical treatment of sfxn1 mutation associated hematological disorders.
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Affiliation(s)
- Binghao Bao
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Wenbin An
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, ,China
| | - Qunwei Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Yaqin Wang
- Department of Pediatrics, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Zhichao Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Jiayi Tu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Yongjuan Duan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, ,China
| | - Weiping Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, ,China.
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, ,China.
| | - Haibo Jia
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China.
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21
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Gueiderikh A, Maczkowiak-Chartois F, Rouvet G, Souquère-Besse S, Apcher S, Diaz JJ, Rosselli F. Fanconi anemia A protein participates in nucleolar homeostasis maintenance and ribosome biogenesis. SCIENCE ADVANCES 2021; 7:7/1/eabb5414. [PMID: 33523834 PMCID: PMC7775781 DOI: 10.1126/sciadv.abb5414] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 10/28/2020] [Indexed: 05/22/2023]
Abstract
Fanconi anemia (FA), the most common inherited bone marrow failure and leukemia predisposition syndrome, is generally attributed to alterations in DNA damage responses due to the loss of function of the DNA repair and replication rescue activities of the FANC pathway. Here, we report that FANCA deficiency, whose inactivation has been identified in two-thirds of FA patients, is associated with nucleolar homeostasis loss, mislocalization of key nucleolar proteins, including nucleolin (NCL) and nucleophosmin 1 (NPM1), as well as alterations in ribosome biogenesis and protein synthesis. FANCA coimmunoprecipitates with NCL and NPM1 in a FANCcore complex-independent manner and, unique among the FANCcore complex proteins, associates with ribosomal subunits, influencing the stoichiometry of the translational machineries. In conclusion, we have identified unexpected nucleolar and translational consequences specifically associated with FANCA deficiency that appears to be involved in both DNA damage and nucleolar stress responses, challenging current hypothesis on FA physiopathology.
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Affiliation(s)
- Anna Gueiderikh
- CNRS-UMR9019, Équipe labellisée "La Ligue contre le Cancer," 94805 Villejuif, France
- Gustave Roussy Cancer Center, 94805 Villejuif, France
- Université Paris-Saclay-Paris Sud, Orsay, France
| | - Frédérique Maczkowiak-Chartois
- CNRS-UMR9019, Équipe labellisée "La Ligue contre le Cancer," 94805 Villejuif, France
- Gustave Roussy Cancer Center, 94805 Villejuif, France
- Université Paris-Saclay-Paris Sud, Orsay, France
| | - Guillaume Rouvet
- CNRS-UMR9019, Équipe labellisée "La Ligue contre le Cancer," 94805 Villejuif, France
- Gustave Roussy Cancer Center, 94805 Villejuif, France
- Université Paris-Saclay-Paris Sud, Orsay, France
| | - Sylvie Souquère-Besse
- Gustave Roussy Cancer Center, 94805 Villejuif, France
- Université Paris-Saclay-Paris Sud, Orsay, France
- CNRS-UMS3655, 94805 Villejuif, France
| | - Sébastien Apcher
- Gustave Roussy Cancer Center, 94805 Villejuif, France
- Université Paris-Saclay-Paris Sud, Orsay, France
- INSERM-UMR1015, 94805 Villejuif, France
| | - Jean-Jacques Diaz
- Université Lyon, Université Claude Bernard Lyon 1, Inserm 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, 69373 Lyon cedex 08, France
| | - Filippo Rosselli
- CNRS-UMR9019, Équipe labellisée "La Ligue contre le Cancer," 94805 Villejuif, France.
- Gustave Roussy Cancer Center, 94805 Villejuif, France
- Université Paris-Saclay-Paris Sud, Orsay, France
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RPL-4 and RPL-9 ̶Mediated Ribosome Purifications Facilitate the Efficient Analysis of Gene Expression in Caenorhabditis elegans Germ Cells. G3-GENES GENOMES GENETICS 2020; 10:4063-4069. [PMID: 32883755 PMCID: PMC7642943 DOI: 10.1534/g3.120.401644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In many organisms, tissue complexity and cellular diversity create a barrier that can hinder our understanding of gene expression programs. To address this problem, methods have been developed that allow for easy isolation of translated mRNAs from genetically defined cell populations. A prominent example is the Translating Ribosome Affinity Purification method also called TRAP. Here, ribosome associated mRNAs are isolated via purification of the ribosomal protein RPL10A/uL1, which is expressed under the control of a tissue specific promoter. Originally developed to investigate gene expression in mouse neurons, it has by now been adopted to many different organisms and tissues. Interestingly, TRAP has never been used successfully to analyze mRNA translation in germ cells. Employing a combination of genetic and biochemical approaches, I assessed several ribosomal proteins for their suitability for TRAP using the Caenorhabditis elegans germline as a target tissue. Surprisingly, I found that RPL10A/uL1 is not the ideal ribosomal component to perform such an analysis in germ cells. Instead other proteins such as RPL4/uL4 or RPL9/eL6 are much better suited for this task. Tagged variants of these proteins are well expressed in germ cells, integrated into translating ribosomes and do not influence germ cell functions. Furthermore, germ cell-specific mRNAs are much more efficiently co-purified with RPL4/uL4 and RPL9/uL6 compared to RPL10A/uL1. This study provides a solid basis upon which future germ cell TRAP experiments can be built, and it highlights the need for rigorous testing when adopting such methods to a new biological system.
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23
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Petibon C, Malik Ghulam M, Catala M, Abou Elela S. Regulation of ribosomal protein genes: An ordered anarchy. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1632. [PMID: 33038057 PMCID: PMC8047918 DOI: 10.1002/wrna.1632] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/08/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023]
Abstract
Ribosomal protein genes are among the most highly expressed genes in most cell types. Their products are generally essential for ribosome synthesis, which is the cornerstone for cell growth and proliferation. Many cellular resources are dedicated to producing ribosomal proteins and thus this process needs to be regulated in ways that carefully balance the supply of nascent ribosomal proteins with the demand for new ribosomes. Ribosomal protein genes have classically been viewed as a uniform interconnected regulon regulated in eukaryotic cells by target of rapamycin and protein kinase A pathway in response to changes in growth conditions and/or cellular status. However, recent literature depicts a more complex picture in which the amount of ribosomal proteins produced varies between genes in response to two overlapping regulatory circuits. The first includes the classical general ribosome‐producing program and the second is a gene‐specific feature responsible for fine‐tuning the amount of ribosomal proteins produced from each individual ribosomal gene. Unlike the general pathway that is mainly controlled at the level of transcription and translation, this specific regulation of ribosomal protein genes is largely achieved through changes in pre‐mRNA splicing efficiency and mRNA stability. By combining general and specific regulation, the cell can coordinate ribosome production, while allowing functional specialization and diversity. Here we review the many ways ribosomal protein genes are regulated, with special focus on the emerging role of posttranscriptional regulatory events in fine‐tuning the expression of ribosomal protein genes and its role in controlling the potential variation in ribosome functions. This article is categorized under:Translation > Ribosome Biogenesis Translation > Ribosome Structure/Function Translation > Translation Regulation
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Affiliation(s)
- Cyrielle Petibon
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Mustafa Malik Ghulam
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Mathieu Catala
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Sherif Abou Elela
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
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24
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Hamabata T, Umeda K, Kouzuki K, Tanaka T, Daifu T, Nodomi S, Saida S, Kato I, Baba S, Hiramatsu H, Osawa M, Niwa A, Saito MK, Kamikubo Y, Adachi S, Hashii Y, Shimada A, Watanabe H, Osafune K, Okita K, Nakahata T, Watanabe K, Takita J, Heike T. Pluripotent stem cell model of Shwachman-Diamond syndrome reveals apoptotic predisposition of hemoangiogenic progenitors. Sci Rep 2020; 10:14859. [PMID: 32908229 PMCID: PMC7481313 DOI: 10.1038/s41598-020-71844-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/11/2020] [Indexed: 11/09/2022] Open
Abstract
Shwachman-Diamond syndrome (SDS), an autosomal recessive disorder characterized by bone marrow failure, exocrine pancreatic insufficiency, and skeletal abnormalities, is caused by mutations in the Shwachman-Bodian-Diamond syndrome (SBDS) gene, which plays a role in ribosome biogenesis. Although the causative genes of congenital disorders frequently involve regulation of embryogenesis, the role of the SBDS gene in early hematopoiesis remains unclear, primarily due to the lack of a suitable experimental model for this syndrome. In this study, we established induced pluripotent stem cells (iPSCs) from patients with SDS (SDS-iPSCs) and analyzed their in vitro hematopoietic and endothelial differentiation potentials. SDS-iPSCs generated hematopoietic and endothelial cells less efficiently than iPSCs derived from healthy donors, principally due to the apoptotic predisposition of KDR+CD34+ common hemoangiogenic progenitors. By contrast, forced expression of SBDS gene in SDS-iPSCs or treatment with a caspase inhibitor reversed the deficiency in hematopoietic and endothelial development, and decreased apoptosis of their progenitors, mainly via p53-independent mechanisms. Patient-derived iPSCs exhibited the hematological abnormalities associated with SDS even at the earliest hematopoietic stages. These findings will enable us to dissect the pathogenesis of multiple disorders associated with ribosomal dysfunction.
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Affiliation(s)
- Takayuki Hamabata
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Katsutsugu Umeda
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
| | - Kagehiro Kouzuki
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Takayuki Tanaka
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Tomoo Daifu
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Seishiro Nodomi
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Satoshi Saida
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Itaru Kato
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Shiro Baba
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Hidefumi Hiramatsu
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Mitsujiro Osawa
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Akira Niwa
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Megumu K Saito
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Yasuhiko Kamikubo
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Souichi Adachi
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Yoshiko Hashii
- Department of Cancer Immunotherapy, Osaka University School of Medicine, Suita, 565-0871, Japan
| | - Akira Shimada
- Department of Pediatric Hematology/Oncology, Okayama University, Okayama, 700-8558, Japan
| | - Hiroyoshi Watanabe
- Department of Pediatrics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8501, Japan
| | - Kenji Osafune
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Keisuke Okita
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Tatsutoshi Nakahata
- Drug Discovery Technology Development Office, Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Kenichiro Watanabe
- Department of Hematology and Oncology, Shizuoka Children's Hospital, Shizuoka, 420-8660, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Toshio Heike
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
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Abstract
Many organisms, including bacteria, code for multiple paralogues of some ribosomal protein subunits. The relative contribution of these alternative subunits to ribosome function and protein synthesis is unknown and controversial. Many studies on alternative ribosomes have been confounded by isolation of alternative and canonical ribosomes from different strains or growth conditions, potentially confounding results. Here, we show that one form of alternative ribosome from Mycobacterium smegmatis has a distinct translational profile compared with canonical ribosomes purified from an identical cellular context. We also identify a role for alternative ribosomes in iron homeostasis. Given the prevalence of alternative ribosomal genes in diverse organisms, our study suggests that alternative ribosomes may represent a further layer of regulation of gene translation. Alternative ribosome subunit proteins are prevalent in the genomes of diverse bacterial species, but their functional significance is controversial. Attempts to study microbial ribosomal heterogeneity have mostly relied on comparing wild-type strains with mutants in which subunits have been deleted, but this approach does not allow direct comparison of alternate ribosome isoforms isolated from identical cellular contexts. Here, by simultaneously purifying canonical and alternative RpsR ribosomes from Mycobacterium smegmatis, we show that alternative ribosomes have distinct translational features compared with their canonical counterparts. Both alternative and canonical ribosomes actively take part in protein synthesis, although they translate a subset of genes with differential efficiency as measured by ribosome profiling. We also show that alternative ribosomes have a relative defect in initiation complex formation. Furthermore, a strain of M. smegmatis in which the alternative ribosome protein operon is deleted grows poorly in iron-depleted medium, uncovering a role for alternative ribosomes in iron homeostasis. Our work confirms the distinct and nonredundant contribution of alternative bacterial ribosomes for adaptation to hostile environments.
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26
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Pervasive changes of mRNA splicing in upf1-deficient zebrafish identify rpl10a as a regulator of T cell development. Proc Natl Acad Sci U S A 2020; 117:15799-15808. [PMID: 32571908 PMCID: PMC7354994 DOI: 10.1073/pnas.1917812117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The transcriptome of eukaryotic cells is constantly monitored for errors to avoid the production of undesired protein variants. The evolutionarily conserved nonsense-mediated mRNA decay (NMD) pathway degrades aberrant mRNAs, but also functions in the regulation of transcript abundance in response to changed physiological states. Here, we describe a zebrafish mutant of upf1, encoding the central component of the NMD machinery. Fish homozygous for the upf1 t20450 allele (Y163X) survive until day 10 after fertilization, presenting with impaired T cell development as one of the most conspicuous features of the mutant phenotype. Analysis of differentially expressed genes identified dysregulation of the pre-mRNA splicing pathway, accompanied by perturbed autoregulation of canonical splicing activators (SRSF) and repressors (HNRNP). In upf1-deficient mutants, NMD-susceptible transcripts of ribosomal proteins that are known for their role as noncanonical splicing regulators were greatly increased, most notably, rpl10a When the levels of NMD-susceptible rpl10a transcripts were artificially increased in zebrafish larvae, T cell development was significantly impaired, suggesting that perturbed autoregulation of rpl10a splicing contributes to failing T cell development in upf1 deficiency. Our results identify an extraribosomal tissue-specific function to rpl10a in the immune system, and thus exemplify the advantages of the zebrafish model to study the effects of upf1-deficiency in the context of a vertebrate organism.
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27
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Li D, Wang J. Ribosome heterogeneity in stem cells and development. J Cell Biol 2020; 219:e202001108. [PMID: 32330234 PMCID: PMC7265316 DOI: 10.1083/jcb.202001108] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 02/08/2023] Open
Abstract
Translation control is critical to regulate protein expression. By directly adjusting protein levels, cells can quickly respond to dynamic transitions during stem cell differentiation and embryonic development. Ribosomes are multisubunit cellular assemblies that mediate translation. Previously seen as invariant machines with the same composition of components in all conditions, recent studies indicate that ribosomes are heterogeneous and that different ribosome types can preferentially translate specific subsets of mRNAs. Such heterogeneity and specialized translation functions are very important in stem cells and development, as they allow cells to quickly respond to stimuli through direct changes of protein abundance. In this review, we discuss ribosome heterogeneity that arises from multiple features of rRNAs, including rRNA variants and rRNA modifications, and ribosomal proteins, including their stoichiometry, compositions, paralogues, and posttranslational modifications. We also discuss alterations of ribosome-associated proteins (RAPs), with a particular focus on their consequent specialized translational control in stem cells and development.
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Affiliation(s)
- Dan Li
- Department of Cell, Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jianlong Wang
- Department of Cell, Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY
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28
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Ribosome and Translational Control in Stem Cells. Cells 2020; 9:cells9020497. [PMID: 32098201 PMCID: PMC7072746 DOI: 10.3390/cells9020497] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/11/2020] [Accepted: 02/17/2020] [Indexed: 12/16/2022] Open
Abstract
Embryonic stem cells (ESCs) and adult stem cells (ASCs) possess the remarkable capacity to self-renew while remaining poised to differentiate into multiple progenies in the context of a rapidly developing embryo or in steady-state tissues, respectively. This ability is controlled by complex genetic programs, which are dynamically orchestrated at different steps of gene expression, including chromatin remodeling, mRNA transcription, processing, and stability. In addition to maintaining stem cell homeostasis, these molecular processes need to be rapidly rewired to coordinate complex physiological modifications required to redirect cell fate in response to environmental clues, such as differentiation signals or tissue injuries. Although chromatin remodeling and mRNA expression have been extensively studied in stem cells, accumulating evidence suggests that stem cell transcriptomes and proteomes are poorly correlated and that stem cell properties require finely tuned protein synthesis. In addition, many studies have shown that the biogenesis of the translation machinery, the ribosome, is decisive for sustaining ESC and ASC properties. Therefore, these observations emphasize the importance of translational control in stem cell homeostasis and fate decisions. In this review, we will provide the most recent literature describing how ribosome biogenesis and translational control regulate stem cell functions and are crucial for accommodating proteome remodeling in response to changes in stem cell fate.
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29
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Feng Z, Zhang L, Wu Y, Wang L, Xu M, Yang M, Li Y, Wei G, Chou M. The Rpf84 gene, encoding a ribosomal large subunit protein, RPL22, regulates symbiotic nodulation in Robinia pseudoacacia. PLANTA 2019; 250:1897-1910. [PMID: 31485773 DOI: 10.1007/s00425-019-03267-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
A homologue of the ribosomal protein L22e, Rpf84, regulates root nodule symbiosis by mediating the infection process of rhizobia and preventing bacteroids from degradation in Robinia pseudoacacia. Ribosomal proteins (RPs) are known to have extraribosomal functions, including developmental regulation and stress responses; however, the effects of RPs on symbiotic nodulation of legumes are still unclear. Ribosomal protein 22 of the large 60S subunit (RPL22), a non-typical RP that is only found in eukaryotes, has been shown to function as a tumour suppressor in animals. Here, a homologue of RPL22, Rpf84, was identified from the leguminous tree R. pseudoacacia. Subcellular localization assays showed that Rpf84 was expressed in the cytoplasm and nucleus. Knockdown of Rpf84 by RNA interference (RNAi) technology impaired the infection process and nodule development. Compared with the control, root and stem length, dry weight and nodule number per plant were drastically decreased in Rpf84-RNAi plants. The numbers of root hair curlings, infection threads and nodule primordia were also significantly reduced. Ultrastructure analyses showed that Rpf84-RNAi nodules contained fewer infected cells with fewer bacteria. In particular, remarkable deformation of bacteroids and fusion of multiple symbiosomes occurred in infected cells. By contrast, overexpression of Rpf84 promoted nodulation, and the overexpression nodules maintained a larger infection/differentiation region and had more infected cells filled with bacteroids than the control at 45 days post inoculation, suggesting a retarded ageing process in nodules. These results indicate for the first time that RP regulates the symbiotic nodulation of legumes and that RPL22 may function in initiating the invasion of rhizobia and preventing bacteroids from degradation in R. pseudoacacia.
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Affiliation(s)
- Zhao Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
- College of Medical Technology, Shaanxi University of Chinese Medicine, Xianyang, 712046, China
| | - Lu Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Yuanyuan Wu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Li Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Mingying Xu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Mo Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Yajuan Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Minxia Chou
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, China.
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30
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Rao S, Peri S, Hoffmann J, Cai KQ, Harris B, Rhodes M, Connolly DC, Testa JR, Wiest DL. RPL22L1 induction in colorectal cancer is associated with poor prognosis and 5-FU resistance. PLoS One 2019; 14:e0222392. [PMID: 31581233 PMCID: PMC6776433 DOI: 10.1371/journal.pone.0222392] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 08/19/2019] [Indexed: 12/22/2022] Open
Abstract
We have previously demonstrated that loss of the tumor suppressive activity of ribosomal protein (RP) RPL22 predisposes to development of leukemia in mouse models and aggressive disease in human patients; however, the role of RPL22 in solid tumors, specifically colorectal cancer (CRC), had not been explored. We report here that RPL22 is either deleted or mutated in 36% of CRC and provide new insights into its mechanism of action. Indeed, Rpl22 inactivation causes the induction of its highly homologous paralog, RPL22L1, which serves as a driver of cell proliferation and anchorage-independent growth in CRC cells. Moreover, RPL22L1 protein is highly expressed in patient CRC samples and correlates with poor survival. Interestingly, the association of high RPL22L1 expression with poor prognosis appears to be linked to resistance to 5-Fluorouracil, which is a core component of most CRC therapeutic regimens. Indeed, in an avatar trial, we found that human CRC samples that were unresponsive to 5-Fluorouracil in patient-derived xenografts exhibited elevated expression levels of RPL22L1. This link between RPL22L1 induction and 5-Fluorouracil resistance appears to be causal, because ectopic expression or knockdown of RPL22L1 in cell lines increases and decreases 5-Fluorouracil resistance, respectively, and this is associated with changes in expression of the DNA-repair genes, MGMT and MLH1. In summary, our data suggest that RPL22L1 might be a prognostic marker in CRC and predict 5-FU responsiveness.
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Affiliation(s)
- Shuyun Rao
- Center for Translational Medicine, Department of Surgery, George Washington University, Washington, DC, United States of America
- * E-mail: (DW); (SR)
| | - Suraj Peri
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States of America
| | - Jens Hoffmann
- Experimental Pharmacology & Oncology Berlin-Buch GMBH, Berlin-Buch, Germany
| | - Kathy Q. Cai
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, United States of America
| | - Bryan Harris
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States of America
| | - Michele Rhodes
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States of America
| | - Denise C. Connolly
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, United States of America
| | - Joseph R. Testa
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, United States of America
| | - David L. Wiest
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States of America
- * E-mail: (DW); (SR)
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31
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Kong J, Han H, Bergalet J, Bouvrette LPB, Hernández G, Moon NS, Vali H, Lécuyer É, Lasko P. A ribosomal protein S5 isoform is essential for oogenesis and interacts with distinct RNAs in Drosophila melanogaster. Sci Rep 2019; 9:13779. [PMID: 31551467 PMCID: PMC6760144 DOI: 10.1038/s41598-019-50357-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/01/2019] [Indexed: 11/09/2022] Open
Abstract
In Drosophila melanogaster there are two genes encoding ribosomal protein S5, RpS5a and RpS5b. Here, we demonstrate that RpS5b is required for oogenesis. Females lacking RpS5b produce ovaries with numerous developmental defects that undergo widespread apoptosis in mid-oogenesis. Females lacking germline RpS5a are fully fertile, but germline expression of interfering RNA targeting germline RpS5a in an RpS5b mutant background worsened the RpS5b phenotype and blocked oogenesis before egg chambers form. A broad spectrum of mRNAs co-purified in immunoprecipitations with RpS5a, while RpS5b-associated mRNAs were specifically enriched for GO terms related to mitochondrial electron transport and cellular metabolic processes. Consistent with this, RpS5b mitochondrial fractions are depleted for proteins linked to oxidative phosphorylation and mitochondrial respiration, and RpS5b mitochondria tended to form large clusters and had more heterogeneous morphology than those from controls. We conclude that RpS5b-containing ribosomes preferentially associate with particular mRNAs and serve an essential function in oogenesis.
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Affiliation(s)
- Jian Kong
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, QC, H3G 0B1, Canada
| | - Hong Han
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, QC, H3G 0B1, Canada
| | - Julie Bergalet
- Montreal Clinical Research Institute (IRCM), 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Louis Philip Benoit Bouvrette
- Montreal Clinical Research Institute (IRCM), 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada.,Département de Biochimie, Université de Montréal, Montréal, QC, H3C 3J7, Canada
| | - Greco Hernández
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, QC, H3G 0B1, Canada.,Unit of Biomedical Research on Cancer, National Institute of Cancer, Tlalpan, 14080, Mexico City, Mexico
| | - Nam-Sung Moon
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, QC, H3G 0B1, Canada
| | - Hojatollah Vali
- Facility for Electron Microscopy Research, Faculty of Dentistry, McGill University, Montréal, QC, Canada
| | - Éric Lécuyer
- Montreal Clinical Research Institute (IRCM), 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Paul Lasko
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, QC, H3G 0B1, Canada.
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Genuth NR, Barna M. Heterogeneity and specialized functions of translation machinery: from genes to organisms. Nat Rev Genet 2019; 19:431-452. [PMID: 29725087 DOI: 10.1038/s41576-018-0008-z] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Regulation of mRNA translation offers the opportunity to diversify the expression and abundance of proteins made from individual gene products in cells, tissues and organisms. Emerging evidence has highlighted variation in the composition and activity of several large, highly conserved translation complexes as a means to differentially control gene expression. Heterogeneity and specialized functions of individual components of the ribosome and of the translation initiation factor complexes eIF3 and eIF4F, which are required for recruitment of the ribosome to the mRNA 5' untranslated region, have been identified. In this Review, we summarize the evidence for selective mRNA translation by components of these macromolecular complexes as a means to dynamically control the translation of the proteome in time and space. We further discuss the implications of this form of gene expression regulation for a growing number of human genetic disorders associated with mutations in the translation machinery.
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Affiliation(s)
- Naomi R Genuth
- Departments of Genetics and Developmental Biology, Stanford University, Stanford, CA, USA.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Maria Barna
- Departments of Genetics and Developmental Biology, Stanford University, Stanford, CA, USA.
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33
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Liang Z, Mou Q, Pan Z, Zhang Q, Gao G, Cao Y, Gao Z, Pan Z, Feng W. Identification of candidate diagnostic and prognostic biomarkers for human prostate cancer: RPL22L1 and RPS21. Med Oncol 2019; 36:56. [DOI: 10.1007/s12032-019-1283-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/07/2019] [Indexed: 12/17/2022]
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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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35
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The Ribosome as a Missing Link in Prebiotic Evolution III: Over-Representation of tRNA- and rRNA-Like Sequences and Plieofunctionality of Ribosome-Related Molecules Argues for the Evolution of Primitive Genomes from Ribosomal RNA Modules. Int J Mol Sci 2019; 20:ijms20010140. [PMID: 30609737 PMCID: PMC6337102 DOI: 10.3390/ijms20010140] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/21/2018] [Accepted: 12/23/2018] [Indexed: 12/18/2022] Open
Abstract
We propose that ribosomal RNA (rRNA) formed the basis of the first cellular genomes, and provide evidence from a review of relevant literature and proteonomic tests. We have proposed previously that the ribosome may represent the vestige of the first self-replicating entity in which rRNAs also functioned as genes that were transcribed into functional messenger RNAs (mRNAs) encoding ribosomal proteins. rRNAs also encoded polymerases to replicate itself and a full complement of the transfer RNAs (tRNAs) required to translate its genes. We explore here a further prediction of our “ribosome-first” theory: the ribosomal genome provided the basis for the first cellular genomes. Modern genomes should therefore contain an unexpectedly large percentage of tRNA- and rRNA-like modules derived from both sense and antisense reading frames, and these should encode non-ribosomal proteins, as well as ribosomal ones with key cell functions. Ribosomal proteins should also have been co-opted by cellular evolution to play extra-ribosomal functions. We review existing literature supporting these predictions. We provide additional, new data demonstrating that rRNA-like sequences occur at significantly higher frequencies than predicted on the basis of mRNA duplications or randomized RNA sequences. These data support our “ribosome-first” theory of cellular evolution.
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36
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Mageeney CM, Kearse MG, Gershman BW, Pritchard CE, Colquhoun JM, Ware VC. Functional interplay between ribosomal protein paralogues in the eRpL22 family in Drosophila melanogaster. Fly (Austin) 2018; 12:143-163. [PMID: 30465696 DOI: 10.1080/19336934.2018.1549419] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Duplicated ribosomal protein (RP) genes in the Drosophila melanogaster eRpL22 family encode structurally-divergent and differentially-expressed rRNA-binding RPs. eRpL22 is expressed ubiquitously and eRpL22-like expression is tissue-restricted with highest levels in the adult male germline. We explored paralogue functional equivalence using the GAL4-UAS system for paralogue knockdown or overexpression and a conditional eRpL22-like knockout in a heat- shock flippase/FRT line. Ubiquitous eRpL22 knockdown with Actin-GAL4 resulted in embryonic lethality, confirming eRpL22 essentiality. eRpL22-like knockdown (60%) was insufficient to cause lethality; yet, conditional eRpL22-like knockout at one hour following egg deposition caused lethality within each developmental stage. Therefore, each paralogue is essential. Variation in timing of heat-shock-induced eRpL22-like knockout highlighted early embryogenesis as the critical period where eRpL22-like expression (not compensated for by eRpL22) is required for normal development of several organ systems, including testis development and subsequent sperm production. To determine if eRpL22-like can substitute for eRpL22, we used Actin-GAL4 for ubiquitous eRpL22 knockdown and eRpL22-like-FLAG (or FLAG-eRpL22: control) overexpression. Emergence of adults demonstrated that ubiquitous eRpL22-like-FLAG or FLAG-eRpL22 expression eliminates embryonic lethality resulting from eRpL22 depletion. Adults rescued by eRpL22-like-FLAG (but not by FLAG-eRpL22) overexpression had reduced fertility and longevity. We conclude that eRpL22 paralogue roles are not completely interchangeable and include functionally-diverse roles in development and spermatogenesis. Testis-specific paralogue knockdown revealed molecular phenotypes, including increases in eRpL22 protein and mRNA levels following eRpL22-like depletion, implicating a negative crosstalk mechanism regulating eRpL22 expression. Paralogue depletion unmasked mechanisms, yet to be defined that impact paralogue co-expression within germ cells.
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Affiliation(s)
| | - Michael G Kearse
- a Department of Biological Sciences , Lehigh University , Bethlehem , PA , USA
| | - Brett W Gershman
- a Department of Biological Sciences , Lehigh University , Bethlehem , PA , USA
| | | | | | - Vassie C Ware
- a Department of Biological Sciences , Lehigh University , Bethlehem , PA , USA
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37
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Ribosome biogenesis: An emerging druggable pathway for cancer therapeutics. Biochem Pharmacol 2018; 159:74-81. [PMID: 30468711 DOI: 10.1016/j.bcp.2018.11.014] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/16/2018] [Indexed: 01/05/2023]
Abstract
Ribosomes are nanomachines essential for protein production in all living cells. Ribosome synthesis increases in cancer cells to cope with a rise in protein synthesis and sustain unrestricted growth. This increase in ribosome biogenesis is reflected by severe morphological alterations of the nucleolus, the cell compartment where the initial steps of ribosome biogenesis take place. Ribosome biogenesis has recently emerged as an effective target in cancer therapy, and several compounds that inhibit ribosome production or function, killing preferentially cancer cells, have entered clinical trials. Recent research indicates that cells express heterogeneous populations of ribosomes and that the composition of ribosomes may play a key role in tumorigenesis, exposing novel therapeutic opportunities. Here, we review recent data demonstrating that ribosome biogenesis is a promising druggable pathway in cancer therapy, and discuss future research perspectives.
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38
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Fan S, Liang Z, Gao Z, Pan Z, Han S, Liu X, Zhao C, Yang W, Pan Z, Feng W. Identification of the key genes and pathways in prostate cancer. Oncol Lett 2018; 16:6663-6669. [PMID: 30405806 PMCID: PMC6202544 DOI: 10.3892/ol.2018.9491] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 09/17/2018] [Indexed: 12/13/2022] Open
Abstract
Prostate cancer (PCa) is one of the most common malignancies in men globally. The aim of the present study was to identify the key genes and pathways involved in the occurrence of PCa. Gene expression profile (GSE55945) was downloaded from Gene Expression Omnibus, and the differentially expressed genes (DEGs) were identified. Subsequently, Gene ontology analysis, KEGG pathway analysis and protein-protein interaction (PPI) analysis of DEGs were performed. Finally, the identified key genes were confirmed by immunohistochemistry. The GO analysis results showed that the DEGs were mainly participated in cell cycle, cell division, cell development and cell junction. The KEGG pathway analysis showed that the DEGs were mainly enriched in proteoglycans in cancer, endocytosis, focal adhesion and hippo signaling pathway. The PPI analysis results showed that RPS21, FOXO1, BIRC5, POLR2H, RPL22L1 and NPM1 were the key genes involved in the occurrence of PCa, and the Module analysis indicated that the occurrence of PCa was associated with cell cycle, oocyte meiosis and ribosome biogenesis. IHC result showed that the expression of RPS21, BIRC5, POLR2H, RPL22L1 and NPM1 were significantly upregulated in PCa, while the expression of FOXO1 was significantly downregulated in PCa, matching with the bioinformatics analysis. Taken together, several key genes and pathways were identified involved in PCa, which might provide the potential biomarker for prognosis, diagnosis and drug targets.
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Affiliation(s)
- Shutong Fan
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Zumu Liang
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Zhiqin Gao
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Zhiwei Pan
- Department of Internal Medicine, Laizhou Development Zone Hospital, Yantai, Shandong 261400, P.R. China
| | - Shaojie Han
- Animal Epidemic Prevention and Epidemic Control Center, Changle County Bureau of Animal Health and Production, Weifang, Shandong 262400, P.R. China
| | - Xiaoying Liu
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Chunling Zhao
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Weiwei Yang
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Zhifang Pan
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Weiguo Feng
- College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053, P.R. China
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39
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Leighton PLA, Kanyo R, Neil GJ, Pollock NM, Allison WT. Prion gene paralogs are dispensable for early zebrafish development and have nonadditive roles in seizure susceptibility. J Biol Chem 2018; 293:12576-12592. [PMID: 29903907 DOI: 10.1074/jbc.ra117.001171] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 06/07/2018] [Indexed: 11/06/2022] Open
Abstract
Normally folded prion protein (PrPC) and its functions in healthy brains remain underappreciated compared with the intense study of its misfolded forms ("prions," PrPSc) during the pathobiology of prion diseases. This impedes the development of therapeutic strategies in Alzheimer's and prion diseases. Disrupting the zebrafish homologs of PrPC has provided novel insights; however, mutagenesis of the zebrafish paralog prp2 did not recapitulate previous dramatic developmental phenotypes, suggesting redundancy with the prp1 paralog. Here, we generated zebrafish prp1 loss-of-function mutant alleles and dual prp1-/-;prp2-/- mutants. Zebrafish prp1-/- and dual prp1-/-;prp2-/- mutants resemble mammalian Prnp knockouts insofar as they lack overt phenotypes, which surprisingly contrasts with reports of severe developmental phenotypes when either prp1 or prp2 is knocked down acutely. Previous studies suggest that PrPC participates in neural cell development/adhesion, including in zebrafish where loss of prp2 affects adhesion and deposition patterns of lateral line neuromasts. In contrast with the expectation that prp1's functions would be redundant to prp2, they appear to have opposing functions in lateral line neurodevelopment. Similarly, loss of prp1 blunted the seizure susceptibility phenotypes observed in prp2 mutants, contrasting the expected exacerbation of phenotypes if these prion gene paralogs were serving redundant roles. In summary, prion mutant fish lack the overt phenotypes previously predicted, and instead they have subtle phenotypes similar to mammals. No evidence was found for functional redundancy in the zebrafish prion gene paralogs, and the phenotypes observed when each gene is disrupted individually are consistent with ancient functions of prion proteins in neurodevelopment and modulation of neural activity.
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Affiliation(s)
- Patricia L A Leighton
- From the Department of Biological Sciences and the Centre for Prion and Protein Folding Diseases, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Richard Kanyo
- From the Department of Biological Sciences and the Centre for Prion and Protein Folding Diseases, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Gavin J Neil
- From the Department of Biological Sciences and the Centre for Prion and Protein Folding Diseases, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Niall M Pollock
- From the Department of Biological Sciences and the Centre for Prion and Protein Folding Diseases, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - W Ted Allison
- From the Department of Biological Sciences and the Centre for Prion and Protein Folding Diseases, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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40
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Abrhámová K, Nemčko F, Libus J, Převorovský M, Hálová M, Půta F, Folk P. Introns provide a platform for intergenic regulatory feedback of RPL22 paralogs in yeast. PLoS One 2018; 13:e0190685. [PMID: 29304067 PMCID: PMC5755908 DOI: 10.1371/journal.pone.0190685] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 12/19/2017] [Indexed: 01/04/2023] Open
Abstract
Ribosomal protein genes (RPGs) in Saccharomyces cerevisiae are a remarkable regulatory group that may serve as a model for understanding genetic redundancy in evolutionary adaptations. Most RPGs exist as pairs of highly conserved functional paralogs with divergent untranslated regions and introns. We examined the roles of introns in strains with various combinations of intron and gene deletions in RPL22, RPL2, RPL16, RPL37, RPL17, RPS0, and RPS18 paralog pairs. We found that introns inhibited the expression of their genes in the RPL22 pair, with the RPL22B intron conferring a much stronger effect. While the WT RPL22A/RPL22B mRNA ratio was 93/7, the rpl22aΔi/RPL22B and RPL22A/rpl22bΔi ratios were >99/<1 and 60/40, respectively. The intron in RPL2A stimulated the expression of its own gene, but the removal of the other introns had little effect on expression of the corresponding gene pair. Rpl22 protein abundances corresponded to changes in mRNAs. Using splicing reporters containing endogenous intron sequences, we demonstrated that these effects were due to the inhibition of splicing by Rpl22 proteins but not by their RNA-binding mutant versions. Indeed, only WT Rpl22A/Rpl22B proteins (but not the mutants) interacted in a yeast three-hybrid system with an RPL22B intronic region between bp 165 and 236. Transcriptome analysis showed that both the total level of Rpl22 and the A/B ratio were important for maintaining the WT phenotype. The data presented here support the contention that the Rpl22B protein has a paralog-specific role. The RPL22 singleton of Kluyveromyces lactis, which did not undergo whole genome duplication, also responded to Rpl22-mediated inhibition in K. lactis cells. Vice versa, the overproduction of the K. lactis protein reduced the expression of RPL22A/B in S. cerevisiae. The extraribosomal function of of the K. lactis Rpl22 suggests that the loop regulating RPL22 paralogs of S. cerevisiae evolved from autoregulation.
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Affiliation(s)
- Kateřina Abrhámová
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Filip Nemčko
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jiří Libus
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martina Hálová
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - František Půta
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Folk
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- * E-mail:
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41
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Kurre P. Hematopoietic development: a gap in our understanding of inherited bone marrow failure. Exp Hematol 2017; 59:1-8. [PMID: 29248612 DOI: 10.1016/j.exphem.2017.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 11/26/2017] [Accepted: 12/07/2017] [Indexed: 12/31/2022]
Abstract
Inherited bone marrow failure syndromes (IBMFS) represent a heterogeneous group of multisystem disorders that typically present with cytopenia in early childhood. Efforts to understand the underlying hematopoietic stem cell (HSC) losses have generally focused on postnatal hematopoiesis. However, reflecting the role of many of the involved genes in core cellular functions and the diverse nonhematologic abnormalities seen in patients at birth, studies have begun to explore IBMFS manifestations during fetal development. Here, I consider the current evidence for fetal deficits in the HSC pool and highlight emerging concepts regarding the origins and unique pathophysiology of hematopoietic failure in IBMFS.
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Affiliation(s)
- Peter Kurre
- Department of Pediatrics, Papé Family Pediatric Research Institute, Pediatric Blood & Cancer Biology Program, Oregon Health & Science University, Portland, Oregon.
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42
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Zhang Y, O'Leary MN, Peri S, Wang M, Zha J, Melov S, Kappes DJ, Feng Q, Rhodes J, Amieux PS, Morris DR, Kennedy BK, Wiest DL. Ribosomal Proteins Rpl22 and Rpl22l1 Control Morphogenesis by Regulating Pre-mRNA Splicing. Cell Rep 2017; 18:545-556. [PMID: 28076796 DOI: 10.1016/j.celrep.2016.12.034] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 10/15/2016] [Accepted: 12/12/2016] [Indexed: 01/13/2023] Open
Abstract
Most ribosomal proteins (RP) are regarded as essential, static components that contribute only to ribosome biogenesis and protein synthesis. However, emerging evidence suggests that RNA-binding RP are dynamic and can influence cellular processes by performing "extraribosomal," regulatory functions involving binding to select critical target mRNAs. We report here that the RP, Rpl22, and its highly homologous paralog Rpl22-Like1 (Rpl22l1 or Like1) play critical, extraribosomal roles in embryogenesis. Indeed, they antagonistically control morphogenesis through developmentally regulated localization to the nucleus, where they modulate splicing of the pre-mRNA encoding smad2, an essential transcriptional effector of Nodal/TGF-β signaling. During gastrulation, Rpl22 binds to intronic sequences of smad2 pre-mRNA and induces exon 9 skipping in cooperation with hnRNP-A1. This action is opposed by its paralog, Like1, which promotes exon 9 inclusion in the mature transcript. The nuclear roles of these RP in controlling morphogenesis represent a fundamentally different and paradigm-shifting mode of action for RP.
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Affiliation(s)
- Yong Zhang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | | | - Suraj Peri
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Minshi Wang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Jikun Zha
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Simon Melov
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Dietmar J Kappes
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Qing Feng
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jennifer Rhodes
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Paul S Amieux
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - David R Morris
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - David L Wiest
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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43
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Somech R, Lev A, Lee YN, Simon AJ, Barel O, Schiby G, Avivi C, Barshack I, Rhodes M, Yin J, Wang M, Yang Y, Rhodes J, Marcus N, Garty BZ, Stein J, Amariglio N, Rechavi G, Wiest DL, Zhang Y. Disruption of Thrombocyte and T Lymphocyte Development by a Mutation in ARPC1B. THE JOURNAL OF IMMUNOLOGY 2017; 199:4036-4045. [PMID: 29127144 DOI: 10.4049/jimmunol.1700460] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 10/06/2017] [Indexed: 01/21/2023]
Abstract
Regulation of the actin cytoskeleton is crucial for normal development and function of the immune system, as evidenced by the severe immune abnormalities exhibited by patients bearing inactivating mutations in the Wiskott-Aldrich syndrome protein (WASP), a key regulator of actin dynamics. WASP exerts its effects on actin dynamics through a multisubunit complex termed Arp2/3. Despite the critical role played by Arp2/3 as an effector of WASP-mediated control over actin polymerization, mutations in protein components of the Arp2/3 complex had not previously been identified as a cause of immunodeficiency. Here, we describe two brothers with hematopoietic and immunologic symptoms reminiscent of Wiskott-Aldrich syndrome (WAS). However, these patients lacked mutations in any of the genes previously associated with WAS. Whole-exome sequencing revealed a homozygous 2 bp deletion, n.c.G623DEL-TC (p.V208VfsX20), in Arp2/3 complex component ARPC1B that causes a frame shift resulting in premature termination. Modeling of the disease in zebrafish revealed that ARPC1B plays a critical role in supporting T cell and thrombocyte development. Moreover, the defects in development caused by ARPC1B loss could be rescued by the intact human ARPC1B ortholog, but not by the p.V208VfsX20 variant identified in the patients. Moreover, we found that the expression of ARPC1B is restricted to hematopoietic cells, potentially explaining why a mutation in ARPC1B has now been observed as a cause of WAS, whereas mutations in other, more widely expressed, components of the Arp2/3 complex have not been observed.
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Affiliation(s)
- Raz Somech
- Pediatric Department A and Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 52621, Israel.,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Tel Aviv 52621, Israel
| | - Atar Lev
- Pediatric Department A and Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 52621, Israel.,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Tel Aviv 52621, Israel
| | - Yu Nee Lee
- Pediatric Department A and Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 52621, Israel.,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Tel Aviv 52621, Israel
| | - Amos J Simon
- Pediatric Department A and Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 52621, Israel.,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Tel Aviv 52621, Israel.,Hematology Laboratory, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
| | - Ortal Barel
- The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Tel Aviv 52621, Israel.,Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
| | - Ginette Schiby
- Department of Pathology, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
| | - Camila Avivi
- Department of Pathology, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
| | - Iris Barshack
- Department of Pathology, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
| | - Michele Rhodes
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Jiejing Yin
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Minshi Wang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Yibin Yang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Jennifer Rhodes
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Nufar Marcus
- Allergy and Immunology Unit, Schneider Children's Medical Center of Israel, Felsenstein Medical Research Center, Kipper Institute of Immunology, Petach Tikva, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 4920235, Israel
| | - Ben-Zion Garty
- Allergy and Immunology Unit, Schneider Children's Medical Center of Israel, Felsenstein Medical Research Center, Kipper Institute of Immunology, Petach Tikva, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 4920235, Israel
| | - Jerry Stein
- Bone Marrow Transplantation Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 4920235, Israel; and
| | - Ninette Amariglio
- The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Tel Aviv 52621, Israel.,Hematology Laboratory, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 52621, Israel.,Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 52621, Israel.,The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Gideon Rechavi
- The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Tel Aviv 52621, Israel.,Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
| | - David L Wiest
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111;
| | - Yong Zhang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111;
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Sulima SO, Hofman IJF, De Keersmaecker K, Dinman JD. How Ribosomes Translate Cancer. Cancer Discov 2017; 7:1069-1087. [PMID: 28923911 PMCID: PMC5630089 DOI: 10.1158/2159-8290.cd-17-0550] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/18/2017] [Accepted: 07/31/2017] [Indexed: 12/13/2022]
Abstract
A wealth of novel findings, including congenital ribosomal mutations in ribosomopathies and somatic ribosomal mutations in various cancers, have significantly increased our understanding of the relevance of ribosomes in oncogenesis. Here, we explore the growing list of mechanisms by which the ribosome is involved in carcinogenesis-from the hijacking of ribosomes by oncogenic factors and dysregulated translational control, to the effects of mutations in ribosomal components on cellular metabolism. Of clinical importance, the recent success of RNA polymerase inhibitors highlights the dependence on "onco-ribosomes" as an Achilles' heel of cancer cells and a promising target for further therapeutic intervention.Significance: The recent discovery of somatic mutations in ribosomal proteins in several cancers has strengthened the link between ribosome defects and cancer progression, while also raising the question of which cellular mechanisms such defects exploit. Here, we discuss the emerging molecular mechanisms by which ribosomes support oncogenesis, and how this understanding is driving the design of novel therapeutic strategies. Cancer Discov; 7(10); 1069-87. ©2017 AACR.
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Affiliation(s)
- Sergey O Sulima
- Department of Oncology, KU Leuven, University of Leuven, LKI, Leuven Cancer Institute, Leuven, Belgium
| | - Isabel J F Hofman
- Department of Oncology, KU Leuven, University of Leuven, LKI, Leuven Cancer Institute, Leuven, Belgium
| | - Kim De Keersmaecker
- Department of Oncology, KU Leuven, University of Leuven, LKI, Leuven Cancer Institute, Leuven, Belgium.
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland.
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Abstract
NMD is a highly conserved pathway that degrades specific subsets of RNAs. There is increasing evidence for roles of NMD in development. In this commentary, we focus on spermatogenesis, a process dramatically impeded upon loss or disruption of NMD. NMD requires strict regulation for normal spermatogenesis, as loss of a newly discovered NMD repressor, UPF3A, also causes spermatogenic defects, most prominently during meiosis. We discuss the unusual evolution of UPF3A, whose paralog, UPF3B, has the opposite biochemical function and acts in brain development. We also discuss the regulation of NMD during germ cell development, including in chromatoid bodies, which are specifically found in haploid germ cells. The ability of NMD to coordinately degrade batteries of RNAs in a regulated fashion during development is akin to the action of transcriptional pathways, yet has the advantage of driving rapid changes in gene expression.
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Affiliation(s)
- Samantha H Jones
- a Department of Reproductive Medicine , School of Medicine, University of California, San Diego , La Jolla , CA , USA
| | - Miles Wilkinson
- a Department of Reproductive Medicine , School of Medicine, University of California, San Diego , La Jolla , CA , USA.,b Institute of Genomic Medicine, University of California , San Diego, La Jolla , CA , USA
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Punwani D, Zhang Y, Yu J, Cowan MJ, Rana S, Kwan A, Adhikari AN, Lizama CO, Mendelsohn BA, Fahl SP, Chellappan A, Srinivasan R, Brenner SE, Wiest DL, Puck JM. Multisystem Anomalies in Severe Combined Immunodeficiency with Mutant BCL11B. N Engl J Med 2016; 375:2165-2176. [PMID: 27959755 PMCID: PMC5215776 DOI: 10.1056/nejmoa1509164] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Severe combined immunodeficiency (SCID) is characterized by arrested T-lymphocyte production and by B-lymphocyte dysfunction, which result in life-threatening infections. Early diagnosis of SCID through population-based screening of newborns can aid clinical management and help improve outcomes; it also permits the identification of previously unknown factors that are essential for lymphocyte development in humans. METHODS SCID was detected in a newborn before the onset of infections by means of screening of T-cell-receptor excision circles, a biomarker for thymic output. On confirmation of the condition, the affected infant was treated with allogeneic hematopoietic stem-cell transplantation. Exome sequencing in the patient and parents was followed by functional analysis of a prioritized candidate gene with the use of human hematopoietic stem cells and zebrafish embryos. RESULTS The infant had "leaky" SCID (i.e., a form of SCID in which a minimal degree of immune function is preserved), as well as craniofacial and dermal abnormalities and the absence of a corpus callosum; his immune deficit was fully corrected by hematopoietic stem-cell transplantation. Exome sequencing revealed a heterozygous de novo missense mutation, p.N441K, in BCL11B. The resulting BCL11B protein had dominant negative activity, which abrogated the ability of wild-type BCL11B to bind DNA, thereby arresting development of the T-cell lineage and disrupting hematopoietic stem-cell migration; this revealed a previously unknown function of BCL11B. The patient's abnormalities, when recapitulated in bcl11ba-deficient zebrafish, were reversed by ectopic expression of functionally intact human BCL11B but not mutant human BCL11B. CONCLUSIONS Newborn screening facilitated the identification and treatment of a previously unknown cause of human SCID. Coupling exome sequencing with an evaluation of candidate genes in human hematopoietic stem cells and in zebrafish revealed that a constitutional BCL11B mutation caused human multisystem anomalies with SCID and also revealed a prethymic role for BCL11B in hematopoietic progenitors. (Funded by the National Institutes of Health and others.).
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Affiliation(s)
- Divya Punwani
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Yong Zhang
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Jason Yu
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Morton J Cowan
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Sadhna Rana
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Antonia Kwan
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Aashish N Adhikari
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Carlos O Lizama
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Bryce A Mendelsohn
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Shawn P Fahl
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Ajithavalli Chellappan
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Rajgopal Srinivasan
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Steven E Brenner
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - David L Wiest
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Jennifer M Puck
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
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Guimaraes JC, Zavolan M. Patterns of ribosomal protein expression specify normal and malignant human cells. Genome Biol 2016; 17:236. [PMID: 27884178 PMCID: PMC5123215 DOI: 10.1186/s13059-016-1104-z] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/09/2016] [Indexed: 02/06/2023] Open
Abstract
Background Ribosomes are highly conserved molecular machines whose core composition has traditionally been regarded as invariant. However, recent studies have reported intriguing differences in the expression of some ribosomal proteins (RPs) across tissues and highly specific effects on the translation of individual mRNAs. Results To determine whether RPs are more generally linked to cell identity, we analyze the heterogeneity of RP expression in a large set of human tissues, primary cells, and tumors. We find that about a quarter of human RPs exhibit tissue-specific expression and that primary hematopoietic cells display the most complex patterns of RP expression, likely shaped by context-restricted transcriptional regulators. Strikingly, we uncover patterns of dysregulated expression of individual RPs across cancer types that arise through copy number variations and are predictive for disease progression. Conclusions Our study reveals an unanticipated plasticity of RP expression across normal and malignant human cell types and provides a foundation for future characterization of cellular behaviors that are orchestrated by specific RPs. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1104-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joao C Guimaraes
- Computational and Systems Biology, Biozentrum, University of Basel, 4056, Basel, Switzerland.
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, 4056, Basel, Switzerland.
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Highly expressed ribosomal protein L34 indicates poor prognosis in osteosarcoma and its knockdown suppresses osteosarcoma proliferation probably through translational control. Sci Rep 2016; 6:37690. [PMID: 27883047 PMCID: PMC5121591 DOI: 10.1038/srep37690] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/01/2016] [Indexed: 01/25/2023] Open
Abstract
Osteosarcoma has devastating health implications on children and adolescents. However, due to its low incidence and high tumor heterogeneity, it is hard to achieve any further improvements in therapy and overall survival. Ribosomal protein L34 (RPL34) has been increasingly recognized to promote the proliferation of malignant cells, but its role in osteosarcoma has not been investigated. In this study, real-time quantitative PCR (RT-qPCR) and immunohistochemistry revealed that RPL34 was highly expressed in osteosarcoma tissues when compared to adjacent tissues and normal bone tissues. Survival analysis showed that high expression of RPL34 predicted a poor prognosis for osteosarcoma patients. Knockdown of RPL34 in Saos-2 cells via lentivirus-mediated small interfering RNA (siRNA) significantly inhibited cell proliferation, induced cell apoptosis and G2/M phase arrest. Moreover, screening of transcription factors using University of California Santa Cruz (UCSC) Genome Browser, protein-protein interaction (PPI) network analysis, Gene Ontology (GO) and pathway enrichment analysis revealed that MYC participates in the transcriptional regulation of RPL34, which interacts with the subunits of eukaryotic translation initiation factor 3 (eIF3) and probably involves the translational control of growth-promoting proteins. Our findings suggest that RPL34 plays an important role in the proliferation of osteosarcoma cells.
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49
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Fahl SP, Wang M, Zhang Y, Duc ACE, Wiest DL. Regulatory Roles of Rpl22 in Hematopoiesis: An Old Dog with New Tricks. Crit Rev Immunol 2016; 35:379-400. [PMID: 26853850 DOI: 10.1615/critrevimmunol.v35.i5.30] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ribosomal proteins have long been known to serve critical roles in facilitating the biogenesis of the ribosome and its ability to synthesize proteins. However, evidence is emerging that suggests ribosomal proteins are also capable of performing tissue-restricted, regulatory functions that impact normal development and pathological conditions, including cancer. The challenge in studying such regulatory functions is that elimination of many ribosomal proteins also disrupts ribosome biogenesis and/or function. Thus, it is difficult to determine whether developmental abnormalities resulting from ablation of a ribosomal protein result from loss of core ribosome functions or from loss of the regulatory function of the ribosomal protein. Rpl22, a ribosomal protein component of the large 60S subunit, provides insight into this conundrum; Rpl22 is dispensable for both ribosome biogenesis and protein synthesis yet its ablation causes tissue-restricted disruptions in development. Here we review evidence supporting the regulatory functions of Rpl22 and other ribosomal proteins.
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Affiliation(s)
- Shawn P Fahl
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Minshi Wang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Yong Zhang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Anne-Cecile E Duc
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - David L Wiest
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
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50
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Lloyd MM, Makukhov AD, Pespeni MH. Loss of genetic diversity as a consequence of selection in response to high pCO 2. Evol Appl 2016; 9:1124-1132. [PMID: 27695520 PMCID: PMC5039325 DOI: 10.1111/eva.12404] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/17/2016] [Indexed: 01/09/2023] Open
Abstract
Standing genetic variation may allow for rapid evolutionary response to the geologically unprecedented changes in global conditions. However, there is little known about the consequences of such rapid evolutionary change. Here, we measure genetic responses to experimental low and high pCO 2 levels in purple sea urchin larvae, Strongylocentrotus purpuratus. We found greater loss of nucleotide diversity in high pCO 2 levels (18.61%; 900 μatm) compared to low pCO 2 levels (10.12%; 400 μatm). In the wild, this loss could limit the evolutionary capacity of future generations. In contrast, we found minimal evidence that purple sea urchin larvae physiologically respond to high pCO 2 through alternative splicing of transcripts (11 genes), despite a strong signal of alternative splicing between different developmental stages (1193 genes). However, in response to high pCO 2, four of the 11 alternatively spliced transcripts encoded ribosomal proteins, suggesting the regulation of translation as a potential response mechanism. The results of this study indicate that while the purple urchin presently may have enough standing genetic variation in response to rapid environmental change, this reservoir of resilience is a finite resource and could quickly diminish.
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