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Yu M, Liu H, Wang Y, Zhou S, Ding X, Xia Z, An M, Wu Y. Synthesis, Anti-TMV Activities, and Action Mechanisms of a Novel Cytidine Peptide Compound. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:20783-20793. [PMID: 39267339 DOI: 10.1021/acs.jafc.4c02767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/17/2024]
Abstract
Cytidine has a broad range of applications in the pharmaceutical field as an intermediate of antitumor or antiviral agent. Here, a series of new cytidine peptide compounds were synthesized using cytidine and Boc group-protected amino acids and analyzed for their antiviral activities against tobacco mosaic virus (TMV). Among these compounds, the structure of an effective antiviral cytidine peptide SN11 was characterized by 1H NMR, 13C NMR, and high-resolution mass spectrometer. The compound SN11 has a molecular formula of C15H22N6O8 and is named 2-amino-N-(2- ((1- (3,4-dihydroxy-5-(hydroxymethyl) tetrahydrofuran-2-yl) -2-oxo-1,2-dihydropyrimidin-4-yl) amino) -2-oxyethyl) amino). The protection, inactivation, and curation activities of SN11 at a concentration of 500 μg/mL against TMV in Nicotiana glutinosa were 82.6%, 84.2%, and 72.8%, respectively. SN11 also effectively suppressed the systemic transportation of a recombinant TMV carrying GFP reporter gene (p35S-30B:GFP) in Nicotiana benthamiana by reducing viral accumulation to 71.3% in the upper uninoculated leaves and inhibited the systemic infection of TMV in Nicotiana tabacum plants. Furthermore, the results of RNA-seq showed that compound SN11 induced differential expression of genes involved in the biogenesis and function of ribosome, plant hormone signal transduction, plant pathogen interaction, and chromatin. These results validate the antiviral mechanisms of the cytidine peptide compound and provide a theoretical basis for their potential application in the management of plant virus diseases.
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Affiliation(s)
- Miao Yu
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling, Shenyang 110866, Liaoning, China
| | - He Liu
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling, Shenyang 110866, Liaoning, China
- Center for Research and Development of Fine Chemicals of Guizhou University, Guiyang 550025, Guizhou, China
| | - Yan Wang
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling, Shenyang 110866, Liaoning, China
| | - Shidong Zhou
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling, Shenyang 110866, Liaoning, China
| | - Xiaojie Ding
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling, Shenyang 110866, Liaoning, China
| | - Zihao Xia
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling, Shenyang 110866, Liaoning, China
| | - Mengnan An
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling, Shenyang 110866, Liaoning, China
| | - Yuanhua Wu
- College of Plant Protection, Shenyang Agricultural University, No. 120 Dongling, Shenyang 110866, Liaoning, China
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Wisitpongpun P, Buakaew W, Pongcharoen S, Apiratmateekul N, Potup P, Daowtak K, Krobthong S, Yingchutrakul Y, Brindley PJ, Usuwanthim K. Proteomic profiling of oleamide-mediated polarization in a primary human monocyte-derived tumor-associated macrophages (TAMs) model: a functional analysis. PeerJ 2024; 12:e18090. [PMID: 39308806 PMCID: PMC11416084 DOI: 10.7717/peerj.18090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 08/22/2024] [Indexed: 09/25/2024] Open
Abstract
Background Tumor-associated macrophages (TAMs) play a critical function in the development of tumors and are associated with protumor M2 phenotypes. Shifting TAMs towards antitumor M1 phenotypes holds promise for tumor immunotherapy. Oleamide, a primary fatty acid amide, has emerged as a potent anticancer and immunomodulatory compound. However, the regulatory effects of oleamide on TAM phenotypes remain unclear. Methods We used real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) and enzyme-linked immunosorbent assay (ELISA) techniques to study the influence of oleamide on primary human monocyte-derived TAM phenotypes, and we investigated the protein expression profiles based on mass spectrometry to analyze the effect of oleamide on macrophage polarization. Moreover, the advantageous binding scores between oleamide and these target candidate proteins are examined using molecular docking. Results Our study revealed that oleamide effectively suppressed the M2-like TAM phenotype by reducing interleukin (IL)-10 production and downregulating M2-like markers, including vascular endothelial growth factor A (VEGFA), MYC proto-oncogene, bHLH transcription factor (c-Myc), and mannose receptor C-type 1 (CD206). Moreover, the conditioned medium derived from oleamide-treated TAMs induces apoptosis of MDA-MB-231 breast cancer cells. Proteomic analysis identified 20 candidate up- and down-regulation proteins targeted by oleamide, showing modulation activity associated with the promotion of the M1-like phenotype. Furthermore, molecular docking demonstrated favorable binding scores between oleamide and these candidate proteins. Collectively, our findings suggest that oleamide exerts a potent antitumor effect by promoting the antitumor M1-like TAM phenotype. These novel insights provide valuable resources for further investigations into oleamide and macrophage polarization which inhibit the progression of breast cancer, which may provide insight into immunotherapeutic approaches for cancer.
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Affiliation(s)
- Prapakorn Wisitpongpun
- Cellular and Molecular Immunology Research Unit (CMIRU), Faculty of Allied Health Sciences, Naresuan University, Mueang, Phitsanulok, Thailand
| | - Watunyoo Buakaew
- Cellular and Molecular Immunology Research Unit (CMIRU), Faculty of Allied Health Sciences, Naresuan University, Mueang, Phitsanulok, Thailand
- Department of Microbiology, Faculty of Medicine, Srinakharinwirot University, Bangkok, Thailand
| | - Sutatip Pongcharoen
- Division of Immunology, Department of Medicine, Faculty of Medicine, Naresuan University, Mueang, Phitsanulok, Thailand
| | - Napaporn Apiratmateekul
- Reference Material and Medical Laboratory Innovation Research Unit, Faculty of Allied Health Sciences, Naresuan University, Mueang, Phitsanulok, Thailand
| | - Pachuen Potup
- Cellular and Molecular Immunology Research Unit (CMIRU), Faculty of Allied Health Sciences, Naresuan University, Mueang, Phitsanulok, Thailand
| | - Krai Daowtak
- Cellular and Molecular Immunology Research Unit (CMIRU), Faculty of Allied Health Sciences, Naresuan University, Mueang, Phitsanulok, Thailand
| | - Sucheewin Krobthong
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- National Center for Genetic Engineering and Biotechnology, NSTDA, Pathum Thani, Thailand
| | - Yodying Yingchutrakul
- National Center for Genetic Engineering and Biotechnology, NSTDA, Pathum Thani, Thailand
| | - Paul J. Brindley
- Department of Microbiology, Immunology and Tropical Medicine, and Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, District of Columbia, WA, United States of America
| | - Kanchana Usuwanthim
- Cellular and Molecular Immunology Research Unit (CMIRU), Faculty of Allied Health Sciences, Naresuan University, Mueang, Phitsanulok, Thailand
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Almutairy AF, Alhamed AS, Grant SG, Falso MJ, Day BW, Simmons CR, Latimer JJ. Cancer-specific alterations in nuclear matrix proteins determined by multi-omics analyses of ductal carcinoma in situ. Front Oncol 2024; 14:1406946. [PMID: 39165691 PMCID: PMC11333849 DOI: 10.3389/fonc.2024.1406946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/20/2024] [Indexed: 08/22/2024] Open
Abstract
Introduction Breast cancer (BC) is the most common cancer affecting women in the United States. Ductal carcinoma in situ (DCIS) is the earliest identifiable pre-invasive BC lesion. Estimates show that 14 to 50% of DCIS cases progress to invasive BC. Methods Our objective was to identify nuclear matrix proteins (NMP) with specifically altered expression in DCIS and later stages of BC compared to non-diseased breast reduction mammoplasty and a contralateral breast explant culture using mass spectrometry and RNA sequencing to accurately identify aggressive DCIS. Results Sixty NMPs were significantly differentially expressed between the DCIS and non-diseased breast epithelium in an isogenic contralateral pair of patient-derived extended explants. Ten of the sixty showed significant mRNA expression level differences that matched the protein expression. These 10 proteins were similarly expressed in non-diseased breast reduction cells. Three NMPs (RPL7A, RPL11, RPL31) were significantly upregulated in DCIS and all other BC stages compared to the matching contralateral breast culture and an unrelated non-diseased breast reduction culture. RNA sequencing analyses showed that these three genes were increasingly upregulated with BC progression. Finally, we identified three NMPs (AHNAK, CDC37 and DNAJB1) that were significantly downregulated in DCIS and all other BC stages compared to the isogenically matched contralateral culture and the non-diseased breast reduction culture using both proteomics and RNA sequencing techniques. Discussion These genes should form the basis of, or contribute to, a molecular diagnostic panel that could identify DCIS lesions likely to be indolent and therefore not requiring aggressive treatment.
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Affiliation(s)
- Ali F. Almutairy
- Department of Pharmacology and Toxicology, College of Pharmacy, Qassim University, Buraidah, Saudi Arabia
- Department of Pharmaceutical Sciences, Barry and Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL, United States
- AutoNation Institute for Breast Cancer Research and Care, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Abdullah S. Alhamed
- Department of Pharmaceutical Sciences, Barry and Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL, United States
- AutoNation Institute for Breast Cancer Research and Care, Nova Southeastern University, Fort Lauderdale, FL, United States
- Pharmacology Department, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Stephen G. Grant
- AutoNation Institute for Breast Cancer Research and Care, Nova Southeastern University, Fort Lauderdale, FL, United States
- Department of Public Health, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Miranda J. Falso
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Billy W. Day
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, United States
| | - Colton R. Simmons
- Department of Pharmaceutical Sciences, Barry and Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL, United States
- AutoNation Institute for Breast Cancer Research and Care, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Jean J. Latimer
- Department of Pharmaceutical Sciences, Barry and Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL, United States
- AutoNation Institute for Breast Cancer Research and Care, Nova Southeastern University, Fort Lauderdale, FL, United States
- Department of Obstetrics and Gynecology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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Almutairy A, Alhamed A, Grant SG, Sarachine Falso MJ, Day BW, Simmons CR, Latimer JJ. Cancer-Specific Alterations in Nuclear Matrix Proteins Determined by Multi-omics Analyses of Ductal Carcinoma in Situ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580215. [PMID: 38405693 PMCID: PMC10888842 DOI: 10.1101/2024.02.13.580215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Breast cancer (BC) is the most common cancer affecting women in the United States. Ductal carcinoma in situ (DCIS) is the earliest identifiable pre-invasive BC lesion. Estimates show that 14 to 50% of DCIS cases progress to invasive BC. Our objective was to identify nuclear matrix proteins (NMP) with specifically altered expression in DCIS and later stages of BC compared to non-diseased breast reduction mammoplasty and a contralateral breast explant using mass spectrometry and RNA sequencing to accurately identify aggressive DCIS. Sixty NMPs were significantly differentially expressed between the DCIS and non-diseased breast epithelium in an isogenic contralateral pair of patient-derived extended explants. Ten of the sixty showed significant mRNA expression level differences that matched the protein expression. These 10 proteins were similarly expressed in non-diseased breast reduction cells. Three NMPs (RPL7A, RPL11, RPL31) were significantly upregulated in DCIS and all other BC stages compared to the matching contralateral breast culture and an unrelated non-diseased breast reduction culture. RNA sequencing analyses showed that these three genes were upregulated increasingly with BC progression. Finally, we identified three NMPs (AHNAK, CDC37 and DNAJB1) that were significantly downregulated in DCIS and all other BC stages compared to the isogenically matched contralateral culture and the non-diseased breast reduction culture using both proteomics and RNA sequencing techniques.
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Temaj G, Hadziselimovic R, Nefic H, Nuhii N. Ribosome biogenesis and ribosome therapy in cancer cells. RESEARCH RESULTS IN PHARMACOLOGY 2022. [DOI: 10.3897/rrpharmacology.8.81706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Introduction: The process of protein synthesis is a vital process for all kingdoms of life. The ribosome is a ribonucleoprotein complex that reads the genetic code, from messenger RNA (mRNA) to produce proteins and to tightly regulate and ensure cells growth. The fact that numerous diseases are caused by defect during the ribosome biogenesis is important to understand this pathway.
Materials and methods: We have analyzed the literature for ribosome biogenesis and its links with different diseases which have been found.
Results and discussion: We have discussed the key aspect of human ribosome biogenesis and its links to diseases. We have also proposed the potential of applying this knowledge to the development of a ribosomal stress-based cancer therapy.
Conclusion: Major challenges in the future will be to determine factors which play a pivotal role during ribosome biogenesis. Therefore, more anti-cancer drugs and gene therapy for genetic diseases will be developed against ribosomal biogenesis in the coming years.
Graphical abstract:
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Redavid I, Conserva MR, Anelli L, Zagaria A, Specchia G, Musto P, Albano F. Single-Cell Sequencing: Ariadne’s Thread in the Maze of Acute Myeloid Leukemia. Diagnostics (Basel) 2022; 12:diagnostics12040996. [PMID: 35454044 PMCID: PMC9024495 DOI: 10.3390/diagnostics12040996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 02/01/2023] Open
Abstract
Acute myeloid leukemia (AML) is a haematological neoplasm resulting from the accumulation of genetic and epigenetic alterations. Patients’ prognoses vary with AML genetic heterogeneity, which hampers successful treatments. Single-cell approaches have provided new insights of the clonal architecture of AML, revealing the mutational history from diagnosis, during treatment and to relapse. In this review, we imagine single-cell technologies as the Ariadne’s thread that will guide us out of the AML maze, provide a precise identikit of the leukemic cell at single-cell resolution and explore genomic, transcriptomic, epigenetic and proteomic levels.
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Affiliation(s)
- Immacolata Redavid
- Hematology Section, Department of Emergency and Organ Transplantation (D.E.T.O.), University of Bari ‘Aldo Moro’, 70124 Bari, Italy; (I.R.); (M.R.C.); (L.A.); (A.Z.); (P.M.)
| | - Maria Rosa Conserva
- Hematology Section, Department of Emergency and Organ Transplantation (D.E.T.O.), University of Bari ‘Aldo Moro’, 70124 Bari, Italy; (I.R.); (M.R.C.); (L.A.); (A.Z.); (P.M.)
| | - Luisa Anelli
- Hematology Section, Department of Emergency and Organ Transplantation (D.E.T.O.), University of Bari ‘Aldo Moro’, 70124 Bari, Italy; (I.R.); (M.R.C.); (L.A.); (A.Z.); (P.M.)
| | - Antonella Zagaria
- Hematology Section, Department of Emergency and Organ Transplantation (D.E.T.O.), University of Bari ‘Aldo Moro’, 70124 Bari, Italy; (I.R.); (M.R.C.); (L.A.); (A.Z.); (P.M.)
| | - Giorgina Specchia
- School of Medicine, University of Bari ‘Aldo Moro’, 70124 Bari, Italy;
| | - Pellegrino Musto
- Hematology Section, Department of Emergency and Organ Transplantation (D.E.T.O.), University of Bari ‘Aldo Moro’, 70124 Bari, Italy; (I.R.); (M.R.C.); (L.A.); (A.Z.); (P.M.)
| | - Francesco Albano
- Hematology Section, Department of Emergency and Organ Transplantation (D.E.T.O.), University of Bari ‘Aldo Moro’, 70124 Bari, Italy; (I.R.); (M.R.C.); (L.A.); (A.Z.); (P.M.)
- Correspondence:
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Deregulation of ribosomal proteins in human cancers. Biosci Rep 2021; 41:230380. [PMID: 34873618 PMCID: PMC8685657 DOI: 10.1042/bsr20211577] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/28/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022] Open
Abstract
The ribosome, the site for protein synthesis, is composed of ribosomal RNAs (rRNAs) and ribosomal proteins (RPs). The latter have been shown to have many ribosomal and extraribosomal functions. RPs are implicated in a variety of pathological processes, especially tumorigenesis and cell transformation. In this review, we will focus on the recent advances that shed light on the effects of RPs deregulation in different types of cancer and their roles in regulating the tumor cell fate.
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Cho SM, Lee HJ, Karuso P, Kwon HJ. Daptomycin suppresses tumor migration and angiogenesis via binding to ribosomal protein S19 in humans. J Antibiot (Tokyo) 2021; 74:726-733. [PMID: 34253886 DOI: 10.1038/s41429-021-00446-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
We have previously reported that daptomycin (DAP), a last resort antibiotic, binds to ribosomal protein S19 (RPS19) in humans and exhibits selective anti-cancer activity against MCF7 breast cancer cells. Here, we investigated the role of RPS19 in the anti-cancer effects of DAP and have found that DAP does not induce autophagy, apoptosis or cell viability but does reduce cell proliferation. Our results suggest that an extraribosomal function of RPS19 involves the regulation of vascular endothelial growth factor (VEGF) but not EGF, PDGF or FGF. Engagement of RPS19 by DAP was shown by CETSA and ITDRFCETSA assays, and knocking down of RPS19 with siRNA increased the potency of DAP in MCF7 cells. In addition, DAP suppressed the secretion of VEGF in cancer cells and thereby inhibited cell migration. Collectively, these data provide an outline of the underlying mechanism of how DAP exhibits anti-cancer activity and suggests that RPS19 could be a promising target for the development of new anticancer drugs.
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Affiliation(s)
- Sung Min Cho
- Chemical Genomics Global Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Hwa Jung Lee
- Chemical Genomics Global Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Peter Karuso
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ho Jeong Kwon
- Chemical Genomics Global Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea.
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Kang J, Brajanovski N, Chan KT, Xuan J, Pearson RB, Sanij E. Ribosomal proteins and human diseases: molecular mechanisms and targeted therapy. Signal Transduct Target Ther 2021; 6:323. [PMID: 34462428 PMCID: PMC8405630 DOI: 10.1038/s41392-021-00728-8] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 07/12/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Ribosome biogenesis and protein synthesis are fundamental rate-limiting steps for cell growth and proliferation. The ribosomal proteins (RPs), comprising the structural parts of the ribosome, are essential for ribosome assembly and function. In addition to their canonical ribosomal functions, multiple RPs have extra-ribosomal functions including activation of p53-dependent or p53-independent pathways in response to stress, resulting in cell cycle arrest and apoptosis. Defects in ribosome biogenesis, translation, and the functions of individual RPs, including mutations in RPs have been linked to a diverse range of human congenital disorders termed ribosomopathies. Ribosomopathies are characterized by tissue-specific phenotypic abnormalities and higher cancer risk later in life. Recent discoveries of somatic mutations in RPs in multiple tumor types reinforce the connections between ribosomal defects and cancer. In this article, we review the most recent advances in understanding the molecular consequences of RP mutations and ribosomal defects in ribosomopathies and cancer. We particularly discuss the molecular basis of the transition from hypo- to hyper-proliferation in ribosomopathies with elevated cancer risk, a paradox termed "Dameshek's riddle." Furthermore, we review the current treatments for ribosomopathies and prospective therapies targeting ribosomal defects. We also highlight recent advances in ribosome stress-based cancer therapeutics. Importantly, insights into the mechanisms of resistance to therapies targeting ribosome biogenesis bring new perspectives into the molecular basis of cancer susceptibility in ribosomopathies and new clinical implications for cancer therapy.
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Affiliation(s)
- Jian Kang
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Natalie Brajanovski
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Keefe T. Chan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Jiachen Xuan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Richard B. Pearson
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, VIC Australia
| | - Elaine Sanij
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Clinical Pathology, University of Melbourne, Melbourne, VIC Australia ,grid.1073.50000 0004 0626 201XSt. Vincent’s Institute of Medical Research, Fitzroy, VIC Australia
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Sim EUH, Lee CW, Narayanan K. The roles of ribosomal proteins in nasopharyngeal cancer: culprits, sentinels or both. Biomark Res 2021; 9:51. [PMID: 34193301 PMCID: PMC8247250 DOI: 10.1186/s40364-021-00311-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/20/2021] [Indexed: 12/15/2022] Open
Abstract
Ribosomal protein genes encode products that are essential for cellular protein biosynthesis and are major components of ribosomes. Canonically, they are involved in the complex system of ribosome biogenesis pivotal to the catalysis of protein translation. Amid this tightly organised process, some ribosomal proteins have unique spatial and temporal physiological activity giving rise to their extra-ribosomal functions. Many of these extra-ribosomal roles pertain to cellular growth and differentiation, thus implicating the involvement of some ribosomal proteins in organogenesis. Consequently, dysregulated functions of these ribosomal proteins could be linked to oncogenesis or neoplastic transformation of human cells. Their suspected roles in carcinogenesis have been reported but not specifically explained for malignancy of the nasopharynx. This is despite the fact that literature since one and half decade ago have documented the association of ribosomal proteins to nasopharyngeal cancer. In this review, we explain the association and contribution of dysregulated expression among a subset of ribosomal proteins to nasopharyngeal oncogenesis. The relationship of these ribosomal proteins with the cancer are explained. We provide information to indicate that the dysfunctional extra-ribosomal activities of specific ribosomal proteins are tightly involved with the molecular pathogenesis of nasopharyngeal cancer albeit mechanisms yet to be precisely defined. The complete knowledge of this will impact future applications in the effective management of nasopharyngeal cancer.
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Affiliation(s)
- Edmund Ui-Hang Sim
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Choon-Weng Lee
- Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kumaran Narayanan
- School of Science, Monash University, 46150, Bandar Sunway, Selangor, Malaysia.,Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY, 10029, USA
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Exploration of the Key Proteins in the Normal-Adenoma-Carcinoma Sequence of Colorectal Cancer Evolution Using In-Depth Quantitative Proteomics. JOURNAL OF ONCOLOGY 2021; 2021:5570058. [PMID: 34194496 PMCID: PMC8214504 DOI: 10.1155/2021/5570058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/30/2021] [Accepted: 05/09/2021] [Indexed: 12/30/2022]
Abstract
Purpose In most cases, the carcinogenesis of colorectal cancer (CRC) follows the normal-adenoma-carcinoma (N-A-C) sequence. In this study, we aimed to identify the key proteins in the N-A-C sequence. Methods Differentially expressed proteins (DEPs) in normal, adenoma, and carcinoma tissues were identified using the Tandem Mass Tag- (TMT-) based quantitative proteomics approach. The landscape of proteomic variation in the N-A-C sequence was explored using gene set enrichment analysis (GSEA) and Proteomaps. Key proteins in the N-A-C sequence were identified, verified, and validated based on our proteomic data, external proteomic data, and external transcriptomic data in the ProteomeXchange, CPTAC, GEO, and TCGA databases. The prognostic value of the key proteins in our database was evaluated by univariate and multivariate Cox regression analysis. The effects of the key proteins on adenoma organoids and colorectal cancer cells were explored in functional studies. Results Based on our proteomic profiles, we identified 1,294 DEPs between the carcinoma (CG) and normal (NG) groups, 919 DEPs between the adenoma group (AG) and NG, and 1,030 DEPs between the CG and AG. Ribosome- and spliceosome-related pathways were mainly enriched in the N-A process. Extracellular matrix- and epithelial-mesenchymal transition- (EMT-) related pathways were mainly enriched in the A-C process. RRP12 and SERPINH1 were identified, verified, and validated as candidate key proteins in the N-A and A-C processes, respectively. Furthermore, RRP12 and SERPINH1 knockdown impeded the viability and proliferation of adenoma organoids. SERPINH1 was validated as a risk factor for disease-free survival (DFS) based on the TCGA and our database, whereas RRP12 did not show prognostic value. SERPINH1 knockdown was accompanied by EMT-related protein variation, increased apoptosis, and reduced proliferation, invasion, and migration of CRC cells in vitro. Conclusions RRP12 and SERPINH1 may play an important role in the N-A and A-C processes, respectively. Furthermore, SERPINH1 showed favorable prognostic value for DFS in CRC patients. We speculate that SERPINH1 might promote not only the A-C process but also the development of CRC.
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Martinez-Seidel F, Beine-Golovchuk O, Hsieh YC, Eshraky KE, Gorka M, Cheong BE, Jimenez-Posada EV, Walther D, Skirycz A, Roessner U, Kopka J, Pereira Firmino AA. Spatially Enriched Paralog Rearrangements Argue Functionally Diverse Ribosomes Arise during Cold Acclimation in Arabidopsis. Int J Mol Sci 2021; 22:6160. [PMID: 34200446 PMCID: PMC8201131 DOI: 10.3390/ijms22116160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/23/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
Ribosome biogenesis is essential for plants to successfully acclimate to low temperature. Without dedicated steps supervising the 60S large subunits (LSUs) maturation in the cytosol, e.g., Rei-like (REIL) factors, plants fail to accumulate dry weight and fail to grow at suboptimal low temperatures. Around REIL, the final 60S cytosolic maturation steps include proofreading and assembly of functional ribosomal centers such as the polypeptide exit tunnel and the P-Stalk, respectively. In consequence, these ribosomal substructures and their assembly, especially during low temperatures, might be changed and provoke the need for dedicated quality controls. To test this, we blocked ribosome maturation during cold acclimation using two independent reil double mutant genotypes and tested changes in their ribosomal proteomes. Additionally, we normalized our mutant datasets using as a blank the cold responsiveness of a wild-type Arabidopsis genotype. This allowed us to neglect any reil-specific effects that may happen due to the presence or absence of the factor during LSU cytosolic maturation, thus allowing us to test for cold-induced changes that happen in the early nucleolar biogenesis. As a result, we report that cold acclimation triggers a reprogramming in the structural ribosomal proteome. The reprogramming alters the abundance of specific RP families and/or paralogs in non-translational LSU and translational polysome fractions, a phenomenon known as substoichiometry. Next, we tested whether the cold-substoichiometry was spatially confined to specific regions of the complex. In terms of RP proteoforms, we report that remodeling of ribosomes after a cold stimulus is significantly constrained to the polypeptide exit tunnel (PET), i.e., REIL factor binding and functional site. In terms of RP transcripts, cold acclimation induces changes in RP families or paralogs that are significantly constrained to the P-Stalk and the ribosomal head. The three modulated substructures represent possible targets of mechanisms that may constrain translation by controlled ribosome heterogeneity. We propose that non-random ribosome heterogeneity controlled by specialized biogenesis mechanisms may contribute to a preferential or ultimately even rigorous selection of transcripts needed for rapid proteome shifts and successful acclimation.
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Affiliation(s)
- Federico Martinez-Seidel
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Olga Beine-Golovchuk
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
- Heidelberg University, Biochemie-Zentrum, Nuclear Pore Complex and Ribosome Assembly, 69120 Heidelberg, Germany
| | - Yin-Chen Hsieh
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
- Institute for Arctic and Marine Biology, UiT Arctic University of Norway, 9037 Tromsø, Norway
| | - Kheloud El Eshraky
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
| | - Michal Gorka
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
| | - Bo-Eng Cheong
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia;
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Malaysia
| | - Erika V. Jimenez-Posada
- Grupo de Biotecnología-Productos Naturales, Universidad Tecnológica de Pereira, Pereira 660003, Colombia;
- Emerging Infectious Diseases and Tropical Medicine Research Group—Sci-Help, Pereira 660009, Colombia
| | - Dirk Walther
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
| | - Aleksandra Skirycz
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
| | - Ute Roessner
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Joachim Kopka
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
| | - Alexandre Augusto Pereira Firmino
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (O.B.-G.); (Y.-C.H.); (K.E.E.); (M.G.); (B.-E.C.); (D.W.); (A.S.); (J.K.); (A.A.P.F.)
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13
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Ladelfa MF, Peche LY, Amato GE, Escalada MC, Zampieri S, Pascucci FA, Benevento AF, Do Porto DF, Dardis A, Schneider C, Monte M. Expression of the tumor-expressed protein MageB2 enhances rRNA transcription. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119015. [PMID: 33741433 DOI: 10.1016/j.bbamcr.2021.119015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 02/22/2021] [Accepted: 03/12/2021] [Indexed: 11/17/2022]
Abstract
An essential requirement for cells to sustain a high proliferating rate is to be paired with enhanced protein synthesis through the production of ribosomes. For this reason, part of the growth-factor signaling pathways, are devoted to activate ribosome biogenesis. Enhanced production of ribosomes is a hallmark in cancer cells, which is boosted by different mechanisms. Here we report that the nucleolar tumor-protein MageB2, whose expression is associated with cell proliferation, also participates in ribosome biogenesis. Studies carried out in both siRNA-mediated MageB2 silenced cells and CRISPR/CAS9-mediated MageB2 knockout (KO) cells showed that its expression is linked to rRNA transcription increase independently of the cell proliferation status. Mechanistically, MageB2 interacts with phospho-UBF, a protein which causes the recruitment of RNA Pol I pre-initiation complex required for rRNA transcription. In addition, cells expressing MageB2 displays enhanced phospho-UBF occupancy at the rDNA gene promoter. Proteomic studies performed in MageB2 KO cells revealed impairment in ribosomal protein (RPs) content. Functionally, enhancement in rRNA production in MageB2 expressing cells, was directly associated with an increased dynamic in protein synthesis. Altogether our results unveil a novel function for a tumor-expressed protein from the MAGE-I family. Findings reported here suggest that nucleolar MageB2 might play a role in enhancing ribosome biogenesis as part of its repertoire to support cancer cell proliferation.
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Affiliation(s)
- María Fátima Ladelfa
- Lab. Oncología Molecular, Departamento de Química Biológica, IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Leticia Yamila Peche
- Laboratorio Nazionale del Consorzio Interuniversitario per le Biotecnologie, Area Science Park, Trieste, Italy
| | - Gastón Ezequiel Amato
- Lab. Oncología Molecular, Departamento de Química Biológica, IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Micaela Carolina Escalada
- Lab. Oncología Molecular, Departamento de Química Biológica, IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Stefania Zampieri
- Centro di Coordinamento Regionale per le Malattie Rare, Ospedale Universitario Santa Maria Della Misericordia, Udine, Italy
| | - Franco Andrés Pascucci
- Lab. Oncología Molecular, Departamento de Química Biológica, IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Andres Fernandez Benevento
- Plataforma de Bioinformática Argentina, Instituto de Cálculo, Pabellón 2, Ciudad Universitaria, Facultad de Ciencias Exactas y Naturales, UBA, Buenos Aires, Argentina
| | - Dario Fernandez Do Porto
- Plataforma de Bioinformática Argentina, Instituto de Cálculo, Pabellón 2, Ciudad Universitaria, Facultad de Ciencias Exactas y Naturales, UBA, Buenos Aires, Argentina
| | - Andrea Dardis
- Centro di Coordinamento Regionale per le Malattie Rare, Ospedale Universitario Santa Maria Della Misericordia, Udine, Italy
| | - Claudio Schneider
- Laboratorio Nazionale del Consorzio Interuniversitario per le Biotecnologie, Area Science Park, Trieste, Italy; Dipartimento di Scienze e Tecnologie Biomediche, Università di Udine, p.le Kolbe 4, Udine, Italy
| | - Martin Monte
- Lab. Oncología Molecular, Departamento de Química Biológica, IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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14
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HumanaFly: high-throughput transgenesis and expression of breast cancer transcripts in Drosophila eye discovers the RPS12-Wingless signaling axis. Sci Rep 2020; 10:21013. [PMID: 33273532 PMCID: PMC7713366 DOI: 10.1038/s41598-020-77942-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 02/03/2023] Open
Abstract
Drosophila melanogaster has been a model for multiple human disease conditions, including cancer. Among Drosophila tissues, the eye development is particularly sensitive to perturbations of the embryonic signaling pathways, whose improper activation in humans underlies various forms of cancer. We have launched the HumanaFly project, whereas human genes expressed in breast cancer patients are screened for their ability to aberrate development of the Drosophila eye, hoping to thus identify novel oncogenes. Here we report identification of a breast cancer transgene, which upon expression in Drosophila produces eye malformation similar to the famous Glazed phenotype discovered by Thomas Morgan and decades later dissected to originate from mis-expression of Wingless (Wg). Wg is the ortholog of human Wnt proteins serving as ligands to initiate the developmental/oncogenic Wnt signaling pathway. Through genetic experiments we identified that this transgene interacted with the Wg production machinery, rather than with Wg signal transduction. In Drosophila imaginal discs, we directly show that the transgene promoted long-range diffusion of Wg, affecting expression of the Wg target genes. The transgene emerged to encode RPS12—a protein of the small ribosomal subunit overexpressed in several cancer types and known to also possess extra-ribosomal functions. Our work identifies RPS12 as an unexpected regulator of secretion and activity of Wnts. As Wnt signaling is particularly important in the context of breast cancer initiation and progression, RPS12 might be implicated in tumorigenesis in this and other Wnt-dependent cancers. Continuation of our HumanaFly project may bring further discoveries on oncogenic mechanisms.
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15
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Iglesias-Pedraz JM, Fossatti-Jara DM, Valle-Riestra-Felice V, Cruz-Visalaya SR, Ayala Felix JA, Comai L. WRN modulates translation by influencing nuclear mRNA export in HeLa cancer cells. BMC Mol Cell Biol 2020; 21:71. [PMID: 33054770 PMCID: PMC7557079 DOI: 10.1186/s12860-020-00315-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/01/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND The Werner syndrome protein (WRN) belongs to the RecQ family of helicases and its loss of function results in the premature aging disease Werner syndrome (WS). We previously demonstrated that an early cellular change induced by WRN depletion is a posttranscriptional decrease in the levels of enzymes involved in metabolic pathways that control macromolecular synthesis and protect from oxidative stress. This metabolic shift is tolerated by normal cells but causes mitochondria dysfunction and acute oxidative stress in rapidly growing cancer cells, thereby suppressing their proliferation. RESULTS To identify the mechanism underlying this metabolic shift, we examined global protein synthesis and mRNA nucleocytoplasmic distribution after WRN knockdown. We determined that WRN depletion in HeLa cells attenuates global protein synthesis without affecting the level of key components of the mRNA export machinery. We further observed that WRN depletion affects the nuclear export of mRNAs and demonstrated that WRN interacts with mRNA and the Nuclear RNA Export Factor 1 (NXF1). CONCLUSIONS Our findings suggest that WRN influences the export of mRNAs from the nucleus through its interaction with the NXF1 export receptor thereby affecting cellular proteostasis. In summary, we identified a new partner and a novel function of WRN, which is especially important for the proliferation of cancer cells.
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Affiliation(s)
- Juan Manuel Iglesias-Pedraz
- Departamento de Investigación, Desarrollo e Innovación, Laboratorio de Genética Molecular y Bioquímica, Universidad Científica del Sur, Villa El Salvador, 15842 Lima, Peru
| | - Diego Matia Fossatti-Jara
- Departamento de Investigación, Desarrollo e Innovación, Laboratorio de Genética Molecular y Bioquímica, Universidad Científica del Sur, Villa El Salvador, 15842 Lima, Peru
- Present address: National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic
| | - Valeria Valle-Riestra-Felice
- Departamento de Investigación, Desarrollo e Innovación, Laboratorio de Genética Molecular y Bioquímica, Universidad Científica del Sur, Villa El Salvador, 15842 Lima, Peru
| | - Sergio Rafael Cruz-Visalaya
- Departamento de Investigación, Desarrollo e Innovación, Laboratorio de Genética Molecular y Bioquímica, Universidad Científica del Sur, Villa El Salvador, 15842 Lima, Peru
| | - Jose Antonio Ayala Felix
- Departamento de Investigación, Desarrollo e Innovación, Laboratorio de Genética Molecular y Bioquímica, Universidad Científica del Sur, Villa El Salvador, 15842 Lima, Peru
| | - Lucio Comai
- Department of Molecular Microbiology and Immunology, Biochemistry and Molecular Medicine, Keck School of Medicine, Longevity Institute, Davis School of Gerontology, University of Southern California, Los Angeles, CA 90033 USA
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16
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Wu J, Xiao Y, Sun J, Sun H, Chen H, Zhu Y, Fu H, Yu C, E W, Lai S, Ma L, Li J, Fei L, Jiang M, Wang J, Ye F, Wang R, Zhou Z, Zhang G, Zhang T, Ding Q, Wang Z, Hao S, Liu L, Zheng W, He J, Huang W, Wang Y, Xie J, Li T, Cheng T, Han X, Huang H, Guo G. A single-cell survey of cellular hierarchy in acute myeloid leukemia. J Hematol Oncol 2020; 13:128. [PMID: 32977829 PMCID: PMC7517826 DOI: 10.1186/s13045-020-00941-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/21/2020] [Indexed: 02/07/2023] Open
Abstract
Background Acute myeloid leukemia (AML) is a fatal hematopoietic malignancy and has a prognosis that varies with its genetic complexity. However, there has been no appropriate integrative analysis on the hierarchy of different AML subtypes. Methods Using Microwell-seq, a high-throughput single-cell mRNA sequencing platform, we analyzed the cellular hierarchy of bone marrow samples from 40 patients and 3 healthy donors. We also used single-cell single-molecule real-time (SMRT) sequencing to investigate the clonal heterogeneity of AML cells. Results From the integrative analysis of 191727 AML cells, we established a single-cell AML landscape and identified an AML progenitor cell cluster with novel AML markers. Patients with ribosomal protein high progenitor cells had a low remission rate. We deduced two types of AML with diverse clinical outcomes. We traced mitochondrial mutations in the AML landscape by combining Microwell-seq with SMRT sequencing. We propose the existence of a phenotypic “cancer attractor” that might help to define a common phenotype for AML progenitor cells. Finally, we explored the potential drug targets by making comparisons between the AML landscape and the Human Cell Landscape. Conclusions We identified a key AML progenitor cell cluster. A high ribosomal protein gene level indicates the poor prognosis. We deduced two types of AML and explored the potential drug targets. Our results suggest the existence of a cancer attractor.
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Affiliation(s)
- Junqing Wu
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Yanyu Xiao
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Jie Sun
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Huiyu Sun
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Yuanyuan Zhu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Huarui Fu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Chengxuan Yu
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Weigao E
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Shujing Lai
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Lifeng Ma
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Jiaqi Li
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Lijiang Fei
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Mengmeng Jiang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Jingjing Wang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Fang Ye
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Renying Wang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Ziming Zhou
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Guodong Zhang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Tingyue Zhang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Qiong Ding
- Wuhan Biobank Co., LTD, Wuhan, 430075, China
| | - Zou Wang
- Wuhan Biobank Co., LTD, Wuhan, 430075, China
| | - Sheng Hao
- Wuhan Biobank Co., LTD, Wuhan, 430075, China
| | - Lizhen Liu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Weiyan Zheng
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jingsong He
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Weijia Huang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yungui Wang
- Institute of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jin Xie
- State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou, 310058, China
| | - Tiefeng Li
- Institute of Applied Mechanics, Zhejiang University, Hangzhou, 310027, China
| | - Tao Cheng
- Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300000, China.,Alliance for Atlas of Blood Cells, Tianjin, China
| | - Xiaoping Han
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China. .,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China. .,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, 311121, China.
| | - He Huang
- Institute of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China. .,Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China. .,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China. .,Alliance for Atlas of Blood Cells, Tianjin, China. .,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, 311121, China.
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China. .,Institute of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China. .,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China. .,Alliance for Atlas of Blood Cells, Tianjin, China. .,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, 311121, China.
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Direct Antiviral Treatments for Hepatitis C Virus Have Off-Target Effects of Oncologic Relevance in Hepatocellular Carcinoma. Cancers (Basel) 2020; 12:cancers12092674. [PMID: 32961688 PMCID: PMC7565876 DOI: 10.3390/cancers12092674] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 12/25/2022] Open
Abstract
Simple Summary Hepatitis C virus (HCV) eradication by direct-acting antiviral agents (DAAs) reduces de novo hepatocellular carcinoma incidence in cirrhosis; however, contrasting evidence on higher incidence of hepatocellular carcinoma (HCC) was reported in patients previously treated for HCC. Here, we showed that sofosbuvir and daclatasvir can modulate cell proliferation, invasion capability and gene expression in HCC-derived cell lines, suggesting that off-target effects of these drugs might be responsible for both the increase and reduction of cell proliferation and migration capability. Off-target gene modulation, mainly affecting mitochondrial functions, ribosomal genes and histones, was consistent with matched phenotypic changes and might account either for pro-oncogenic or tumor-suppressive functions of DAAs, that seemed to be dictated by the molecular background. Abstract Background and Aims: HCV eradication by direct-acting antiviral agents (DAAs) reduces de novo hepatocellular carcinoma (HCC) incidence in cirrhosis; however, contrasting evidence about beneficial or detrimental effects still exists in patients who have already developed HCC. Methods: we investigated whether sofosbuvir and daclatasvir modulate cell proliferation, invasion capability and gene expression (RNA-seq) in HCC-derived cell lines, hypothesizing possible off-target effects of these drugs. Results observed in HCC cell lines were validated in non-HCC cancer-derived cell lines and a preliminary series of human HCC tissues by qPCR and IHC. Results: DAAs can affect HCC cell proliferation and migration capability by either increasing or reducing them, showing transcriptomic changes consistent with some unexpected drug-associated effects. Off-target gene modulation, mainly affecting ribosomal genes, mitochondrial functions and histones, points to epigenetics and proliferation as relevant events, consistent with matched phenotypic changes. A preliminary validation of in vitro findings was performed in a restricted cohort of HCC patients previously treated with DAAs, with immunohistochemical correlations suggesting DAA-treated HCCs to be more aggressive in terms of migration and epidermal-to-mesenchymal transition. Conclusions: Our findings suggested the possible occurrence of off-target effects ultimately modulating cell proliferation and/or migration and potentially justified previous findings showing some instances of particularly aggressive HCC recurrence as well as reduced incidence of recurrence of HCC following treatment with DAAs.
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18
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De novo Transcriptome of the Non-saxitoxin Producing Alexandrium tamutum Reveals New Insights on Harmful Dinoflagellates. Mar Drugs 2020; 18:md18080386. [PMID: 32722301 PMCID: PMC7460133 DOI: 10.3390/md18080386] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/17/2022] Open
Abstract
Many dinoflagellates species, especially of the Alexandrium genus, produce a series of toxins with tremendous impacts on human and environmental health, and tourism economies. Alexandrium tamutum was discovered for the first time in the Gulf of Naples, and it is not known to produce saxitoxins. However, a clone of A. tamutum from the same Gulf showed copepod reproduction impairment and antiproliferative activity. In this study, the full transcriptome of the dinoflagellate A. tamutum is presented in both control and phosphate starvation conditions. RNA-seq approach was used for in silico identification of transcripts that can be involved in the synthesis of toxic compounds. Phosphate starvation was selected because it is known to induce toxin production for other Alexandrium spp. Results showed the presence of three transcripts related to saxitoxin synthesis (sxtA, sxtG and sxtU), and others potentially related to the synthesis of additional toxic compounds (e.g., 44 transcripts annotated as "polyketide synthase"). These data suggest that even if this A. tamutum clone does not produce saxitoxins, it has the potential to produce toxic metabolites, in line with the previously observed activity. These data give new insights into toxic microalgae, toxin production and their potential applications for the treatment of human pathologies.
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Banerjee A, Kulkarni S, Mukherjee A. Herpes Simplex Virus: The Hostile Guest That Takes Over Your Home. Front Microbiol 2020; 11:733. [PMID: 32457704 PMCID: PMC7221137 DOI: 10.3389/fmicb.2020.00733] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 03/30/2020] [Indexed: 12/15/2022] Open
Abstract
Alpha (α)-herpesviruses (HSV-1 and HSV-2), like other viruses, are obligate intracellular parasites. They hijack the cellular machinery to survive and replicate through evading the defensive responses by the host. The viral genome of herpes simplex viruses (HSVs) contains viral genes, the products of which are destined to exploit the host apparatus for their own existence. Cellular modulations begin from the entry point itself. The two main gateways that the virus has to penetrate are the cell membrane and the nuclear membrane. Changes in the cell membrane are triggered when the glycoproteins of HSV interact with the surface receptors of the host cell, and from here, the components of the cytoskeleton take over. The rearrangement in the cytoskeleton components help the virus to enter as well as transport to the nucleus and back to the cell membrane to spread out to the other cells. The entire carriage process is also mediated by the motor proteins of the kinesin and dynein superfamily and is directed by the viral tegument proteins. Also, the virus captures the cell’s most efficient cargo carrying system, the endoplasmic reticulum (ER)–Golgi vesicular transport machinery for egress to the cell membrane. For these reasons, the host cell has its own checkpoints where the normal functions are halted once a danger is sensed. However, a cell may be prepared for the adversities from an invading virus, and it is simply commendable that the virus has the antidote to these cellular strategies as well. The HSV viral proteins are capable of limiting the use of the transcriptional and translational tools for the cell itself, so that its own transcription and translation pathways remain unhindered. HSV prefers to constrain any self-destruction process of the cell—be it autophagy in the lysosome or apoptosis by the mitochondria, so that it can continue to parasitize the cell for its own survival. This review gives a detailed account of the significance of compartmentalization during HSV pathogenesis. It also highlights the undiscovered areas in the HSV cell biology research which demand attention for devising improved therapeutics against the infection.
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Affiliation(s)
- Anwesha Banerjee
- Division of Virology, Indian Council of Medical Research-National AIDS Research Institute, Pune, India
| | - Smita Kulkarni
- Division of Virology, Indian Council of Medical Research-National AIDS Research Institute, Pune, India
| | - Anupam Mukherjee
- Division of Virology, Indian Council of Medical Research-National AIDS Research Institute, Pune, India
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20
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Ebright RY, Lee S, Wittner BS, Niederhoffer KL, Nicholson BT, Bardia A, Truesdell S, Wiley DF, Wesley B, Li S, Mai A, Aceto N, Vincent-Jordan N, Szabolcs A, Chirn B, Kreuzer J, Comaills V, Kalinich M, Haas W, Ting DT, Toner M, Vasudevan S, Haber DA, Maheswaran S, Micalizzi DS. Deregulation of ribosomal protein expression and translation promotes breast cancer metastasis. Science 2020; 367:1468-1473. [PMID: 32029688 DOI: 10.1126/science.aay0939] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 12/01/2019] [Accepted: 01/26/2020] [Indexed: 12/11/2022]
Abstract
Circulating tumor cells (CTCs) are shed into the bloodstream from primary tumors, but only a small subset of these cells generates metastases. We conducted an in vivo genome-wide CRISPR activation screen in CTCs from breast cancer patients to identify genes that promote distant metastasis in mice. Genes coding for ribosomal proteins and regulators of translation were enriched in this screen. Overexpression of RPL15, which encodes a component of the large ribosomal subunit, increased metastatic growth in multiple organs and selectively enhanced translation of other ribosomal proteins and cell cycle regulators. RNA sequencing of freshly isolated CTCs from breast cancer patients revealed a subset with strong ribosome and protein synthesis signatures; these CTCs expressed proliferation and epithelial markers and correlated with poor clinical outcome. Therapies targeting this aggressive subset of CTCs may merit exploration as potential suppressors of metastatic progression.
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Affiliation(s)
- Richard Y Ebright
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Sooncheol Lee
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Ben S Wittner
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Kira L Niederhoffer
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Benjamin T Nicholson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Aditya Bardia
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Samuel Truesdell
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Devon F Wiley
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Benjamin Wesley
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Selena Li
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Andy Mai
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Nicola Aceto
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Nicole Vincent-Jordan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Annamaria Szabolcs
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Brian Chirn
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Johannes Kreuzer
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Valentine Comaills
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Mark Kalinich
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - David T Ting
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Mehmet Toner
- Center for Bioengineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Shriners Hospital for Children, Boston, MA 02114, USA.,Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Shobha Vasudevan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA. .,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02114, USA
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA. .,Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Douglas S Micalizzi
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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21
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Sim EUH, Talwar SP. In silico evidence of de novo interactions between ribosomal and Epstein - Barr virus proteins. BMC Mol Cell Biol 2019; 20:34. [PMID: 31416416 PMCID: PMC6694676 DOI: 10.1186/s12860-019-0219-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/08/2019] [Indexed: 12/29/2022] Open
Abstract
Background Association of Epstein-Barr virus (EBV) encoded latent gene products with host ribosomal proteins (RPs) has not been fully explored, despite their involvement in the aetiology of several human cancers. To gain an insight into their plausible interactions, we employed a computational approach that encompasses structural alignment, gene ontology analysis, pathway analysis, and molecular docking. Results In this study, the alignment analysis based on structural similarity allows the prediction of 48 potential interactions between 27 human RPs and the EBV proteins EBNA1, LMP1, LMP2A, and LMP2B. Gene ontology analysis of the putative protein-protein interactions (PPIs) reveals their probable involvement in RNA binding, ribosome biogenesis, metabolic and biosynthetic processes, and gene regulation. Pathway analysis shows their possible participation in viral infection strategies (viral translation), as well as oncogenesis (Wnt and EGFR signalling pathways). Finally, our molecular docking assay predicts the functional interactions of EBNA1 with four RPs individually: EBNA1-eS10, EBNA1-eS25, EBNA1-uL10 and EBNA1-uL11. Conclusion These interactions have never been revealed previously via either experimental or in silico approach. We envisage that the calculated interactions between the ribosomal and EBV proteins herein would provide a hypothetical model for future experimental studies on the functional relationship between ribosomal proteins and EBV infection. Electronic supplementary material The online version of this article (10.1186/s12860-019-0219-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Edmund Ui-Hang Sim
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Shruti Prashant Talwar
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
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22
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Piazzi M, Bavelloni A, Gallo A, Faenza I, Blalock WL. Signal Transduction in Ribosome Biogenesis: A Recipe to Avoid Disaster. Int J Mol Sci 2019; 20:ijms20112718. [PMID: 31163577 PMCID: PMC6600399 DOI: 10.3390/ijms20112718] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 12/27/2022] Open
Abstract
Energetically speaking, ribosome biogenesis is by far the most costly process of the cell and, therefore, must be highly regulated in order to avoid unnecessary energy expenditure. Not only must ribosomal RNA (rRNA) synthesis, ribosomal protein (RP) transcription, translation, and nuclear import, as well as ribosome assembly, be tightly controlled, these events must be coordinated with other cellular events, such as cell division and differentiation. In addition, ribosome biogenesis must respond rapidly to environmental cues mediated by internal and cell surface receptors, or stress (oxidative stress, DNA damage, amino acid depletion, etc.). This review examines some of the well-studied pathways known to control ribosome biogenesis (PI3K-AKT-mTOR, RB-p53, MYC) and how they may interact with some of the less well studied pathways (eIF2α kinase and RNA editing/splicing) in higher eukaryotes to regulate ribosome biogenesis, assembly, and protein translation in a dynamic manner.
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Affiliation(s)
- Manuela Piazzi
- Istituto di Genetica Molecolare-Luigi Luca Cavalli Sforza, UOS Bologna, Consiglio Nazionale delle Ricerche (IGM-CNR), 40136 Bologna, Italy.
- IRCCS, Istituto Ortopedico Rizzoli, 40136 Bologna, Italy.
| | | | - Angela Gallo
- RNA Editing Laboratory, Dipartimento di Oncoematologia, IRCCS, Ospedale Pediatrica Bambino Gesù, 00146 Rome, Italy.
| | - Irene Faenza
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, 40126 Bologna, Italy.
| | - William L Blalock
- Istituto di Genetica Molecolare-Luigi Luca Cavalli Sforza, UOS Bologna, Consiglio Nazionale delle Ricerche (IGM-CNR), 40136 Bologna, Italy.
- IRCCS, Istituto Ortopedico Rizzoli, 40136 Bologna, Italy.
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23
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Li S. Regulation of Ribosomal Proteins on Viral Infection. Cells 2019; 8:E508. [PMID: 31137833 PMCID: PMC6562653 DOI: 10.3390/cells8050508] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/17/2019] [Accepted: 05/21/2019] [Indexed: 12/20/2022] Open
Abstract
Ribosomal proteins (RPs), in conjunction with rRNA, are major components of ribosomes involved in the cellular process of protein biosynthesis, known as "translation". The viruses, as the small infectious pathogens with limited genomes, must recruit a variety of host factors to survive and propagate, including RPs. At present, more and more information is available on the functional relationship between RPs and virus infection. This review focuses on advancements in my own understanding of critical roles of RPs in the life cycle of viruses. Various RPs interact with viral mRNA and proteins to participate in viral protein biosynthesis and regulate the replication and infection of virus in host cells. Most interactions are essential for viral translation and replication, which promote viral infection and accumulation, whereas the minority represents the defense signaling of host cells by activating immune pathway against virus. RPs provide a new platform for antiviral therapy development, however, at present, antiviral therapeutics with RPs involving in virus infection as targets is limited, and exploring antiviral strategy based on RPs will be the guides for further study.
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Affiliation(s)
- Shuo Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
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24
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Bowlt Blacklock KL, Birand Z, Selmic LE, Nelissen P, Murphy S, Blackwood L, Bass J, McKay J, Fox R, Beaver S, Starkey M. Genome-wide analysis of canine oral malignant melanoma metastasis-associated gene expression. Sci Rep 2019; 9:6511. [PMID: 31019223 PMCID: PMC6482147 DOI: 10.1038/s41598-019-42839-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 04/04/2019] [Indexed: 12/12/2022] Open
Abstract
Oral malignant melanoma (OMM) is the most common canine melanocytic neoplasm. Overlap between the somatic mutation profiles of canine OMM and human mucosal melanomas suggest a shared UV-independent molecular aetiology. In common with human mucosal melanomas, most canine OMM metastasise. There is no reliable means of predicting canine OMM metastasis, and systemic therapies for metastatic disease are largely palliative. Herein, we employed exon microarrays for comparative expression profiling of FFPE biopsies of 18 primary canine OMM that metastasised and 10 primary OMM that did not metastasise. Genes displaying metastasis-associated expression may be targets for anti-metastasis treatments, and biomarkers of OMM metastasis. Reduced expression of CXCL12 in the metastasising OMMs implies that the CXCR4/CXCL12 axis may be involved in OMM metastasis. Increased expression of APOBEC3A in the metastasising OMMs may indicate APOBEC3A-induced double-strand DNA breaks and pro-metastatic hypermutation. DNA double strand breakage triggers the DNA damage response network and two Fanconi anaemia DNA repair pathway members showed elevated expression in the metastasising OMMs. Cross-validation was employed to test a Linear Discriminant Analysis classifier based upon the RT-qPCR-measured expression levels of CXCL12, APOBEC3A and RPL29. Classification accuracies of 94% (metastasising OMMs) and 86% (non-metastasising OMMs) were estimated.
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Affiliation(s)
| | - Z Birand
- Animal Health Trust, Newmarket, Suffolk, UK
| | - L E Selmic
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, Ohio, USA
| | - P Nelissen
- Dick White Referrals, Newmarket, Suffolk, UK
| | - S Murphy
- Animal Health Trust, Newmarket, Suffolk, UK
- The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - L Blackwood
- Institute of Veterinary Science, University of Liverpool, Liverpool, UK
| | - J Bass
- Animal Health Trust, Newmarket, Suffolk, UK
- Finn Pathologists, Harleston, UK
| | - J McKay
- IDEXX Laboratories, Ltd, Wetherby, UK
| | - R Fox
- Finn Pathologists, Harleston, UK
| | - S Beaver
- Nationwide Laboratory Services, Poulton-le-Fylde, UK
| | - M Starkey
- Animal Health Trust, Newmarket, Suffolk, UK.
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25
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Halim VA, García-Santisteban I, Warmerdam DO, van den Broek B, Heck AJR, Mohammed S, Medema RH. Doxorubicin-induced DNA Damage Causes Extensive Ubiquitination of Ribosomal Proteins Associated with a Decrease in Protein Translation. Mol Cell Proteomics 2018; 17:2297-2308. [PMID: 29438997 PMCID: PMC6283304 DOI: 10.1074/mcp.ra118.000652] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Indexed: 11/06/2022] Open
Abstract
Protein posttranslational modifications (PTMs) play a central role in the DNA damage response. In particular, protein phosphorylation and ubiquitination have been shown to be essential in the signaling cascade that coordinates break repair with cell cycle progression. Here, we performed whole-cell quantitative proteomics to identify global changes in protein ubiquitination that are induced by DNA double-strand breaks. In total, we quantified more than 9,400 ubiquitin sites and found that the relative abundance of ∼10% of these sites was altered in response to DNA double-strand breaks. Interestingly, a large proportion of ribosomal proteins, including those from the 40S as well as the 60S subunit, were ubiquitinated in response to DNA damage. In parallel, we discovered that DNA damage leads to the inhibition of ribosome function. Taken together, these data uncover the ribosome as a major target of the DNA damage response.
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Affiliation(s)
- Vincentius A Halim
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, 3584 CH Utrecht, The Netherlands; Division of Cell Biology and Cancer Genomics Center, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Iraia García-Santisteban
- Division of Cell Biology and Cancer Genomics Center, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Daniel O Warmerdam
- Division of Cell Biology and Cancer Genomics Center, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; European Research Institute for the Biology of Ageing, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Bram van den Broek
- Division of Cell Biology and Cancer Genomics Center, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, 3584 CH Utrecht, The Netherlands
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, 3584 CH Utrecht, The Netherlands; Department of Biochemistry, University of Oxford, OX13TA Oxford, United Kingdom; Chemistry Research Laboratory, Department of Chemistry, University of Oxford, OX13TA Oxford, United Kingdom
| | - René H Medema
- Division of Cell Biology and Cancer Genomics Center, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands.
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26
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Wang P, Gao L, Hu Y, Li F. Feature related multi-view nonnegative matrix factorization for identifying conserved functional modules in multiple biological networks. BMC Bioinformatics 2018; 19:394. [PMID: 30373534 PMCID: PMC6206826 DOI: 10.1186/s12859-018-2434-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 10/15/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Comprehensive analyzing multi-omics biological data in different conditions is important for understanding biological mechanism in system level. Multiple or multi-layer network model gives us a new insight into simultaneously analyzing these data, for instance, to identify conserved functional modules in multiple biological networks. However, because of the larger scale and more complicated structure of multiple networks than single network, how to accurate and efficient detect conserved functional biological modules remains a significant challenge. RESULTS Here, we propose an efficient method, named ConMod, to discover conserved functional modules in multiple biological networks. We introduce two features to characterize multiple networks, thus all networks are compressed into two feature matrices. The module detection is only performed in the feature matrices by using multi-view non-negative matrix factorization (NMF), which is independent of the number of input networks. Experimental results on both synthetic and real biological networks demonstrate that our method is promising in identifying conserved modules in multiple networks since it improves the accuracy and efficiency comparing with state-of-the-art methods. Furthermore, applying ConMod to co-expression networks of different cancers, we find cancer shared gene modules, the majority of which have significantly functional implications, such as ribosome biogenesis and immune response. In addition, analyzing on brain tissue-specific protein interaction networks, we detect conserved modules related to nervous system development, mRNA processing, etc. CONCLUSIONS: ConMod facilitates finding conserved modules in any number of networks with a low time and space complexity, thereby serve as a valuable tool for inference shared traits and biological functions of multiple biological system.
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Affiliation(s)
- Peizhuo Wang
- School of Computer Science and Technology, Xidian University, Xi’an, 710071 China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, Xi’an, 710071 China
| | - Yuxuan Hu
- School of Computer Science and Technology, Xidian University, Xi’an, 710071 China
| | - Feng Li
- School of Computer Science and Technology, Xidian University, Xi’an, 710071 China
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27
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Altered patterns of global protein synthesis and translational fidelity in RPS15-mutated chronic lymphocytic leukemia. Blood 2018; 132:2375-2388. [PMID: 30181176 DOI: 10.1182/blood-2017-09-804401] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 08/24/2018] [Indexed: 12/17/2022] Open
Abstract
Genomic studies have recently identified RPS15 as a new driver gene in aggressive and chemorefractory cases of chronic lymphocytic leukemia (CLL). RPS15 encodes a ribosomal protein whose conserved C-terminal domain extends into the decoding center of the ribosome. We demonstrate that mutations in highly conserved residues of this domain affect protein stability, by increasing its ubiquitin-mediated degradation, and cell-proliferation rates. On the other hand, we show that mutated RPS15 can be loaded into the ribosomes, directly impacting on global protein synthesis and/or translational fidelity in a mutation-specific manner. Quantitative mass spectrometry analyses suggest that RPS15 variants may induce additional alterations in the translational machinery, as well as a metabolic shift at the proteome level in HEK293T and MEC-1 cells. These results indicate that CLL-related RPS15 mutations might act following patterns known for other ribosomal diseases, likely switching from a hypo- to a hyperproliferative phenotype driven by mutated ribosomes. In this scenario, loss of translational fidelity causing altered cell proteostasis can be proposed as a new molecular mechanism involved in CLL pathobiology.
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28
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Ba Q, Li X, Huang C, Li J, Fu Y, Chen P, Duan J, Hao M, Zhang Y, Li J, Sun C, Ying H, Song H, Zhang R, Shen Z, Wang H. BCCIPβ modulates the ribosomal and extraribosomal function of S7 through a direct interaction. J Mol Cell Biol 2018; 9:209-219. [PMID: 28510697 PMCID: PMC5907838 DOI: 10.1093/jmcb/mjx019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 05/14/2017] [Indexed: 11/14/2022] Open
Abstract
Extraribosomal functions of ribosomal proteins (RPs) have gained much attention for their implications in tumorigenesis and progression. However, the regulations for transition between the ribosomal and extraribosomal functions of RPs are rarely reported. Herein, we identified a ribosomal protein S7-interacting partner, BCCIPβ, which modulates the functional conversion of S7. Through the N-terminal acidic domain, BCCIPβ interacts with the central basic region in S7 and regulates the extraribosomal distribution of S7. BCCIPβ deficiency abrogates the ribosomal accumulation but enhances the ribosome-free location of S7. This translocation further impairs protein synthesis and triggers ribosomal stress. Consequently, BCCIPβ deficiency suppresses the ribosomal function and initiates the extraribosomal function of S7, resulting in restriction of cell proliferation. Moreover, clinically relevant S7 mutations were found to dampen the interaction with BCCIPβ and facilitate the functional transition of S7. In conclusion, BCCIPβ, as a S7 modulator, contributes to the regulation of ribosomal and extraribosomal functions of S7 and has implications in cell growth and tumor development.
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Affiliation(s)
- Qian Ba
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaoguang Li
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chao Huang
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Junyang Li
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yijing Fu
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Peizhan Chen
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Juan Duan
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Miao Hao
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yinghua Zhang
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jingquan Li
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chuanqi Sun
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hao Ying
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Haiyun Song
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ruiwen Zhang
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA
| | - Zhiyuan Shen
- Rutgers Cancer Institute of New Jersey, Department of Radiation Oncology of Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
| | - Hui Wang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Correspondence to: Hui Wang, E-mail:
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29
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Shi C, Wang Y, Guo Y, Chen Y, Liu N. Cooperative down-regulation of ribosomal protein L10 and NF-κB signaling pathway is responsible for the anti-proliferative effects by DMAPT in pancreatic cancer cells. Oncotarget 2018; 8:35009-35018. [PMID: 28388532 PMCID: PMC5471030 DOI: 10.18632/oncotarget.16557] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 03/09/2017] [Indexed: 01/05/2023] Open
Abstract
Dimethylaminoparthenolide (DMAPT), a water-soluble analogue of natural product parthenolide, possesses anti-inflammatory and anti-tumor activities. Despite that the anti-inflammatory mechanism of DMAPT has been well studied, specific target(s) for DMPAT and its anti-tumor mechanism remain poorly understood. In this study, to assess the anti-proliferative effects of DMAPT in pancreatic cancer cell lines and exploit its anti-tumor mechanism, serial affinity chromatograph was implemented to probe potential targets for DMAPT, revealing that ribosomal protein L10 (RPL10) is a specific binding protein of DMAPT in PANC-1 cells. DMAPT could decrease the expression of RPL10 accompanying its anti-proliferative effects. Mechanistically, in both PANC-1 cells and MiaPaca-2 cells, reduced expression of RPL10 triggered by DMAPT binding decreased the expression of either p65 or IKKγ through the direct binding between RPL10 and p65 or IKKγ. Together, the present study strongly implies that RPL10 is a novel target with therapeutic potential for the treatment of pancreatic cancer.
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Affiliation(s)
- Chen Shi
- State Key Laboratory of Natural Medicines and Laboratory of Chemical Biology, China Pharmaceutical University, Nanjing, Jiangsu Province, 210009, People's Republic of China
| | - Yang Wang
- State Key Laboratory of Natural Medicines and Laboratory of Chemical Biology, China Pharmaceutical University, Nanjing, Jiangsu Province, 210009, People's Republic of China
| | - Yuna Guo
- State Key Laboratory of Natural Medicines and Laboratory of Chemical Biology, China Pharmaceutical University, Nanjing, Jiangsu Province, 210009, People's Republic of China
| | - Yijun Chen
- State Key Laboratory of Natural Medicines and Laboratory of Chemical Biology, China Pharmaceutical University, Nanjing, Jiangsu Province, 210009, People's Republic of China
| | - Nan Liu
- State Key Laboratory of Natural Medicines and Laboratory of Chemical Biology, China Pharmaceutical University, Nanjing, Jiangsu Province, 210009, People's Republic of China
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30
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Chang CYY, Lai MT, Chen Y, Yang CW, Chang HW, Lu CC, Chen CM, Chan C, Chung C, Tseng CC, Hwang T, Sheu JJC, Tsai FJ. Up-regulation of ribosome biogenesis by MIR196A2 genetic variation promotes endometriosis development and progression. Oncotarget 2018; 7:76713-76725. [PMID: 27741504 PMCID: PMC5363543 DOI: 10.18632/oncotarget.11536] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 08/09/2016] [Indexed: 12/28/2022] Open
Abstract
Aberrant miRNA expression has been reported in endometriosis and miRNA gene polymorphisms have been linked to cancer. Because certain ovarian cancers arise from endometriosis, we genotyped seven cancer-related miRNA single nucleotide polymorphisms (MiRSNPs) to investigate their possible roles in endometriosis. Genetic variants in MIR196A2 (rs11614913) and MIR100 (rs1834306) were found to be associated with endometriosis development and related clinical phenotypes, such as infertility and pain. Downstream analysis of the MIR196A2 risk allele revealed upregulation of rRNA editing and protein synthesis genes, suggesting hyper-activation of ribosome biogenesis as a driving force for endometriosis progression. Clinical studies confirmed higher levels of small nucleolar RNAs and ribosomal proteins in atypical endometriosis lesions, and this was more pronounced in the associated ovarian clear cell carcinomas. Treating ovarian clear cells with CX5461, an RNA polymerase I inhibitor, suppressed cell growth and mobility followed by cell cycle arrest at G2/M stage and apoptosis. Our study thus uncovered a novel tumorigenesis pathway triggered by the cancer-related MIR196A2 risk allele during endometriosis development and progression. We suggest that anti-RNA polymerase I therapy may be efficacious for treating endometriosis and associated malignancies.
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Affiliation(s)
- Cherry Yin-Yi Chang
- Department of Obstetrics and Gynecology, China Medical University Hospital, Taichung, Taiwan.,Institute of Environmental Health, China Medical University, Taichung, Taiwan
| | - Ming-Tsung Lai
- Department of Pathology, Taichung Hospital, Ministry of Health and Welfare, Taichung, Taiwan
| | - Yi Chen
- Human Genetic Center, China Medical University Hospital, Taichung, Taiwan
| | - Ching-Wen Yang
- The Institute of Basic Medical Sciences, National Cheng Kung University, Tainan, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Hui-Wen Chang
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Cheng-Chan Lu
- The Institute of Basic Medical Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Chih-Mei Chen
- Human Genetic Center, China Medical University Hospital, Taichung, Taiwan
| | - Carmen Chan
- Human Genetic Center, China Medical University Hospital, Taichung, Taiwan
| | - Ching Chung
- Human Genetic Center, China Medical University Hospital, Taichung, Taiwan
| | - Chun-Cheng Tseng
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Tritium Hwang
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Jim Jinn-Chyuan Sheu
- Human Genetic Center, China Medical University Hospital, Taichung, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan.,School of Chinese Medicine, China Medical University, Taichung, Taiwan.,Department of Health and Nutrition Biotechnology, Asia University, Taichung, Taiwan
| | - Fuu-Jen Tsai
- Human Genetic Center, China Medical University Hospital, Taichung, Taiwan.,School of Post-Baccalaureate Chinese Medicine, China Medical University, Taichung, Taiwan
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31
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Russo A, Maiolino S, Pagliara V, Ungaro F, Tatangelo F, Leone A, Scalia G, Budillon A, Quaglia F, Russo G. Enhancement of 5-FU sensitivity by the proapoptotic rpL3 gene in p53 null colon cancer cells through combined polymer nanoparticles. Oncotarget 2018; 7:79670-79687. [PMID: 27835895 PMCID: PMC5346744 DOI: 10.18632/oncotarget.13216] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/14/2016] [Indexed: 01/09/2023] Open
Abstract
Colon cancer is one of the leading causes of cancer-related death worldwide and the therapy with 5-fluorouracil (5-FU) is mainly limited due to resistance. Recently, we have demonstrated that nucleolar stress upon 5-FU treatment leads to the activation of ribosome-free rpL3 (L3) as proapoptotic factor. In this study, we analyzed L3 expression profile in colon cancer tissues and demonstrated that L3 mRNA amount decreased with malignant progression and the intensity of its expression was inversely related to tumor grade and Bcl-2/Bax ratio. With the aim to develop a combined therapy of 5-FU plus plasmid encoding L3 (pL3), we firstly assessed the potentiation of the cytotoxic effect of 5-FU on colon cancer cells by L3. Next, 10 μM 5-FU and 2 μg of pL3 were encapsulated in biocompatible nanoparticles (NPs) chemically conjugated with HA to achieve active tumor-targeting ability in CD44 overexpressing cancer cells. We showed the specific intracellular accumulation of NPs in cells and a sustained release for 5-FU and L3. Analysis of cytotoxicity and apoptotic induction potential of combined NPs clearly showed that the 5-FU plus L3 were more effective in inducing apoptosis than 5-FU or L3 alone. Furthermore, we show that the cancer-specific chemosensitizer effect of combined NPs may be dependent on L3 ability to affect 5-FU efflux by controlling P-gp (P-glycoprotein) expression. These results led us to propose a novel combined therapy with the use of 5-FU plus L3 in order to establish individualized therapy by examining L3 profiles in tumors to yield a better clinical outcomes.
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Affiliation(s)
- Annapina Russo
- Laboratory of Biochemistry, Department of Pharmacy, University of Napoli Federico II, 80131 Napoli, Italy
| | - Sara Maiolino
- Laboratory of Drug Delivery, Department of Pharmacy, University of Napoli Federico II, 80131 Napoli, Italy
| | - Valentina Pagliara
- Laboratory of Biochemistry, Department of Pharmacy, University of Napoli Federico II, 80131 Napoli, Italy
| | - Francesca Ungaro
- Laboratory of Drug Delivery, Department of Pharmacy, University of Napoli Federico II, 80131 Napoli, Italy
| | - Fabiana Tatangelo
- Istituto Nazionale Tumori "Fondazione Pascale"-IRCCS, 80131 Napoli, Italy
| | - Alessandra Leone
- Istituto Nazionale Tumori "Fondazione Pascale"-IRCCS, 80131 Napoli, Italy
| | | | - Alfredo Budillon
- Istituto Nazionale Tumori "Fondazione Pascale"-IRCCS, 80131 Napoli, Italy
| | - Fabiana Quaglia
- Laboratory of Drug Delivery, Department of Pharmacy, University of Napoli Federico II, 80131 Napoli, Italy
| | - Giulia Russo
- Laboratory of Biochemistry, Department of Pharmacy, University of Napoli Federico II, 80131 Napoli, Italy
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32
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Wilking-Busch MJ, Ndiaye MA, Liu X, Ahmad N. RNA interference-mediated knockdown of SIRT1 and/or SIRT2 in melanoma: Identification of downstream targets by large-scale proteomics analysis. J Proteomics 2017; 170:99-109. [PMID: 28882678 DOI: 10.1016/j.jprot.2017.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/14/2017] [Accepted: 09/03/2017] [Indexed: 02/07/2023]
Abstract
Melanoma is the most notorious and fatal of all skin cancers and the existing treatment options have not been proven to effectively manage this neoplasm, especially the metastatic disease. Sirtuin (SIRT) proteins have been shown to be differentially expressed in melanoma. We have shown that SIRTs 1 and 2 were overexpressed in melanoma and inhibition of SIRT1 imparts anti-proliferative responses in human melanoma cells. To elucidate the impact of SIRT 1 and/or 2 in melanoma, we created stable knockdowns of SIRTs 1, 2, and their combination using shRNA mediated RNA interference in A375 human melanoma cells. We found that SIRT1 and SIRT1&2 combination knockdown caused a decreased cellular proliferation in melanoma cells. Further, the knockdown of SIRT 1 and/or 2 resulted in a decreased colony formation in melanoma cells. To explore the downstream targets of SIRTs 1 and/or 2, we employed a label-free quantitative nano-LC-MS/MS proteomics analysis using the stable lines. We found aberrant levels of proteins involved in many vital cellular processes, including cytoskeletal organization, ribosomal activity, oxidative stress response, and angiogenesis. These findings provide clear evidence of cellular systems undergoing alterations in response to sirtuin inhibition, and have unveiled several excellent candidates for future study. SIGNIFICANCE Melanoma is the deadliest form of skin cancer, due to its aggressive nature, metastatic potential, and a lack of sufficient treatment options for advanced disease. Therefore, detailed investigations into the molecular mechanisms of melanoma growth and progression are needed. In the search for candidate genes to serve as therapeutic targets, the sirtuins show promise as they have been found to be upregulated in melanoma and they regulate a large number of proteins involved in cellular processes known to affect tumor growth, such as DNA damage repair, cell cycle arrest, and apoptosis. In this study, we used a large-scale label-free comparative proteomics system to identify novel protein targets that are affected following knockdown of SIRT1 and/or 2 in A375 metastatic melanoma cell line. Our study offers important insight into the potential downstream targets of SIRTs 1 and/or 2. This may unravel new potential areas of exploration in melanoma research.
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Affiliation(s)
- Melissa J Wilking-Busch
- Department of Dermatology, University of Wisconsin, 1300 University Avenue, Madison, WI 53706, USA
| | - Mary A Ndiaye
- Department of Dermatology, University of Wisconsin, 1300 University Avenue, Madison, WI 53706, USA
| | - Xiaoqi Liu
- Department of Biochemistry, Purdue University, 175 S. University Street, West Lafayette, IN, USA
| | - Nihal Ahmad
- Department of Dermatology, University of Wisconsin, 1300 University Avenue, Madison, WI 53706, USA; William S. Middleton VA Medical Center, 2500 Overlook Terrace, Madison, WI 53705, USA.
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33
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Qi Y, Li X, Chang C, Xu F, He Q, Zhao Y, Wu L. Ribosomal protein L23 negatively regulates cellular apoptosis via the RPL23/Miz-1/c-Myc circuit in higher-risk myelodysplastic syndrome. Sci Rep 2017; 7:2323. [PMID: 28539603 PMCID: PMC5443795 DOI: 10.1038/s41598-017-02403-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 04/10/2017] [Indexed: 01/30/2023] Open
Abstract
Ribosomal protein (RP) L23 is a negative regulator of cellular apoptosis, and RPL23 overexpression is associated with abnormal apoptotic resistance in CD34+ cells derived from patients with higher-risk myelodysplastic syndrome (MDS). However, the mechanism underlying RPL23-induced apoptotic resistance in higher-risk MDS patients is poorly understood. In this study, we showed that reduced RPL23 expression led to suppressed cellular viability, increased apoptosis and G1-S cell cycle arrest. Gene microarray analysis comparing RPL23-knockdown and control cells identified an array of differentially expressed genes, of which, Miz-1, was upregulated with transactivation of the cell cycle inhibitors p15Ink4b and p21Cip1, and Miz-1’s functional repressor, c-Myc, was downregulated. Cells derived from higher-risk MDS patients demonstrated consistently increased expression of RPL23 and c-Myc and decreased Miz-1 expression compared with cells from lower-risk patients. In conclusion, Miz-1-dependent induction of p15Ink4b and p21Cip1 was depressed with decreased Miz-1 and increased c-Myc expression under conditions of elevated RPL23 expression, leading to apoptotic resistance in higher-risk MDS patients. Because RPL23 is encoded by a target gene of c-Myc, the RPL23/Miz-1/c-Myc regulatory circuit provides a feedback loop that links efficient RPL23 expression with c-Myc’s function to suppress Miz-1-induced Cdk inhibitors and thereby leads to apoptotic resistance in higher-risk MDS patients.
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Affiliation(s)
- Yuekun Qi
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Xiao Li
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Chunkang Chang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Feng Xu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Qi He
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Youshan Zhao
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Lingyun Wu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China.
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34
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Grosheva AS, Zharkov DO, Stahl J, Gopanenko AV, Tupikin AE, Kabilov MR, Graifer DM, Karpova GG. Recognition but no repair of abasic site in single-stranded DNA by human ribosomal uS3 protein residing within intact 40S subunit. Nucleic Acids Res 2017; 45:3833-3843. [PMID: 28334742 PMCID: PMC5397187 DOI: 10.1093/nar/gkx052] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 01/13/2017] [Accepted: 01/19/2017] [Indexed: 01/04/2023] Open
Abstract
Isolated human ribosomal protein uS3 has extra-ribosomal functions including those related to base excision DNA repair, e.g. AP lyase activity that nicks double-stranded (ds) DNA 3΄ to the abasic (AP) site. However, the ability of uS3 residing within ribosome to recognize and cleave damaged DNA has never been addressed. Here, we compare interactions of single-stranded (ss) DNA and dsDNA bearing AP site with human ribosome-bound uS3 and with the isolated protein, whose interactions with ssDNA were not yet studied. The AP lyase activity of free uS3 was much higher with ssDNA than with dsDNA, whereas ribosome-bound uS3 was completely deprived of this activity. Nevertheless, an exposed peptide of ribosome-bound uS3 located far away from the putative catalytic center previously suggested for isolated uS3 cross-linked to full-length uncleaved ssDNA, but not to dsDNA. In contrast, free uS3 cross-linked mainly to the 5΄-part of the damaged DNA strand after its cleavage at the AP site. ChIP-seq analysis showed preferential uS3 binding to nucleolus-associated chromatin domains. We conclude that free and ribosome-bound uS3 proteins interact with AP sites differently, exhibiting their non-translational functions in DNA repair in and around the nucleolus and in regulation of DNA damage response in looped DNA structures, respectively.
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Affiliation(s)
- Anastasia S. Grosheva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
| | - Dmitry O. Zharkov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Joachim Stahl
- Max-Delbrück-Center for Molecular Medicine, D-13092 Berlin, Germany
| | - Alexander V. Gopanenko
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
| | - Dmitri M. Graifer
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Galina G. Karpova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
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35
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Owczarek TB, Kobayashi T, Ramirez R, Rong L, Puzio-Kuter AM, Iyer G, Teo MY, Sánchez-Vega F, Wang J, Schultz N, Zheng T, Solit DB, Al-Ahmadie HA, Abate-Shen C. ARF Confers a Context-Dependent Response to Chemotherapy in Muscle-Invasive Bladder Cancer. Cancer Res 2017; 77:1035-1046. [PMID: 28082400 PMCID: PMC5313321 DOI: 10.1158/0008-5472.can-16-2621] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/12/2016] [Accepted: 12/12/2016] [Indexed: 12/14/2022]
Abstract
Muscle-invasive bladder cancer (MIBC) generally responds poorly to treatment and tends to exhibit significant mortality. Here we show that expression of the tumor suppressor p14ARF (ARF) is upregulated in aggressive subtypes of MIBC. Accumulation of ARF in the nucleolus is associated with poor outcome and attenuated response to chemotherapy. In both genetically engineered mouse models and murine xenograft models of human MIBC, we demonstrate that tumors expressing ARF failed to respond to treatment with the platinum-based chemotherapy agent cisplatin. Resistance was mediated in part by the integrin-binding protein ITGB3BP (CENPR) and reflected ARF-dependent impairment of protein translation, which was exaggerated by drug treatment. Overall, our results highlight a context-dependent role for ARF in modulating the drug response of bladder cancer. Cancer Res; 77(4); 1035-46. ©2017 AACR.
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Affiliation(s)
- Tomasz B Owczarek
- Department of Medicine, Columbia University Medical Center, New York, New York
- Department of Urology, Columbia University Medical Center, New York, New York
| | - Takashi Kobayashi
- Department of Urology, Columbia University Medical Center, New York, New York
| | - Ricardo Ramirez
- Department of Human Oncology and Pathogenesis, Memorial Sloan-Kettering Cancer Center, New York, New York
- Weill Cornell Graduate School, Cornell University, New York, New York
| | - Lijie Rong
- Department of Medicine, Columbia University Medical Center, New York, New York
- Department of Urology, Columbia University Medical Center, New York, New York
| | - Anna M Puzio-Kuter
- Department of Urology, Columbia University Medical Center, New York, New York
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
- Weill Medical College, Cornell University, New York, New York
| | - Min Yuen Teo
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Francisco Sánchez-Vega
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Jingqiang Wang
- Department of Urology, Columbia University Medical Center, New York, New York
| | - Nikolaus Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Tian Zheng
- Department of Statistics, Columbia University, New York, New York
| | - David B Solit
- Department of Human Oncology and Pathogenesis, Memorial Sloan-Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York
- Weill Medical College, Cornell University, New York, New York
| | - Hikmat A Al-Ahmadie
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Cory Abate-Shen
- Department of Medicine, Columbia University Medical Center, New York, New York.
- Department of Urology, Columbia University Medical Center, New York, New York
- Department of Systems Biology, Columbia University Medical Center, New York, New York
- Department of Pathology & Cell Biology, Columbia University Medical Center, New York, New York
- Institute of Cancer Genetics, Columbia University Medical Center, New York, New York
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York
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36
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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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37
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Yadav A, Radhakrishnan A, Panda A, Singh A, Sinha H, Bhanot G. The Modular Adaptive Ribosome. PLoS One 2016; 11:e0166021. [PMID: 27812193 PMCID: PMC5094737 DOI: 10.1371/journal.pone.0166021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/23/2016] [Indexed: 11/18/2022] Open
Abstract
The ribosome is an ancient machine, performing the same function across organisms. Although functionally unitary, recent experiments suggest specialized roles for some ribosomal proteins. Our central thesis is that ribosomal proteins function in a modular fashion to decode genetic information in a context dependent manner. We show through large data analyses that although many ribosomal proteins are essential with consistent effect on growth in different conditions in yeast and similar expression across cell and tissue types in mice and humans, some ribosomal proteins are used in an environment specific manner. The latter set of variable ribosomal proteins further function in a coordinated manner forming modules, which are adapted to different environmental cues in different organisms. We show that these environment specific modules of ribosomal proteins in yeast have differential genetic interactions with other pathways and their 5’UTRs show differential signatures of selection in yeast strains, presumably to facilitate adaptation. Similarly, we show that in higher metazoans such as mice and humans, different modules of ribosomal proteins are expressed in different cell types and tissues. A clear example is nervous tissue that uses a ribosomal protein module distinct from the rest of the tissues in both mice and humans. Our results suggest a novel stratification of ribosomal proteins that could have played a role in adaptation, presumably to optimize translation for adaptation to diverse ecological niches and tissue microenvironments.
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Affiliation(s)
- Anupama Yadav
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Aparna Radhakrishnan
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Anshuman Panda
- Department of Physics, Rutgers University, Piscataway, New Jersey 08854, United States of America
| | - Amartya Singh
- Department of Physics, Rutgers University, Piscataway, New Jersey 08854, United States of America
| | - Himanshu Sinha
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
- Initiative for Biological Systems Engineering, Indian Institute of Technology Madras, Chennai 600036, India
- * E-mail: (HS); (GB)
| | - Gyan Bhanot
- Department of Physics, Rutgers University, Piscataway, New Jersey 08854, United States of America
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, United States of America
- The Cancer Institute of New Jersey, New Brunswick, New Jersey 08903, United States of America
- * E-mail: (HS); (GB)
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38
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Shaikho S, Dobson CC, Naing T, Samanfar B, Moteshareie H, Hajikarimloo M, Golshani A, Holcik M. Elevated levels of ribosomal proteins eL36 and eL42 control expression of Hsp90 in rhabdomyosarcoma. ACTA ACUST UNITED AC 2016; 4:e1244395. [PMID: 28090422 DOI: 10.1080/21690731.2016.1244395] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/13/2016] [Accepted: 09/28/2016] [Indexed: 01/08/2023]
Abstract
Mammalian 90 kDa heat shock protein (Hsp90) is a ubiquitous molecular chaperone whose expression is selectively upregulated during stress, although the precise control mechanism of this increase is yet to be fully elucidated. We used polysome profiling to show that Hsp90α mRNA is selectively translated, while global translation is inhibited during heat stress. Furthermore, we have identified 2 ribosomal proteins, eL36 and eL42 that modulate Hsp90α expression under both normal and heat shock conditions. Importantly, we noted that expression of eL36 and eL42 is elevated in a panel of human rhabdomyosarcomas where it drives high expression of Hsp90 and modulates sensitivity of these cells to an Hsp90 inhibitor 17-AAG.
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Affiliation(s)
- Sarah Shaikho
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute , Ottawa, Ontario, Canada
| | - Christine C Dobson
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute , Ottawa, Ontario, Canada
| | - Thet Naing
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute , Ottawa, Ontario, Canada
| | - Bahram Samanfar
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University , Ottawa, Ontario, Canada
| | - Houman Moteshareie
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University , Ottawa, Ontario, Canada
| | - Maryam Hajikarimloo
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University , Ottawa, Ontario, Canada
| | - Ashkan Golshani
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University , Ottawa, Ontario, Canada
| | - Martin Holcik
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute , Ottawa, Ontario, Canada
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39
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Fast MS/MS acquisition without dynamic exclusion enables precise and accurate quantification of proteome by MS/MS fragment intensity. Sci Rep 2016; 6:26392. [PMID: 27198003 PMCID: PMC4873735 DOI: 10.1038/srep26392] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/28/2016] [Indexed: 12/25/2022] Open
Abstract
Most currently proteomic studies use data-dependent acquisition with dynamic exclusion to identify and quantify the peptides generated by the digestion of biological sample. Although dynamic exclusion permits more identifications and higher possibility to find low abundant proteins, stochastic and irreproducible precursor ion selection caused by dynamic exclusion limit the quantification capabilities, especially for MS/MS based quantification. This is because a peptide is usually triggered for fragmentation only once due to dynamic exclusion. Therefore the fragment ions used for quantification only reflect the peptide abundances at that given time point. Here, we propose a strategy of fast MS/MS acquisition without dynamic exclusion to enable precise and accurate quantification of proteome by MS/MS fragment intensity. The results showed comparable proteome identification efficiency compared to the traditional data-dependent acquisition with dynamic exclusion, better quantitative accuracy and reproducibility regardless of label-free based quantification or isobaric labeling based quantification. It provides us with new insights to fully explore the potential of modern mass spectrometers. This strategy was applied to the relative quantification of two human disease cell lines, showing great promises for quantitative proteomic applications.
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40
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Shen CL, Liu CD, You RI, Ching YH, Liang J, Ke L, Chen YL, Chen HC, Hsu HJ, Liou JW, Kieff E, Peng CW. Ribosome Protein L4 is essential for Epstein-Barr Virus Nuclear Antigen 1 function. Proc Natl Acad Sci U S A 2016; 113:2229-34. [PMID: 26858444 PMCID: PMC4776490 DOI: 10.1073/pnas.1525444113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Epstein-Barr Virus (EBV) Nuclear Antigen 1 (EBNA1)-mediated origin of plasmid replication (oriP) DNA episome maintenance is essential for EBV-mediated tumorigenesis. We have now found that EBNA1 binds to Ribosome Protein L4 (RPL4). RPL4 shRNA knockdown decreased EBNA1 activation of an oriP luciferase reporter, EBNA1 DNA binding in lymphoblastoid cell lines, and EBV genome number per lymphoblastoid cell line. EBV infection increased RPL4 expression and redistributed RPL4 to cell nuclei. RPL4 and Nucleolin (NCL) were a scaffold for an EBNA1-induced oriP complex. The RPL4 N terminus cooperated with NCL-K429 to support EBNA1 and oriP-mediated episome binding and maintenance, whereas the NCL C-terminal K380 and K393 induced oriP DNA H3K4me2 modification and promoted EBNA1 activation of oriP-dependent transcription. These observations provide new insights into the mechanisms by which EBV uses NCL and RPL4 to establish persistent B-lymphoblastoid cell infection.
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Affiliation(s)
- Chih-Lung Shen
- Institute of Medical Sciences, Tzu Chi University, Hualien 97004, Taiwan
| | - Cheng-Der Liu
- Institute of Medical Sciences, Tzu Chi University, Hualien 97004, Taiwan
| | - Ren-In You
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Sec. 3, Hualien 97004, Taiwan
| | - Yung-Hao Ching
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Sec. 3, Hualien 97004, Taiwan
| | - Jun Liang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Liangru Ke
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Ya-Lin Chen
- Department of Life Sciences, Tzu Chi University, Sec. 3, Hualien 97004, Taiwan
| | - Hong-Chi Chen
- Department of Life Sciences, Tzu Chi University, Sec. 3, Hualien 97004, Taiwan
| | - Hao-Jen Hsu
- Department of Life Sciences, Tzu Chi University, Sec. 3, Hualien 97004, Taiwan
| | - Je-Wen Liou
- Institute of Biochemical Sciences, Tzu Chi University, Sec. 3, Hualien 97004, Taiwan
| | - Elliott Kieff
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115;
| | - Chih-Wen Peng
- Institute of Medical Sciences, Tzu Chi University, Hualien 97004, Taiwan; Department of Life Sciences, Tzu Chi University, Sec. 3, Hualien 97004, Taiwan;
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41
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Goudarzi KM, Lindström MS. Role of ribosomal protein mutations in tumor development (Review). Int J Oncol 2016; 48:1313-24. [PMID: 26892688 PMCID: PMC4777597 DOI: 10.3892/ijo.2016.3387] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/07/2016] [Indexed: 12/16/2022] Open
Abstract
Ribosomes are cellular machines essential for protein synthesis. The biogenesis of ribosomes is a highly complex and energy consuming process that initiates in the nucleolus. Recently, a series of studies applying whole-exome or whole-genome sequencing techniques have led to the discovery of ribosomal protein gene mutations in different cancer types. Mutations in ribosomal protein genes have for example been found in endometrial cancer (RPL22), T-cell acute lymphoblastic leukemia (RPL10, RPL5 and RPL11), chronic lymphocytic leukemia (RPS15), colorectal cancer (RPS20), and glioma (RPL5). Moreover, patients suffering from Diamond-Blackfan anemia, a bone marrow failure syndrome caused by mutant ribosomal proteins are also at higher risk for developing leukemia, or solid tumors. Different experimental models indicate potential mechanisms whereby ribosomal proteins may initiate cancer development. In particular, deregulation of the p53 tumor suppressor network and altered mRNA translation are mechanisms likely to be involved. We envisage that changes in expression and the occurrence of ribosomal protein gene mutations play important roles in cancer development. Ribosome biology constitutes a re-emerging vital area of basic and translational cancer research.
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Affiliation(s)
- Kaveh M Goudarzi
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, CCK R8:05, Karolinska University Hospital in Solna, Stockholm, Sweden
| | - Mikael S Lindström
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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42
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Stabilization of SIRT7 deacetylase by viral oncoprotein HBx leads to inhibition of growth restrictive RPS7 gene and facilitates cellular transformation. Sci Rep 2015; 5:14806. [PMID: 26442981 PMCID: PMC4595800 DOI: 10.1038/srep14806] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 09/09/2015] [Indexed: 02/06/2023] Open
Abstract
Sirtuin-7 (SIRT7) deacetylase exhibits a high selectivity for acetylated H3K18 and has been implicated in the maintenance of malignant phenotype. However, it remains unclear if SIRT7 and H3K18ac play a role in the tumorigenic program driven by oncogenic viruses. We show that ectopically expressed HBx oncoprotein of hepatitis B virus promoted intracellular stability of SIRT7 by salvaging it from ubiquitin-mediated proteasomal degradation. HBx-dependent accumulation of SIRT7 favored H3K18 deacetylation and down-regulated the small ribosomal protein gene, RPS7, involved in cell death and DNA damage response. HBx facilitated the recruitment of SIRT7 to RPS7 promoter thus impeding H3K18ac occupancy and hindering RPS7 transcription. The antagonistic relationship between SIRT7 and RPS7 was also observed in the HBx transgenic mice, where elevated levels of SIRT7 protein were coincident with low levels of H3K18ac and RPS7. Strikingly, inhibition of cellular deubiquitinase activity restored RPS7 gene transcription. Further, depletion of endogenous SIRT7 led to decreased cell viability and transformation. The biological relevance of RPS7 suppression by HBx-SIRT7 axis was evident from ectopic expression of RPS7 which attenuated clonogenicity of cells. Thus, our findings suggest that SIRT7 is a critical regulator of HBx-driven oncogenic program, through its antagonistic impact on growth restrictive ribosomal protein RPS7.
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43
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Zhou X, Liao WJ, Liao JM, Liao P, Lu H. Ribosomal proteins: functions beyond the ribosome. J Mol Cell Biol 2015; 7:92-104. [PMID: 25735597 DOI: 10.1093/jmcb/mjv014] [Citation(s) in RCA: 427] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 12/05/2014] [Indexed: 01/05/2023] Open
Abstract
Although ribosomal proteins are known for playing an essential role in ribosome assembly and protein translation, their ribosome-independent functions have also been greatly appreciated. Over the past decade, more than a dozen of ribosomal proteins have been found to activate the tumor suppressor p53 pathway in response to ribosomal stress. In addition, these ribosomal proteins are involved in various physiological and pathological processes. This review is composed to overview the current understanding of how ribosomal stress provokes the accumulation of ribosome-free ribosomal proteins, as well as the ribosome-independent functions of ribosomal proteins in tumorigenesis, immune signaling, and development. We also propose the potential of applying these pieces of knowledge to the development of ribosomal stress-based cancer therapeutics.
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Affiliation(s)
- Xiang Zhou
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Wen-Juan Liao
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jun-Ming Liao
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Peng Liao
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Hua Lu
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
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44
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Perucho L, Artero-Castro A, Guerrero S, Ramón y Cajal S, LLeonart ME, Wang ZQ. RPLP1, a crucial ribosomal protein for embryonic development of the nervous system. PLoS One 2014; 9:e99956. [PMID: 24959908 PMCID: PMC4069005 DOI: 10.1371/journal.pone.0099956] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 05/20/2014] [Indexed: 12/22/2022] Open
Abstract
Ribosomal proteins are pivotal to development and tissue homeostasis. RP Large P1 (Rplp1) overexpression is associated with tumorigenesis. However, the physiological function of Rplp1 in mammalian development remains unknown. In this study, we disrupted Rplp1 in the mouse germline and central nervous system (Rplp1CNSΔ). Rplp1 heterozygosity caused body size reductions, male infertility, systemic abnormalities in various tissues and a high frequency of early postnatal death. Rplp1CNSΔ</emph> newborn mice exhibited perinatal lethality and brain atrophy with size reductions of the neocortex, midbrain and ganglionic eminence. The Rplp1 knockout neocortex exhibited progenitor cell proliferation arrest and apoptosis due to the dysregulation of key cell cycle and apoptosis regulators (cyclin A, cyclin E, p21CIP1, p27KIP1, p53). Similarly, Rplp1 deletion in pMEFs led to proliferation arrest and premature senescence. Importantly, Rplp1 deletion in primary mouse embryonic fibroblasts did not alter global protein synthesis, but did change the expression patterns of specific protein subsets involved in protein folding and the unfolded protein response, cell death, protein transport and signal transduction, among others. Altogether, we demonstrated that the translation “fine-tuning” exerted by Rplp1 is essential for embryonic and brain development and for proper cell proliferation.
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Affiliation(s)
- Laura Perucho
- Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Ana Artero-Castro
- Oncology and Pathology Group, Institut de Recerca Hospital Vall d'Hebron, Barcelona, Spain
| | - Sergi Guerrero
- Oncology and Pathology Group, Institut de Recerca Hospital Vall d'Hebron, Barcelona, Spain
| | - Santiago Ramón y Cajal
- Oncology and Pathology Group, Institut de Recerca Hospital Vall d'Hebron, Barcelona, Spain
| | - Matilde E. LLeonart
- Oncology and Pathology Group, Institut de Recerca Hospital Vall d'Hebron, Barcelona, Spain
- * E-mail:
| | - Zhao-Qi Wang
- Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Jena, Germany
- Faculty of Biology and Pharmacy, Friedrich Schiller University of Jena, Jena, Germany
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