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Xu AF, Molinuevo R, Fazzari E, Tom H, Zhang Z, Menendez J, Casey KM, Ruggero D, Hinck L, Pritchard JK, Barna M. Subfunctionalized expression drives evolutionary retention of ribosomal protein paralogs Rps27 and Rps27l in vertebrates. eLife 2023; 12:e78695. [PMID: 37306301 PMCID: PMC10313321 DOI: 10.7554/elife.78695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/09/2023] [Indexed: 06/13/2023] Open
Abstract
The formation of paralogs through gene duplication is a core evolutionary process. For paralogs that encode components of protein complexes such as the ribosome, a central question is whether they encode functionally distinct proteins or whether they exist to maintain appropriate total expression of equivalent proteins. Here, we systematically tested evolutionary models of paralog function using the ribosomal protein paralogs Rps27 (eS27) and Rps27l (eS27L) as a case study. Evolutionary analysis suggests that Rps27 and Rps27l likely arose during whole-genome duplication(s) in a common vertebrate ancestor. We show that Rps27 and Rps27l have inversely correlated mRNA abundance across mouse cell types, with the highest Rps27 in lymphocytes and the highest Rps27l in mammary alveolar cells and hepatocytes. By endogenously tagging the Rps27 and Rps27l proteins, we demonstrate that Rps27- and Rps27l-ribosomes associate preferentially with different transcripts. Furthermore, murine Rps27 and Rps27l loss-of-function alleles are homozygous lethal at different developmental stages. However, strikingly, expressing Rps27 protein from the endogenous Rps27l locus or vice versa completely rescues loss-of-function lethality and yields mice with no detectable deficits. Together, these findings suggest that Rps27 and Rps27l are evolutionarily retained because their subfunctionalized expression patterns render both genes necessary to achieve the requisite total expression of two equivalent proteins across cell types. Our work represents the most in-depth characterization of a mammalian ribosomal protein paralog to date and highlights the importance of considering both protein function and expression when investigating paralogs.
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Affiliation(s)
- Adele Francis Xu
- Department of Genetics, Stanford UniversityStanfordUnited States
- Medical Scientist Training Program, Stanford School of MedicineStanfordUnited States
| | - Rut Molinuevo
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | - Elisa Fazzari
- Helen Diller Family Comprehensive Cancer Center, University of California, Los AngelesLos AngelesUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Department of Urology, University of California, San FranciscoSan FranciscoUnited States
| | - Harrison Tom
- Helen Diller Family Comprehensive Cancer Center, University of California, Los AngelesLos AngelesUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Department of Urology, University of California, San FranciscoSan FranciscoUnited States
| | - Zijian Zhang
- Department of Chemical and Systems Biology, Stanford UniversityStanfordUnited States
| | - Julien Menendez
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | - Kerriann M Casey
- Department of Biology, Stanford UniversityStanfordUnited States
- Department of Comparative Medicine, Stanford School of MedicineStanfordUnited States
| | - Davide Ruggero
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Department of Urology, University of California, San FranciscoSan FranciscoUnited States
| | - Lindsay Hinck
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | | | - Maria Barna
- Department of Genetics, Stanford UniversityStanfordUnited States
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2
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Cook J, Greene ES, Ramser A, Mullenix G, Dridi JS, Liyanage R, Wideman R, Dridi S. Comparative- and network-based proteomic analysis of bacterial chondronecrosis with osteomyelitis lesions in broiler's proximal tibiae identifies new molecular signatures of lameness. Sci Rep 2023; 13:5947. [PMID: 37045932 PMCID: PMC10097873 DOI: 10.1038/s41598-023-33060-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 04/06/2023] [Indexed: 04/14/2023] Open
Abstract
Bacterial Chondronecrosis with Osteomyelitis (BCO) is a specific cause of lameness in commercial fast-growing broiler (meat-type) chickens and represents significant economic, health, and wellbeing burdens. However, the molecular mechanisms underlying the pathogenesis remain poorly understood. This study represents the first comprehensive characterization of the proximal tibia proteome from healthy and BCO chickens. Among a total of 547 proteins identified, 222 were differentially expressed (DE) with 158 up- and 64 down-regulated proteins in tibia of BCO vs. normal chickens. Biological function analysis using Ingenuity Pathways showed that the DE proteins were associated with a variety of diseases including cell death, organismal injury, skeletal and muscular disorder, immunological and inflammatory diseases. Canonical pathway and protein-protein interaction network analysis indicated that these DE proteins were involved in stress response, unfolded protein response, ribosomal protein dysfunction, and actin cytoskeleton signaling. Further, we identified proteins involved in bone resorption (osteoclast-stimulating factor 1, OSFT1) and bone structural integrity (collagen alpha-2 (I) chain, COL2A1), as potential key proteins involved in bone attrition. These results provide new insights by identifying key protein candidates involved in BCO and will have significant impact in understanding BCO pathogenesis.
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Affiliation(s)
- Jennifer Cook
- Department of Poultry Science, University of Arkansas, 1260 W. Maple Street, Fayetteville, AR, 72701, USA
| | - Elizabeth S Greene
- Department of Poultry Science, University of Arkansas, 1260 W. Maple Street, Fayetteville, AR, 72701, USA
| | - Alison Ramser
- Department of Poultry Science, University of Arkansas, 1260 W. Maple Street, Fayetteville, AR, 72701, USA
| | - Garrett Mullenix
- Department of Poultry Science, University of Arkansas, 1260 W. Maple Street, Fayetteville, AR, 72701, USA
| | - Jalila S Dridi
- École Universitaire de Kinésithérapie, Université d'Orléans, Rue de Chartres, 45100, Orléans, France
| | - Rohana Liyanage
- Department of Poultry Science, University of Arkansas, 1260 W. Maple Street, Fayetteville, AR, 72701, USA
| | - Robert Wideman
- Department of Poultry Science, University of Arkansas, 1260 W. Maple Street, Fayetteville, AR, 72701, USA
| | - Sami Dridi
- Department of Poultry Science, University of Arkansas, 1260 W. Maple Street, Fayetteville, AR, 72701, USA.
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3
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Yang IP, Yip KL, Chang YT, Chen YC, Huang CW, Tsai HL, Yeh YS, Wang JY. MicroRNAs as Predictive Biomarkers in Patients with Colorectal Cancer Receiving Chemotherapy or Chemoradiotherapy: A Narrative Literature Review. Cancers (Basel) 2023; 15:cancers15051358. [PMID: 36900159 PMCID: PMC10000071 DOI: 10.3390/cancers15051358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/12/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies and is associated with high mortality rates worldwide. The underlying mechanism of tumorigenesis in CRC is complex, involving genetic, lifestyle-related, and environmental factors. Although radical resection with adjuvant FOLFOX (5-fluorouracil, leucovorin, and oxaliplatin) chemotherapy and neoadjuvant chemoradiotherapy have remained mainstays of treatment for patients with stage III CRC and locally advanced rectal cancer, respectively, the oncological outcomes of these treatments are often unsatisfactory. To improve patients' chances of survival, researchers are actively searching for new biomarkers to facilitate the development of more effective treatment strategies for CRC and metastatic CRC (mCRC). MicroRNAs (miRs), small, single-stranded, noncoding RNAs, can post-transcriptionally regulate mRNA translation and trigger mRNA degradation. Recent studies have documented aberrant miR levels in patients with CRC or mCRC, and some miRs are reportedly associated with chemoresistance or radioresistance in CRC. Herein, we present a narrative review of the literature on the roles of oncogenic miRs (oncomiRs) and tumor suppressor miRs (anti-oncomiRs), some of which can be used to predict the responses of patients with CRC to chemotherapy or chemoradiotherapy. Moreover, miRs may serve as potential therapeutic targets because their functions can be manipulated using synthetic antagonists and miR mimics.
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Affiliation(s)
- I-Ping Yang
- Department of Nursing, Shu-Zen College of Medicine and Management, Kaohsiung 82144, Taiwan
| | - Kwan-Ling Yip
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yu-Tang Chang
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Division of Pediatric Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yen-Cheng Chen
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Ching-Wen Huang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Hsiang-Lin Tsai
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yung-Sung Yeh
- Division of Trauma and Surgical Critical Care, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Emergency Medicine, Faculty of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Graduate Institute of Injury Prevention and Control, College of Public Health, Taipei Medical University, Taipei 11031, Taiwan
| | - Jaw-Yuan Wang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Pingtung Hospital, Ministry of Health and Welfare, Pingtung 90054, Taiwan
- Correspondence:
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4
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Yi Y, Zeng Y, Sam TW, Hamashima K, Tan RJR, Warrier T, Phua JX, Taneja R, Liou YC, Li H, Xu J, Loh YH. Ribosomal proteins regulate 2-cell-stage transcriptome in mouse embryonic stem cells. Stem Cell Reports 2023; 18:463-474. [PMID: 36638791 PMCID: PMC9968990 DOI: 10.1016/j.stemcr.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 01/14/2023] Open
Abstract
A rare sub-population of mouse embryonic stem cells (mESCs), the 2-cell-like cell, is defined by the expression of MERVL and 2-cell-stage-specific transcript (2C transcript). Here, we report that the ribosomal proteins (RPs) RPL14, RPL18, and RPL23 maintain the identity of mESCs and regulate the expression of 2C transcripts. Disregulation of the RPs induces DUX-dependent expression of 2C transcripts and alters the chromatin landscape. Mechanically, knockdown (KD) of RPs triggers the binding of RPL11 to MDM2, an interaction known to prevent P53 protein degradation. Increased P53 protein upon RP KD further activates its downstream pathways, including DUX. Our study delineates the critical roles of RPs in 2C transcript activation, ascribing a novel function to these essential proteins.
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Affiliation(s)
- Yao Yi
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Yingying Zeng
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Tsz Wing Sam
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Department of Physiology, Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Kiyofumi Hamashima
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Rachel Jun Rou Tan
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Tushar Warrier
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Jun Xiang Phua
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Reshma Taneja
- Department of Physiology, Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Yih-Cherng Liou
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Xu
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore; Joint Center for Single Cell Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Yuin-Han Loh
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; NUS Graduate School for Integrative Sciences and Engineering Programme, National University of Singapore, Singapore 119077, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore.
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5
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Archaea/eukaryote-specific ribosomal proteins - guardians of a complex structure. Comput Struct Biotechnol J 2023; 21:1249-1261. [PMID: 36817958 PMCID: PMC9932298 DOI: 10.1016/j.csbj.2023.01.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/09/2023] [Accepted: 01/26/2023] [Indexed: 01/29/2023] Open
Abstract
In three domains of life, proteins are synthesized by large ribonucleoprotein particles called ribosomes. All ribosomes are composed of ribosomal RNAs (rRNA) and numerous ribosomal proteins (r-protein). The three-dimensional shape of ribosomes is mainly defined by a tertiary structure of rRNAs. In addition, rRNAs have a major role in decoding the information carried by messenger RNAs and catalyzing the peptide bond formation. R-proteins are essential for shaping the network of interactions that contribute to a various aspects of the protein synthesis machinery, including assembly of ribosomes and interaction of ribosomal subunits. Structural studies have revealed that many key components of ribosomes are conserved in all life domains. Besides the core structure, ribosomes contain domain-specific structural features that include additional r-proteins and extensions of rRNA and r-proteins. This review focuses specifically on those r-proteins that are found only in archaeal and eukaryotic ribosomes. The role of these archaea/eukaryote specific r-proteins in stabilizing the ribosome structure is discussed. Several examples illustrate their functions in the formation of the internal network of ribosomal subunits and interactions between the ribosomal subunits. In addition, the significance of these r-proteins in ribosome biogenesis and protein synthesis is highlighted.
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6
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Hoellerbauer P, Biery MC, Arora S, Rao Y, Girard EJ, Mitchell K, Dighe P, Kufeld M, Kuppers DA, Herman JA, Holland EC, Soroceanu L, Vitanza NA, Olson JM, Pritchard JR, Paddison PJ. Functional genomic analysis of adult and pediatric brain tumor isolates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522885. [PMID: 36711964 PMCID: PMC9881972 DOI: 10.1101/2023.01.05.522885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Background Adult and pediatric tumors display stark differences in their mutation spectra and chromosome alterations. Here, we attempted to identify common and unique gene dependencies and their associated biomarkers among adult and pediatric tumor isolates using functional genetic lethal screens and computational modeling. Methods We performed CRISRP-Cas9 lethality screens in two adult glioblastoma (GBM) tumor isolates and five pediatric brain tumor isolates representing atypical teratoid rhabdoid tumors (ATRT), diffuse intrinsic pontine glioma, GBM, and medulloblastoma. We then integrated the screen results with machine learning-based gene-dependency models generated from data from >900 cancer cell lines. Results We found that >50% of candidate dependencies of 280 identified were shared between adult GBM tumors and individual pediatric tumor isolates. 68% of screen hits were found as nodes in our network models, along with shared and tumor-specific predictors of gene dependencies. We investigated network predictors associated with ADAR, EFR3A, FGFR1 (pediatric-specific), and SMARCC2 (ATRT-specific) gene dependency among our tumor isolates. Conclusions The results suggest that, despite harboring disparate genomic signatures, adult and pediatric tumor isolates share a preponderance of genetic dependences. Further, combining data from primary brain tumor lethality screens with large cancer cell line datasets produced valuable insights into biomarkers of gene dependency, even for rare cancers. Importance of the Study Our results demonstrate that large cancer cell lines data sets can be computationally mined to identify known and novel gene dependency relationships in adult and pediatric human brain tumor isolates. Gene dependency networks and lethality screen results represent a key resource for neuro-oncology and cancer research communities. We also highlight some of the challenges and limitations of this approach.
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Affiliation(s)
- Pia Hoellerbauer
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA USA
| | - Matt C Biery
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Yiyun Rao
- Huck Institute for the Life Sciences, Pennsylvania State University, State College, PA, USA
| | - Emily J Girard
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Kelly Mitchell
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Pratiksha Dighe
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA
| | - Megan Kufeld
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Daniel A Kuppers
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Jacob A Herman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Liliana Soroceanu
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA
| | - Nicholas A Vitanza
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Justin R Pritchard
- Huck Institute for the Life Sciences, Pennsylvania State University, State College, PA, USA
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA USA
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7
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Sakthivel D, Brown-Suedel A, Bouchier-Hayes L. The role of the nucleolus in regulating the cell cycle and the DNA damage response. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:203-241. [PMID: 37061332 DOI: 10.1016/bs.apcsb.2023.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The nucleolus has long been perceived as the site for ribosome biogenesis, but numerous studies suggest that the nucleolus carefully sequesters crucial proteins involved in multiple cellular functions. Among these, the role of nucleolus in cell cycle regulation is the most evident. The nucleolus is the first responder of growth-related signals to mediate normal cell cycle progression. The nucleolus also senses different cellular stress insults by activating diverse pathways that arrest the cell cycle, promote DNA repair, or initiate apoptosis. Here, we review the emerging concepts on how the ribosomal and nonribosomal nucleolar proteins mediate such cellular effects.
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8
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Kiron V, Kathiresan P, Fernandes JM, Sørensen M, Vasanth GK, Qingsong L, Lin Q, Kwang LT, Dahle D, Dias J, Trichet VV. Clues from the intestinal mucus proteome of Atlantic salmon to counter inflammation. J Proteomics 2022; 255:104487. [DOI: 10.1016/j.jprot.2022.104487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 10/19/2022]
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9
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Cui D, Qu R, Liu D, Xiong X, Liang T, Zhao Y. The Cross Talk Between p53 and mTOR Pathways in Response to Physiological and Genotoxic Stresses. Front Cell Dev Biol 2021; 9:775507. [PMID: 34869377 PMCID: PMC8638743 DOI: 10.3389/fcell.2021.775507] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/03/2021] [Indexed: 12/25/2022] Open
Abstract
The tumor suppressor p53 is activated upon multiple cellular stresses, including DNA damage, oncogene activation, ribosomal stress, and hypoxia, to induce cell cycle arrest, apoptosis, and senescence. Mammalian target of rapamycin (mTOR), an evolutionarily conserved serine/threonine protein kinase, serves as a central regulator of cell growth, proliferation, and survival by coordinating nutrients, energy, growth factors, and oxygen levels. p53 dysfunction and mTOR pathway hyperactivation are hallmarks of human cancer. The balance between response to stresses or commitment to cell proliferation and survival is governed by various regulatory loops between the p53 and mTOR pathways. In this review, we first briefly introduce the tumor suppressor p53 and then describe the upstream regulators and downstream effectors of the mTOR pathway. Next, we discuss the role of p53 in regulating the mTOR pathway through its transcriptional and non-transcriptional effects. We further describe the complicated role of the mTOR pathway in modulating p53 activity. Finally, we discuss the current knowledge and future perspectives on the coordinated regulation of the p53 and mTOR pathways.
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Affiliation(s)
- Danrui Cui
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
| | - Ruirui Qu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Dian Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiufang Xiong
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
| | - Yongchao Zhao
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
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10
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Chandra PK, Cikic S, Baddoo MC, Rutkai I, Guidry JJ, Flemington EK, Katakam PV, Busija DW. Transcriptome analysis reveals sexual disparities in gene expression in rat brain microvessels. J Cereb Blood Flow Metab 2021; 41:2311-2328. [PMID: 33715494 PMCID: PMC8392780 DOI: 10.1177/0271678x21999553] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sex is an important determinant of brain microvessels (MVs) function and susceptibility to cerebrovascular and neurological diseases, but underlying mechanisms are unclear. Using high throughput RNA sequencing analysis, we examined differentially expressed (DE) genes in brain MVs from young, male, and female rats. Bioinformatics analysis of the 23,786 identified genes indicates that 298 (1.2%) genes were DE using False Discovery Rate criteria (FDR; p < 0.05), of which 119 (40%) and 179 (60%) genes were abundantly expressed in male and female MVs, respectively. Nucleic acid binding, enzyme modulator, and transcription factor were the top three DE genes, which were more highly expressed in male than female MVs. Synthesis of glycosylphosphatidylinositol (GPI), biosynthesis of GPI-anchored proteins, steroid and cholesterol synthesis, were the top three significantly enriched canonical pathways in male MVs. In contrast, respiratory chain, ribosome, and 3 ́-UTR-mediated translational regulation were the top three enriched canonical pathways in female MVs. Different gene functions of MVs were validated by proteomic analysis and western blotting. Our novel findings reveal major sex disparities in gene expression and canonical pathways of MVs and these differences provide a foundation to study the underlying mechanisms and consequences of sex-dependent differences in cerebrovascular and other neurological diseases.
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Affiliation(s)
- Partha K Chandra
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Sinisa Cikic
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Melody C Baddoo
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, USA.,Department of Pathology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Ibolya Rutkai
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA.,Department of Pathology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Jessie J Guidry
- Tulane Brain Institute, Tulane University, New Orleans, LA, USA
| | - Erik K Flemington
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, USA.,Department of Pathology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Prasad Vg Katakam
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA.,Department of Pathology, Tulane University School of Medicine, New Orleans, LA, USA
| | - David W Busija
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA.,Department of Pathology, Tulane University School of Medicine, New Orleans, LA, USA
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11
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Serin N, Dihazi GH, Tayyeb A, Lenz C, Müller GA, Zeisberg M, Dihazi H. Calreticulin Deficiency Disturbs Ribosome Biogenesis and Results in Retardation in Embryonic Kidney Development. Int J Mol Sci 2021; 22:ijms22115858. [PMID: 34070742 PMCID: PMC8198291 DOI: 10.3390/ijms22115858] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 11/27/2022] Open
Abstract
Nephrogenesis is driven by complex signaling pathways that control cell growth and differentiation. The endoplasmic reticulum chaperone calreticulin (Calr) is well known for its function in calcium storage and in the folding of glycoproteins. Its role in kidney development is still not understood. We provide evidence for a pivotal role of Calr in nephrogenesis in this investigation. We show that Calr deficiency results in the disrupted formation of an intact nephrogenic zone and in retardation of nephrogenesis, as evidenced by the disturbance in the formation of comma-shaped and s-shaped bodies. Using proteomics and transcriptomics approaches, we demonstrated that in addition to an alteration in Wnt-signaling key proteins, embryonic kidneys from Calr−/− showed an overall impairment in expression of ribosomal proteins which reveals disturbances in protein synthesis and nephrogenesis. CRISPR/cas9 mediated knockout confirmed that Calr deficiency is associated with a deficiency of several ribosomal proteins and key proteins in ribosome biogenesis. Our data highlights a direct link between Calr expression and the ribosome biogenesis.
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Affiliation(s)
- Nazli Serin
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany; (N.S.); (G.A.M.); (M.Z.)
- Department of Hematology and Oncology, University of Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | - Gry H. Dihazi
- Institute of Clinical Chemistry/UMG-Laboratories, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany; (G.H.D.); (C.L.)
| | - Asima Tayyeb
- School of Biological Sciences, University of the Punjab, Lahore 54590, Pakistan;
| | - Christof Lenz
- Institute of Clinical Chemistry/UMG-Laboratories, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany; (G.H.D.); (C.L.)
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Gerhard A. Müller
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany; (N.S.); (G.A.M.); (M.Z.)
| | - Michael Zeisberg
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany; (N.S.); (G.A.M.); (M.Z.)
| | - Hassan Dihazi
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany; (N.S.); (G.A.M.); (M.Z.)
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075 Göttingen, Germany
- Correspondence: ; Tel.: +49-551-39-60350; Fax: +49-551-39-60351
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12
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Cui D, Dai X, Gong L, Chen X, Wang L, Xiong X, Zhao Y. DEPTOR is a direct p53 target that suppresses cell growth and chemosensitivity. Cell Death Dis 2020; 11:976. [PMID: 33184290 PMCID: PMC7661726 DOI: 10.1038/s41419-020-03185-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022]
Abstract
DEP-domain containing mTOR-interacting protein (DEPTOR), a natural mTOR inhibitor, has essential roles in several processes, including cell growth, metabolism, apoptosis, and immunity. DEPTOR expression has been shown to be diversely controlled at transcriptional levels in cell- and context-specific manners. However, whether there is a general mechanism for the regulation of DEPTOR expression remains largely unknown. Here, we report that DEPTOR is a downstream target of the tumor suppressor, p53, whose activity is positively correlated with DEPTOR expression both in vitro in cell cultures and in vivo in mouse tissues. Mechanistically, p53 directly binds to the DEPTOR promoter and transactivates its expression. Depletion of the p53-binding site on the DEPTOR promoter by CRISPR-Cas9 technology decreases DEPTOR expression and promotes cell proliferation and survival by activating AKT signaling. Importantly, inhibition of AKT by small molecular inhibitors or genetic knockdown abrogates the induction of cell growth and survival induced by deletion of the p53-binding region on the DEPTOR promoter. Furthermore, p53, upon activation by the genotoxic agent doxorubicin, induces DEPTOR expression, leading to cancer cell resistance to doxorubicin. Together, DEPTOR is a direct p53 downstream target and contributes to p53-mediated inhibition of cell proliferation, survival, and chemosensitivity.
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Affiliation(s)
- Danrui Cui
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoqing Dai
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Longyuan Gong
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoyu Chen
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Linchen Wang
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiufang Xiong
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yongchao Zhao
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China.
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13
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Sun S, He H, Ma Y, Xu J, Chen G, Sun Y, Xiong X. Inactivation of ribosomal protein S27-like impairs DNA interstrand cross-link repair by destabilization of FANCD2 and FANCI. Cell Death Dis 2020; 11:852. [PMID: 33051438 PMCID: PMC7555897 DOI: 10.1038/s41419-020-03082-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 12/16/2022]
Abstract
Ribosomal protein S27-like (RPS27L), an evolutionarily conserved ribosomal protein and a direct p53 target, plays an important role in maintenance of genome integrity. We have previously reported that RPS27L regulates radiation sensitivity via the MDM2-p53 and MDM2-MRN-ATM axes. Whether and how RPS27L modulates DNA interstrand cross-link (ICL) repair is unknown. Here we identified that RPS27L binds to FANCD2 and FANCI, two Fanconi anemia (FA) proteins functioning in ICL repair pathway. Upon RPS27L knockdown, the levels of FANCD2 and FANCI are reduced due to accelerated degradation via p62-mediated autophagy-lysosome pathway, which is abrogated by chloroquine (CQ) treatment or Beclin 1 knockdown. Biologically, RPS27L knockdown suppresses FANCD2 foci formation and impairs ICL repair upon exposure to ICL-inducing agent mitomycin C (MMC) in lung cancer cells. This effect of MMC sensitization can be partially reversed by CQ treatment. Together, our study shows that RPS27L positively regulates ICL repair by binding with FANCD2 and FANCI to prevent their degradation via autophagy-lysosome system.
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Affiliation(s)
- Siyuan Sun
- Cancer Institute of the Second Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P. R. China
| | - Hengqian He
- Cancer Institute of the Second Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P. R. China
| | - Yuanyuan Ma
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Xu
- Department of Urology, the Second Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing, P. R. China
| | - Guoan Chen
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, P. R. China
| | - Yi Sun
- Cancer Institute of the Second Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P. R. China
| | - Xiufang Xiong
- Cancer Institute of the Second Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P. R. China.
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14
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Xiong X, Cui D, Bi Y, Sun Y, Zhao Y. Neddylation modification of ribosomal protein RPS27L or RPS27 by MDM2 or NEDP1 regulates cancer cell survival. FASEB J 2020; 34:13419-13429. [PMID: 32779270 DOI: 10.1096/fj.202000530rrr] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 11/11/2022]
Abstract
Neddylation plays a distinct role in stabilization of a subset of ribosomal proteins. Whether the family of ribosomal proteins S27 (RPS27 and RPS27-like) is subjected to neddylation regulation with associated biological consequence is totally unknown. Here, we report that both family members are subjected to neddylation by MDM2 E3 ubiquitin ligase, and deneddylation by NEDP1. Blockage of neddylation with MLN4924, a small molecule inhibitor of neddylation-activating enzyme, destabilizes RPS27L and RPS27 by shortening their protein half-lives. Biologically, knockdown of RPS27L and RPS27 sensitizes, whereas ectopic expression of RPS27L and RPS27 desensitizes cancer cells to MLN4924-induced apoptosis. Taken together, our study demonstrates that neddylation stabilizes RPS27L and RPS27 to confer the survival of cancer cells.
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Affiliation(s)
- Xiufang Xiong
- Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, P. R. China
| | - Danrui Cui
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, P. R. China
| | - Yanli Bi
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, P. R. China
| | - Yi Sun
- Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, P. R. China
| | - Yongchao Zhao
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, P. R. China
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15
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Suzuki S, Tsutsumi S, Chen Y, Ozeki C, Okabe A, Kawase T, Aburatani H, Ohki R. Identification and characterization of the binding sequences and target genes of p53 lacking the 1st transactivation domain. Cancer Sci 2020; 111:451-466. [PMID: 31834974 PMCID: PMC7004532 DOI: 10.1111/cas.14279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 02/06/2023] Open
Abstract
The tumor suppressor gene p53 encodes a transcriptional activator that has two transactivation domains (TAD) located in its amino terminus. These two TAD can transactivate genes independently, and at least one TAD is required for p53 transactivation function. The 1st TAD (a.a. 1‐40) is essential for the induction of numerous classical p53 target genes, while the second TAD (a.a. 41‐61) suffices for tumor suppression, although its precise molecular function remains unclear. In this study, we comprehensively identified the sites to which p53 lacking the 1st TAD (Δ1stTAD‐p53) binds, as well as its potential target genes. We found that the binding sequences for Δ1stTAD‐p53 are divergent and include not only the canonical p53 consensus binding sequences but also sequences similar to those recognized by a number of other known transcription factors. We identified and analyzed the functions of three Δ1stTAD‐p53 target genes, PTP4A1, PLK2 and RPS27L. All three genes were induced by both full‐length p53 and Δ1stTAD‐p53, and were dependent on the transactivation activity of the 2nd TAD. We also found that two of these, PTP4A1 and PLK2, are endoplasmic reticulum (ER) stress‐inducible genes. We found that upon ER stress, PTP4A1 suppresses apoptosis while PLK2 induces apoptosis. These results reveal a novel Δ1stTAD‐p53 downstream pathway that is dependent on the transcription activation activity of the 2nd TAD.
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Affiliation(s)
- Shiori Suzuki
- Laboratory of Fundamental Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Shuichi Tsutsumi
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Yu Chen
- Laboratory of Fundamental Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Chikako Ozeki
- Laboratory of Fundamental Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Atsushi Okabe
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.,Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tatsuya Kawase
- Laboratory of Fundamental Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Rieko Ohki
- Laboratory of Fundamental Oncology, National Cancer Center Research Institute, Tokyo, Japan
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16
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Yamaguchi M, Nishida T, Sato Y, Nakai Y, Kashiwakura I. Identification of Radiation-Dose-Dependent Expressive Genes in Individuals Exposed to External Ionizing Radiation. Radiat Res 2020; 193:274-285. [DOI: 10.1667/rr15532.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Masaru Yamaguchi
- Department of Radiation Science, Hirosaki University Graduate School of Health Sciences, Hirosaki, 036-8564, Japan
| | - Teruki Nishida
- Department of Radiation Science, Hirosaki University Graduate School of Health Sciences, Hirosaki, 036-8564, Japan
| | - Yoshiaki Sato
- Department of Radiation Science, Hirosaki University Graduate School of Health Sciences, Hirosaki, 036-8564, Japan
| | - Yuji Nakai
- Institute of Regional Innovation, Section of Food Sciences, Laboratory of Foods, Hirosaki University, Aomori 038-0012, Japan
| | - Ikuo Kashiwakura
- Department of Radiation Science, Hirosaki University Graduate School of Health Sciences, Hirosaki, 036-8564, Japan
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17
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Wang S, Tian J, Wang J, Liu S, Ke L, Shang C, Yang J, Wang L. Identification of the Biomarkers and Pathological Process of Heterotopic Ossification: Weighted Gene Co-Expression Network Analysis. Front Endocrinol (Lausanne) 2020; 11:581768. [PMID: 33391181 PMCID: PMC7774600 DOI: 10.3389/fendo.2020.581768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/12/2020] [Indexed: 12/19/2022] Open
Abstract
Heterotopic ossification (HO) is the formation of abnormal mature lamellar bone in extra-skeletal sites, including soft tissues and joints, which result in high rates of disability. The understanding of the mechanism of HO is insufficient. The aim of this study was to explore biomarkers and pathological processes in HO+ samples. The gene expression profile GSE94683 was downloaded from the Gene Expression Omnibus database. Sixteen samples from nine HO- and seven HO+ subjects were analyzed. After data preprocessing, 3,529 genes were obtained for weighted gene co-expression network analysis. Highly correlated genes were divided into 13 modules. Finally, the cyan and purple modules were selected for further study. Gene ontology functional annotation and Kyoto Encyclopedia of Genes and Genomes pathway enrichment indicated that the cyan module was enriched in a variety of components, including protein binding, membrane, nucleoplasm, cytosol, poly(A) RNA binding, biosynthesis of antibiotics, carbon metabolism, endocytosis, citrate cycle, and metabolic pathways. In addition, the purple module was enriched in cytosol, mitochondrion, protein binding, structural constituent of ribosome, rRNA processing, oxidative phosphorylation, ribosome, and non-alcoholic fatty liver disease. Finally, 10 hub genes in the cyan module [actin related protein 3 (ACTR3), ADP ribosylation factor 4 (ARF4), progesterone receptor membrane component 1 (PGRMC1), ribosomal protein S23 (RPS23), mannose-6-phosphate receptor (M6PR), WD repeat domain 12 (WDR12), synaptosome associated protein 23 (SNAP23), actin related protein 2 (ACTR2), siah E3 ubiquitin protein ligase 1 (SIAH1), and glomulin (GLMN)] and 2 hub genes in the purple module [proteasome 20S subunit alpha 3 (PSMA3) and ribosomal protein S27 like (RPS27L)] were identified. Hub genes were validated through quantitative real-time polymerase chain reaction. In summary, 12 hub genes were identified in two modules that were associated with HO. These hub genes could provide new biomarkers, therapeutic ideas, and targets in HO.
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18
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Ghandhi SA, Shuryak I, Morton SR, Amundson SA, Brenner DJ. New Approaches for Quantitative Reconstruction of Radiation Dose in Human Blood Cells. Sci Rep 2019; 9:18441. [PMID: 31804590 PMCID: PMC6895166 DOI: 10.1038/s41598-019-54967-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/19/2019] [Indexed: 12/22/2022] Open
Abstract
In the event of a nuclear attack or large-scale radiation event, there would be an urgent need for assessing the dose to which hundreds or thousands of individuals were exposed. Biodosimetry approaches are being developed to address this need, including transcriptomics. Studies have identified many genes with potential for biodosimetry, but, to date most have focused on classification of samples by exposure levels, rather than dose reconstruction. We report here a proof-of-principle study applying new methods to select radiation-responsive genes to generate quantitative, rather than categorical, radiation dose reconstructions based on a blood sample. We used a new normalization method to reduce effects of variability of signal intensity in unirradiated samples across studies; developed a quantitative dose-reconstruction method that is generally under-utilized compared to categorical methods; and combined these to determine a gene set as a reconstructor. Our dose-reconstruction biomarker was trained using two data sets and tested on two independent ones. It was able to reconstruct dose up to 4.5 Gy with root mean squared error (RMSE) of ± 0.35 Gy on a test dataset using the same platform, and up to 6.0 Gy with RMSE of ± 1.74 Gy on a test set using a different platform.
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Affiliation(s)
- Shanaz A Ghandhi
- Columbia University Irving Medical Center, 630, W 168th street, VC11-237, New York, NY, 10032, USA.
| | - Igor Shuryak
- Columbia University Irving Medical Center, 630, W 168th street, VC11-237, New York, NY, 10032, USA
| | - Shad R Morton
- Columbia University Irving Medical Center, 630, W 168th street, VC11-237, New York, NY, 10032, USA
| | - Sally A Amundson
- Columbia University Irving Medical Center, 630, W 168th street, VC11-237, New York, NY, 10032, USA
| | - David J Brenner
- Columbia University Irving Medical Center, 630, W 168th street, VC11-237, New York, NY, 10032, USA
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19
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Moreno-Villanueva M, Zhang Y, Feiveson A, Mistretta B, Pan Y, Chatterjee S, Wu W, Clanton R, Nelman-Gonzalez M, Krieger S, Gunaratne P, Crucian B, Wu H. Single-Cell RNA-Sequencing Identifies Activation of TP53 and STAT1 Pathways in Human T Lymphocyte Subpopulations in Response to Ex Vivo Radiation Exposure. Int J Mol Sci 2019; 20:ijms20092316. [PMID: 31083348 PMCID: PMC6539494 DOI: 10.3390/ijms20092316] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 11/16/2022] Open
Abstract
Detrimental health consequences from exposure to space radiation are a major concern for long-duration human exploration missions to the Moon or Mars. Cellular responses to radiation are expected to be heterogeneous for space radiation exposure, where only high-energy protons and other particles traverse a fraction of the cells. Therefore, assessing DNA damage and DNA damage response in individual cells is crucial in understanding the mechanisms by which cells respond to different particle types and energies in space. In this project, we identified a cell-specific signature for radiation response by using single-cell transcriptomics of human lymphocyte subpopulations. We investigated gene expression in individual human T lymphocytes 3 h after ex vivo exposure to 2-Gy gamma rays while using the single-cell sequencing technique (10X Genomics). In the process, RNA was isolated from ~700 irradiated and ~700 non-irradiated control cells, and then sequenced with ~50 k reads/cell. RNA in each of the cells was distinctively barcoded prior to extraction to allow for quantification for individual cells. Principal component and clustering analysis of the unique molecular identifier (UMI) counts classified the cells into three groups or sub-types, which correspond to CD4+, naïve, and CD8+/NK cells. Gene expression changes after radiation exposure were evaluated using negative binomial regression. On average, BBC3, PCNA, and other TP53 related genes that are known to respond to radiation in human T cells showed increased activation. While most of the TP53 responsive genes were upregulated in all groups of cells, the expressions of IRF1, STAT1, and BATF were only upregulated in the CD4+ and naïve groups, but were unchanged in the CD8+/NK group, which suggests that the interferon-gamma pathway does not respond to radiation in CD8+/NK cells. Thus, single-cell RNA sequencing technique was useful for simultaneously identifying the expression of a set of genes in individual cells and T lymphocyte subpopulation after gamma radiation exposure. The degree of dependence of UMI counts between pairs of upregulated genes was also evaluated to construct a similarity matrix for cluster analysis. The cluster analysis identified a group of TP53-responsive genes and a group of genes that are involved in the interferon gamma pathway, which demonstrate the potential of this method for identifying previously unknown groups of genes with similar expression patterns.
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Affiliation(s)
- Maria Moreno-Villanueva
- NASA Johnson Space Center, Houston, TX 77058, USA.
- Human Performance Research Center, University of Konstanz, 78457 Konstanz, Germany.
| | - Ye Zhang
- NASA Kennedy Space Center, Cape Canaveral, FL 32899, USA.
| | | | - Brandon Mistretta
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.
| | - Yinghong Pan
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.
| | - Sujash Chatterjee
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.
| | - Winston Wu
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Ryan Clanton
- NASA Johnson Space Center, Houston, TX 77058, USA.
| | | | | | - Preethi Gunaratne
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.
| | | | - Honglu Wu
- NASA Johnson Space Center, Houston, TX 77058, USA.
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20
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Kuplik Z, Novak L, Shenkar N. Proteomic profiling of ascidians as a tool for biomonitoring marine environments. PLoS One 2019; 14:e0215005. [PMID: 30964904 PMCID: PMC6456167 DOI: 10.1371/journal.pone.0215005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/25/2019] [Indexed: 02/04/2023] Open
Abstract
Applying a proteomic approach for biomonitoring marine environments offers a useful tool for identifying organisms' stress responses, with benthic filter-feeders being ideal candidates for this practice. Here, we investigated the proteomic profile of two solitary ascidians (Chordata, Ascidiacea): Microcosmus exasperatus, collected from five sites along the Mediterranean coast of Israel; and Polycarpa mytiligera collected from four sites along the Red Sea coast. 193 and 13 proteins in M. exasperatus and P. mytiligera, respectively, demonstrated a significant differential expression. Significant differences were found between the proteomes from the northern and the southern sites along both the Mediterranean and the Red Sea coasts. Some of the significant proteins had previously been shown to be affected by environmental stressors, and thus have the potential to be further developed as biomarkers. Obtaining a proteomic profile of field-collected ascidians provides a useful tool for the early-detection of a stress response in ascidians worldwide.
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Affiliation(s)
- Zafrir Kuplik
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Lion Novak
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Noa Shenkar
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies Tel Aviv University, Tel Aviv, Israel
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21
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Balusamy SR, Ramani S, Natarajan S, Kim YJ, Perumalsamy H. Integrated transcriptome and in vitro analysis revealed anti-proliferative effect of citral in human stomach cancer through apoptosis. Sci Rep 2019; 9:4883. [PMID: 30890753 PMCID: PMC6425008 DOI: 10.1038/s41598-019-41406-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/05/2019] [Indexed: 12/13/2022] Open
Abstract
Cancer is the second leading cause of death globally, particularly stomach cancer is third most common causes of cancer death worldwide. Citral possesses anti-tumor activity in various cancer cell lines, However its effect toward stomach cancer and its mechanism of action is have yet to be elucidated. The goal of the present study is to elucidate the role of citral in stomach cancer using transcriptome and in vitro approaches. We performed transcriptome analysis using RNA-seq and explored its capability to persuade apoptosis in AGS human stomach cancer cell lines in vitro. Furthermore, the enrichment and KEGG pathway results suggested that there are several genes involved to induce apoptosis pathway. Furthermore, our study also demonstrated that citral arrested colony formation and migration of cancer cells significantly than that of untreated cells. RNA-seq revealed a total of 125 million trimmed reads obtained from both control and citral treated groups respectively. A total number of 612 differentially expressed genes (DEGs) were identified which includes 216 genes up-regulated and 396 genes down-regulated genes after treatment. The enrichment analysis identified DEGs genes from transcriptome libraries including cell death, cell cycle, apoptosis and cell growth. The present study showed the significant inhibition effect upon citral by regulating various genes involved in signaling pathways, inhibits metastasis, colony formation and induced apoptosis both in silico and in vitro.
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Affiliation(s)
- Sri Renukadevi Balusamy
- Department of Food Science and Biotechnology Sejong University, Gwangjin-gu, Seoul, Republic of Korea.
| | - Sivasubramanian Ramani
- Department of Food Science and Biotechnology Sejong University, Gwangjin-gu, Seoul, Republic of Korea
| | | | - Yeon Ju Kim
- Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin, 446- 701, Republic of Korea.
| | - Haribalan Perumalsamy
- Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin, 446- 701, Republic of Korea.
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22
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Zhao Y, Wilmarth PA, Cheng C, Limi S, Fowler VM, Zheng D, David LL, Cvekl A. Proteome-transcriptome analysis and proteome remodeling in mouse lens epithelium and fibers. Exp Eye Res 2019; 179:32-46. [PMID: 30359574 PMCID: PMC6360118 DOI: 10.1016/j.exer.2018.10.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 08/31/2018] [Accepted: 10/20/2018] [Indexed: 12/21/2022]
Abstract
Epithelial cells and differentiated fiber cells represent distinct compartments in the ocular lens. While previous studies have revealed proteins that are preferentially expressed in epithelial vs. fiber cells, a comprehensive proteomics library comparing the molecular compositions of epithelial vs. fiber cells is essential for understanding lens formation, function, disease and regenerative potential, and for efficient differentiation of pluripotent stem cells for modeling of lens development and pathology in vitro. To compare protein compositions between the lens epithelium and fibers, we employed tandem mass spectrometry (2D-LC/MS) analysis of microdissected mouse P0.5 lenses. Functional classifications of the top 525 identified proteins into gene ontology categories by molecular processes and subcellular localizations, were adapted for the lens. Expression levels of both epithelial and fiber proteomes were compared with whole lens proteome and mRNA levels using E14.5, E16.5, E18.5, and P0.5 RNA-Seq data sets. During this developmental time window, multiple complex biosynthetic and catabolic processes generate the molecular and structural foundation for lens transparency. As expected, crystallins showed a high correlation between their mRNA and protein levels. Comprehensive data analysis confirmed and/or predicted roles for transcription factors (TFs), RNA-binding proteins (e.g. Carhsp1), translational apparatus including ribosomal heterogeneity and initiation factors, microtubules, cytoskeletal [e.g. non-muscle myosin IIA heavy chain (Myh9) and βB2-spectrin (Sptbn2)] and membrane proteins in lens formation and maturation. Our data highlighted many proteins with unknown functions in the lens that were preferentially enriched in epithelium or fibers, setting the stage for future studies to further dissect the roles of these proteins in fiber cell differentiation vs. epithelial cell maintenance. In conclusion, the present proteomic datasets represent the first mouse lens epithelium and fiber cell proteomes, establish comparative analyses of protein and RNA-Seq data, and characterize the major proteome remodeling required to form the mature lens fiber cells.
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Affiliation(s)
- Yilin Zhao
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Phillip A Wilmarth
- Department of Biochemistry & Molecular Biology, Oregon Health Sciences University, 3181 Southwest Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Catherine Cheng
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Saima Limi
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Velia M Fowler
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Deyou Zheng
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Neurology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Neuroscience, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Larry L David
- Department of Biochemistry & Molecular Biology, Oregon Health Sciences University, 3181 Southwest Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Ales Cvekl
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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23
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Liang J, Liu Z, Zou Z, Wang X, Tang Y, Zhou C, Wu K, Zhang F, Lu Y. Knockdown of ribosomal protein S15A inhibits human kidney cancer cell growth in vitro and in vivo. Mol Med Rep 2018; 19:1117-1127. [PMID: 30569143 PMCID: PMC6323228 DOI: 10.3892/mmr.2018.9751] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/31/2018] [Indexed: 02/05/2023] Open
Abstract
Ribosomal protein S15A (RPS15A), a member of the ribosomal protein gene family, was demonstrated to be closely associated with tumorigenesis in multiple human malignancies. Nevertheless, the role of RPS15A in the progression of renal cell carcinoma (RCC) remains unknown. In the present study, by comparing the publicly available data from RCC tissues and reverse transcription-quantitative polymerase chain reaction results, it was identified that RPS15A was upregulated in RCC tissues and cell lines (P<0.001). Notably, knockdown of RPS15A suppressed 786-O cell proliferation (P<0.001) and promoted its apoptosis/necrotic (P=0.0001) in vitro. Additionally, tumour formation and growth of transfected 786-O cells were observed to be restrained in a mouse model (P<0.05). Subsequent to analysing the microarray data, 747 genes were differentially expressed in the RPS15A-knockdown 786-O cells. The enriched canonical pathways, diseases and functions of differentially expressed genes, and the interactive network of RPS15A in RCC were successfully constructed by ingenuity pathway analysis. Overall, the present results provided a preliminary experimental basis for RPS15A as a novel oncogene and potential therapeutic target in RCC.
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Affiliation(s)
- Jiayu Liang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Zhihong Liu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Zijun Zou
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xiangxiu Wang
- Core Facility, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yongquan Tang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Chuan Zhou
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Kan Wu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Fuxun Zhang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yiping Lu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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24
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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: 18] [Impact Index Per Article: 3.0] [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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25
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Ribosomal protein S27-like regulates autophagy via the β-TrCP-DEPTOR-mTORC1 axis. Cell Death Dis 2018; 9:1131. [PMID: 30425236 PMCID: PMC6234217 DOI: 10.1038/s41419-018-1168-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/07/2018] [Accepted: 10/24/2018] [Indexed: 02/07/2023]
Abstract
RPS27L (Ribosomal protein S27-like), an evolutionarily conserved ribosomal protein, is a p53 target and a physiological p53 regulator. We previously reported that Rps27l disruption enhanced lymphomagenesis in Trp53+/− mice by triggering genome instability and sensitized Trp53+/− mice to radiation by blocking DNA damage response. Whether and how RPS27L modulates autophagy is totally unknown. Here we report that RPS27L silencing significantly induced autophagy in breast cancer MB231 and SK-BR3 cells harboring mutant p53. Mechanistically, RPS27L silencing remarkably inactivated mTORC1, a major negative autophagy regulator, but not mTORC2. Autophagy induction and mTORC1 inactivation was also observed in MEFs with Rps27l deletion. More specifically, RPS27L silencing shortened the protein half-life of β-TrCP, a substrate receptor of Skp1-Cullin 1-F-box (SCF) ubiquitin ligase, which is responsible for DEPTOR degradation, leading to DEPTOR accumulation to inhibit mTORC1 activity. Furthermore, RPS27L silencing-induced autophagy and mTORC1 inactivation can be partially rescued by simultaneous DEPTOR silencing, suggesting a causal role of DEPTOR. Biologically, autophagy inhibitor, chloroquine (CQ), or Bafilomycin A1 (BAF A1), significantly induced apoptosis in RPS27L silenced cells, indicating that autophagy is a cellular survival mechanism in response to RPS27L loss. Finally, RPS27L levels were reduced in human breast cancers, as compared to adjacent normal tissues. Collectively, our study suggests that RPS27L reduction might play a promoting role during breast tumorigenesis by autophagy induction via the β-TrCP-DEPTOR-mTORC1 axis.
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26
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Macaeva E, Mysara M, De Vos WH, Baatout S, Quintens R. Gene expression-based biodosimetry for radiological incidents: assessment of dose and time after radiation exposure. Int J Radiat Biol 2018; 95:64-75. [PMID: 30247087 DOI: 10.1080/09553002.2018.1511926] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
PURPOSE In order to ensure efficient use of medical resources following a radiological incident, there is an urgent need for high-throughput time-efficient biodosimetry tools. In the present study, we tested the applicability of a gene expression signature for the prediction of exposure dose as well as the time elapsed since irradiation. MATERIALS AND METHODS We used whole blood samples from seven healthy volunteers as reference samples (X-ray doses: 0, 25, 50, 100, 500, 1000, and 2000 mGy; time points: 8, 12, 24, 36 and 48 h) and samples from seven other individuals as 'blind samples' (20 samples in total). RESULTS Gene expression values normalized to the reference gene without normalization to the unexposed controls were sufficient to predict doses with a correlation coefficient between the true and the predicted doses of 0.86. Importantly, we could also classify the samples according to the time since exposure with a correlation coefficient between the true and the predicted time point of 0.96. Because of the dynamic nature of radiation-induced gene expression, this feature will be of critical importance for adequate gene expression-based dose prediction in a real emergency situation. In addition, in this study we also compared different methodologies for RNA extraction available on the market and suggested the one most suitable for emergency situation which does not require on-spot availability of any specific reagents or equipment. CONCLUSIONS Our results represent an important advancement in the application of gene expression for biodosimetry purposes.
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Affiliation(s)
- Ellina Macaeva
- a Interdisciplinary Biosciences Group, Belgian Nuclear Research Centre, SCK•CEN, Mol , Belgium.,b Department of Molecular Biotechnology , Ghent University , Ghent , Belgium
| | - Mohamed Mysara
- a Interdisciplinary Biosciences Group, Belgian Nuclear Research Centre, SCK•CEN, Mol , Belgium
| | - Winnok H De Vos
- b Department of Molecular Biotechnology , Ghent University , Ghent , Belgium.,c Department of Veterinary Sciences , University of Antwerp , Belgium
| | - Sarah Baatout
- a Interdisciplinary Biosciences Group, Belgian Nuclear Research Centre, SCK•CEN, Mol , Belgium.,b Department of Molecular Biotechnology , Ghent University , Ghent , Belgium
| | - Roel Quintens
- a Interdisciplinary Biosciences Group, Belgian Nuclear Research Centre, SCK•CEN, Mol , Belgium
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27
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Marcel V, Nguyen Van Long F, Diaz JJ. 40 Years of Research Put p53 in Translation. Cancers (Basel) 2018; 10:E152. [PMID: 29883412 PMCID: PMC5977125 DOI: 10.3390/cancers10050152] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/15/2018] [Accepted: 05/18/2018] [Indexed: 12/18/2022] Open
Abstract
Since its discovery in 1979, p53 has shown multiple facets. Initially the tumor suppressor p53 protein was considered as a stress sensor able to maintain the genome integrity by regulating transcription of genes involved in cell cycle arrest, apoptosis and DNA repair. However, it rapidly came into light that p53 regulates gene expression to control a wider range of biological processes allowing rapid cell adaptation to environmental context. Among them, those related to cancer have been extensively documented. In addition to its role as transcription factor, scattered studies reported that p53 regulates miRNA processing, modulates protein activity by direct interaction or exhibits RNA-binding activity, thus suggesting a role of p53 in regulating several layers of gene expression not restricted to transcription. After 40 years of research, it appears more and more clearly that p53 is strongly implicated in translational regulation as well as in the control of the production and activity of the translational machinery. Translation control of specific mRNAs could provide yet unsuspected capabilities to this well-known guardian of the genome.
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Affiliation(s)
- Virginie Marcel
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France.
| | - Flora Nguyen Van Long
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France.
| | - Jean-Jacques Diaz
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France.
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28
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Zhao Y, Tan M, Liu X, Xiong X, Sun Y. Inactivation of ribosomal protein S27-like confers radiosensitivity via the Mdm2-p53 and Mdm2-MRN-ATM axes. Cell Death Dis 2018; 9:145. [PMID: 29396424 PMCID: PMC5833388 DOI: 10.1038/s41419-017-0192-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 01/21/2023]
Abstract
RPS27L (ribosomal protein S27-like) is an evolutionarily conserved ribosomal protein and a direct p53 target. We recently reported that Rps27l disruption triggers ribosomal stress to induce p53, causing postnatal death, which can be rescued by Trp53+/−. Whether and how Rps27l modulates radiosensitivity is unknown. Here we report that Rps27l−/−; Trp53+/− mice are extremely sensitive to radiation due to reduced proliferation and massive induction of apoptosis in radiation-sensitive organs. Mechanistically, the radiation sensitivity is mediated by two signaling pathways: (1) activated p53 pathway due to imbalanced Mdm2/Mdm4 levels and reduced E3 ligase activity; and (2) reduced DNA damage response due to reduced MRN/Atm signal as a result of elevated Mdm2 binding of Nbs1 to inhibit Nbs1–Atm binding and subsequent Atm activation. Indeed, heterozygous deletion of Mdm2 restores the MRN/Atm signal. Collectively, our study revealed a physiological condition under which Rps27l regulates the Mdm2/p53 and MRN/Atm axes to maintain DNA damage response and to confer radioprotection in vivo.
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Affiliation(s)
- Yongchao Zhao
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China. .,Division of Radiation and Cancer Biology, Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA. .,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Mingjia Tan
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Xia Liu
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiufang Xiong
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China. .,Division of Radiation and Cancer Biology, Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.
| | - Yi Sun
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China. .,Division of Radiation and Cancer Biology, Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China.
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29
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Trilla-Fuertes L, Gámez-Pozo A, Arevalillo JM, Díaz-Almirón M, Prado-Vázquez G, Zapater-Moros A, Navarro H, Aras-López R, Dapía I, López-Vacas R, Nanni P, Llorente-Armijo S, Arias P, Borobia AM, Maín P, Feliú J, Espinosa E, Fresno Vara JÁ. Molecular characterization of breast cancer cell response to metabolic drugs. Oncotarget 2018. [PMID: 29515760 PMCID: PMC5839391 DOI: 10.18632/oncotarget.24047] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Metabolic reprogramming is a hallmark of cancer. It has been described that breast cancer subtypes present metabolism differences and this fact enables the possibility of using metabolic inhibitors as targeted drugs in specific scenarios. In this study, breast cancer cell lines were treated with metformin and rapamycin, showing a heterogeneous response to treatment and leading to cell cycle disruption. The genetic causes and molecular effects of this differential response were characterized by means of SNP genotyping and mass spectrometry-based proteomics. Protein expression was analyzed using probabilistic graphical models, showing that treatments elicit various responses in some biological processes such as transcription. Moreover, flux balance analysis using protein expression values showed that predicted growth rates were comparable with cell viability measurements and suggesting an increase in reactive oxygen species response enzymes due to metformin treatment. In addition, a method to assess flux differences in whole pathways was proposed. Our results show that these diverse approaches provide complementary information and allow us to suggest hypotheses about the response to drugs that target metabolism and their mechanisms of action.
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Affiliation(s)
- Lucía Trilla-Fuertes
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain.,Biomedica Molecular Medicine SL, Madrid, Spain
| | - Angelo Gámez-Pozo
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain.,Biomedica Molecular Medicine SL, Madrid, Spain
| | - Jorge M Arevalillo
- Operational Research and Numerical Analysis, National Distance Education University (UNED), Madrid, Spain
| | | | - Guillermo Prado-Vázquez
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Andrea Zapater-Moros
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Hilario Navarro
- Operational Research and Numerical Analysis, National Distance Education University (UNED), Madrid, Spain
| | - Rosa Aras-López
- Congenital Malformations Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital, IdiPAZ, Madrid, Spain
| | - Irene Dapía
- Pharmacogenetics Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Autonomous University of Madrid, Madrid, Spain.,Biomedical Research Networking Center on Rare Diseases-CIBERER, ISCIII, Madrid, Spain
| | - Rocío López-Vacas
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Paolo Nanni
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Sara Llorente-Armijo
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Pedro Arias
- Pharmacogenetics Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Autonomous University of Madrid, Madrid, Spain.,Biomedical Research Networking Center on Rare Diseases-CIBERER, ISCIII, Madrid, Spain
| | - Alberto M Borobia
- Clinical Pharmacology Department, La Paz University Hospital School of Medicine, IdiPAZ, Autonomous University of Madrid, Madrid, Spain
| | - Paloma Maín
- Department of Statistics and Operations Research, Faculty of Mathematics, Complutense University of Madrid, Madrid, Spain
| | - Jaime Feliú
- Medical Oncology Service, La Paz University Hospital-IdiPAZ, Madrid, Spain.,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain.,Cátedra UAM-AMGEN, Universidad Autónoma de Madrid, Madrid, Spain
| | - Enrique Espinosa
- Medical Oncology Service, La Paz University Hospital-IdiPAZ, Madrid, Spain.,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain.,Biomedica Molecular Medicine SL, Madrid, Spain.,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
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30
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Xie X, Guo P, Yu H, Wang Y, Chen G. Ribosomal proteins: insight into molecular roles and functions in hepatocellular carcinoma. Oncogene 2017; 37:277-285. [PMID: 28945227 DOI: 10.1038/onc.2017.343] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/21/2017] [Accepted: 08/14/2017] [Indexed: 02/07/2023]
Abstract
Ribosomes, which are important sites for the synthesis of proteins related to expression and transmission of genetic information in humans, have a complex structure and diverse functions. They consist of a variety of ribosomal proteins (RPs), ribosomal RNAs (rRNAs) and small nucleolar RNAs. Owing to the involvement of ribosomes in many important biological processes of cells, their major components, rRNAs and RPs, have an important role in human diseases, including the initiation and evolvement of malignancies. However, the main mechanisms underlying the involvement of ribosomes in cancer remain unclear. This review describes the crucial role of ribosomes in various common malignant tumors; in particular, it examines the effects of RPs, including S6, the receptor for activated C-kinase and RPS15A, on the development and progression of hepatocellular carcinoma.
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Affiliation(s)
- X Xie
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - P Guo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - H Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Y Wang
- Research Center of Evidence-Based Medicine and Clinical Epidemiology, School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - G Chen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
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31
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Zhang L, McGraw KL, Sallman DA, List AF. The role of p53 in myelodysplastic syndromes and acute myeloid leukemia: molecular aspects and clinical implications. Leuk Lymphoma 2016; 58:1777-1790. [PMID: 27967292 DOI: 10.1080/10428194.2016.1266625] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
TP53 gene mutations occurring in patients with myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) are associated with high-risk karyotypes including 17p abnormalities, monosomal and complex cytogenetics. TP53 mutations in these disorders portend rapid disease progression and resistance to conventional therapeutics. Notably, the size of the TP53 mutant clone as measured by mutation allele burden is directly linked to overall survival (OS) confirming the importance of p53 as a negative prognostic variable. In nucleolar stress-induced ribosomopathies, such as del(5q) MDS, disassociation of MDM2 and p53 results in p53 accumulation in erythroid precursors manifested as erythroid hypoplasia. P53 antagonism by lenalidomide or other therapeutics such as antisense oligonucleotides, repopulates erythroid precursors and enhances effective erythropoiesis. These findings demonstrate that p53 is an intriguing therapeutic target that is currently under investigation in MDS and AML. This study reviews molecular advances in understanding the role of p53 in MDS and AML, and explores potential therapeutic strategies in this era of personalized medicine.
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Affiliation(s)
- Ling Zhang
- a Department of Hematopathology and Laboratory Medicine , H. Lee Moffitt Cancer Center and Research Institute , Tampa , FL , USA
| | - Kathy L McGraw
- b Department of Malignant Hematology , H. Lee Moffitt Cancer Center and Research Institute , Tampa , FL , USA
| | - David A Sallman
- b Department of Malignant Hematology , H. Lee Moffitt Cancer Center and Research Institute , Tampa , FL , USA
| | - Alan F List
- b Department of Malignant Hematology , H. Lee Moffitt Cancer Center and Research Institute , Tampa , FL , USA
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32
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Xu X, Xiong X, Sun Y. The role of ribosomal proteins in the regulation of cell proliferation, tumorigenesis, and genomic integrity. SCIENCE CHINA-LIFE SCIENCES 2016; 59:656-72. [DOI: 10.1007/s11427-016-0018-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 04/06/2016] [Indexed: 01/29/2023]
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Liu Y, Deisenroth C, Zhang Y. RP-MDM2-p53 Pathway: Linking Ribosomal Biogenesis and Tumor Surveillance. Trends Cancer 2016; 2:191-204. [PMID: 28741571 DOI: 10.1016/j.trecan.2016.03.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/03/2016] [Accepted: 03/04/2016] [Indexed: 12/18/2022]
Abstract
Ribosomal biogenesis is tightly associated with cellular activities, such as growth, proliferation, and cell cycle progression. Perturbations in ribosomal biogenesis can initiate so-called nucleolar stress. The process through which ribosomal proteins (RPs) transduce nucleolar stress signals via MDM2 to p53 has been described as a crucial tumor-suppression mechanism. In this review we focus on recent progress pertaining to the function and mechanism of RPs in association with the MDM2-p53 tumor-suppression network, and the potential implications this surveillance network has for cancer development.
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Affiliation(s)
- Yong Liu
- Department of Radiation Oncology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chad Deisenroth
- The Hamner Institutes for Health Sciences, Institute for Chemical Safety Sciences, 6 Davis Drive, PO Box 12137, Research Triangle Park, NC 27709, USA
| | - Yanping Zhang
- Department of Radiation Oncology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical College, Xuzhou, Jiangsu 221002, China.
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Grozav A, Balacescu O, Balacescu L, Cheminel T, Berindan-Neagoe I, Therrien B. Synthesis, Anticancer Activity, and Genome Profiling of Thiazolo Arene Ruthenium Complexes. J Med Chem 2015; 58:8475-90. [PMID: 26488797 DOI: 10.1021/acs.jmedchem.5b00855] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Sixteen hydrazinyl-thiazolo arene ruthenium complexes of the general formula [(η(6)-p-cymene)Ru(N,N'-hydrazinyl-thiazolo)Cl]Cl were synthesized. All complexes were tested in vitro for their antiproliferative activity on three tumor cell lines (HeLa, A2780, and A2780cisR) and on a noncancerous cell line (HFL-1). A superior cytotoxic activity of the ruthenium complexes as compared to cisplatin and oxaliplatin, on both cisplatin-sensitive and cisplatin resistant ovarian cancer cells, was observed. In addition, the biological activity of two selected derivatives was evaluated using microarray gene expression assay and ingenuity pathway analysis. p53 signaling was identified as an important pathway modulated by both arene ruthenium compounds. New activated molecules such as FAS, ZMAT3, PRMT2, BBC3/PUMA, and PDCD4, whose overexpressions are correlated with overcoming resistance to cisplatin therapy, were also identified as potential targets. Moreover, the arene ruthenium complexes can be used in association with cisplatin to prevent cisplatin resistance development and synergistically to induce cell death in ovarian cancer cells.
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Affiliation(s)
- Adriana Grozav
- Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy , Victor Babes Str. 41, RO-400012 Cluj-Napoca, Romania
| | - Ovidiu Balacescu
- Department of Functional Genomics, Proteomics and Experimental Pathology, The Oncology Institute "Prof Dr. Ion Chiricuta" , 34-36 Republicii Str, RO-400015, Cluj-Napoca, Romania
| | - Loredana Balacescu
- Department of Functional Genomics, Proteomics and Experimental Pathology, The Oncology Institute "Prof Dr. Ion Chiricuta" , 34-36 Republicii Str, RO-400015, Cluj-Napoca, Romania
| | - Thomas Cheminel
- Institut de Chimie, Université de Neuchâtel , 51 Avenue de Bellevaux, CH-2000 Neuchâtel, Switzerland
| | - Ioana Berindan-Neagoe
- Department of Functional Genomics, Proteomics and Experimental Pathology, The Oncology Institute "Prof Dr. Ion Chiricuta" , 34-36 Republicii Str, RO-400015, Cluj-Napoca, Romania.,Research Center of Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu″ University of Medicine and Pharmacy , 23 Marinescu Str, RO-400337 Cluj-Napoca, Romania
| | - Bruno Therrien
- Institut de Chimie, Université de Neuchâtel , 51 Avenue de Bellevaux, CH-2000 Neuchâtel, Switzerland
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Wang T, Guo S, Liu Z, Wu L, Li M, Yang J, Chen R, Liu X, Xu H, Cai S, Chen H, Li W, Xu S, Wang L, Hu Z, Zhuang Q, Wang L, Wu K, Liu J, Ye Z, Ji JY, Wang C, Chen K. CAMK2N1 inhibits prostate cancer progression through androgen receptor-dependent signaling. Oncotarget 2015; 5:10293-306. [PMID: 25296973 PMCID: PMC4279373 DOI: 10.18632/oncotarget.2511] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/24/2014] [Indexed: 12/13/2022] Open
Abstract
Castration resistance is a major obstacle to hormonal therapy for prostate cancer patients. Although androgen independence of prostate cancer growth is a known contributing factor to endocrine resistance, the mechanism of androgen receptor deregulation in endocrine resistance is still poorly understood. Herein, the CAMK2N1 was shown to contribute to the human prostate cancer cell growth and survival through AR-dependent signaling. Reduced expression of CAMK2N1 was correlated to recurrence-free survival of prostate cancer patients with high levels of AR expression in their tumor. CAMK2N1 and AR signaling form an auto-regulatory negative feedback loop: CAMK2N1 expression was down-regulated by AR activation; while CAMK2N1 inhibited AR expression and transactivation through CAMKII and AKT pathways. Knockdown of CAMK2N1 in prostate cancer cells alleviated Casodex inhibition of cell growth, while re-expression of CAMK2N1 in castration-resistant cells sensitized the cells to Casodex treatment. Taken together, our findings suggest that CAMK2N1 plays a tumor suppressive role and serves as a crucial determinant of the resistance of prostate cancer to endocrine therapies.
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Affiliation(s)
- Tao Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shuiming Guo
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhuo Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Licheng Wu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mingchao Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jun Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ruibao Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaming Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shaoxin Cai
- Department of Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hui Chen
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Weiyong Li
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shaohua Xu
- Department of Gynecology, Shanghai First Matenity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Liang Wang
- Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhiquan Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qianyuan Zhuang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Liping Wang
- Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Kongming Wu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jihong Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jun-Yuan Ji
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX, USA
| | - Chenguang Wang
- Key Laboratory of Tianjin Radiation and Molecular Nuclear Medicine; Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, China
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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36
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Jeay S, Gaulis S, Ferretti S, Bitter H, Ito M, Valat T, Murakami M, Ruetz S, Guthy DA, Rynn C, Jensen MR, Wiesmann M, Kallen J, Furet P, Gessier F, Holzer P, Masuya K, Würthner J, Halilovic E, Hofmann F, Sellers WR, Graus Porta D. A distinct p53 target gene set predicts for response to the selective p53-HDM2 inhibitor NVP-CGM097. eLife 2015; 4. [PMID: 25965177 PMCID: PMC4468608 DOI: 10.7554/elife.06498] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 05/11/2015] [Indexed: 11/13/2022] Open
Abstract
Biomarkers for patient selection are essential for the successful and rapid development of emerging targeted anti-cancer therapeutics. In this study, we report the discovery of a novel patient selection strategy for the p53-HDM2 inhibitor NVP-CGM097, currently under evaluation in clinical trials. By intersecting high-throughput cell line sensitivity data with genomic data, we have identified a gene expression signature consisting of 13 up-regulated genes that predicts for sensitivity to NVP-CGM097 in both cell lines and in patient-derived tumor xenograft models. Interestingly, these 13 genes are known p53 downstream target genes, suggesting that the identified gene signature reflects the presence of at least a partially activated p53 pathway in NVP-CGM097-sensitive tumors. Together, our findings provide evidence for the use of this newly identified predictive gene signature to refine the selection of patients with wild-type p53 tumors and increase the likelihood of response to treatment with p53-HDM2 inhibitors, such as NVP-CGM097.
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Affiliation(s)
- Sébastien Jeay
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Swann Gaulis
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Stéphane Ferretti
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Hans Bitter
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Moriko Ito
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Thérèse Valat
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Masato Murakami
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Stephan Ruetz
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Daniel A Guthy
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Caroline Rynn
- Metabolism and Pharmacokinetics, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Michael R Jensen
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Marion Wiesmann
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Joerg Kallen
- Center of Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Pascal Furet
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - François Gessier
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Philipp Holzer
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Keiichi Masuya
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Jens Würthner
- Translational Clinical Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Ensar Halilovic
- Translational Clinical Oncology, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Francesco Hofmann
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - William R Sellers
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Diana Graus Porta
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
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37
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A long-range foresight for the medical application of apoptosis specifically induced by Dd-MRP4, Dictyostelium mitochondrial ribosomal protein S4, to cancer therapy. Biomolecules 2015; 5:113-20. [PMID: 25675329 PMCID: PMC4384114 DOI: 10.3390/biom5010113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 01/31/2015] [Indexed: 01/11/2023] Open
Abstract
Apoptosis (programmed cell death) is regarded as ultimate differentiation of the cell. We have recently demonstrated that a targeted delivery of Dd-MRP4 (Dictyostelium mitochondrial ribosomal protein S4) suppresses specifically the proliferation of the human cancer cells, by inducing their apoptotic cell death (Chida et al., 2014, doi:10.1186/1475-2867-14-56). This amazing fact was discovered, simply based on the finding that Dd-MRP4 expression is absolutely required for transition of Dictyostelium cells from growth to differentiation (Chida et al., 2008, doi:10.1186/1471-2156-9-25; Maeda et al., 2013, doi:10.3390/biom3040943). Dd-MRP4 protein has quite unique structural characters, in that it is highly basic (pI: about 11.5) and interestingly has several nuclear-localization signals within the molecule. In this review, we introduce briefly the efficacy of several apoptosis-inducing substances reported thus far for cancer therapy, and speculate the possible mechanisms, by which apoptosis is specifically induced by Dd-MRP4, on the basis of its structural uniqueness. We also discuss several issues to be solved for the medical application of ectopically expressed Dd-MRP4 in human cancer cells.
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38
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Wang W, Nag S, Zhang X, Wang MH, Wang H, Zhou J, Zhang R. Ribosomal proteins and human diseases: pathogenesis, molecular mechanisms, and therapeutic implications. Med Res Rev 2014; 35:225-85. [PMID: 25164622 DOI: 10.1002/med.21327] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ribosomes are essential components of the protein synthesis machinery. The process of ribosome biogenesis is well organized and tightly regulated. Recent studies have shown that ribosomal proteins (RPs) have extraribosomal functions that are involved in cell proliferation, differentiation, apoptosis, DNA repair, and other cellular processes. The dysfunction of RPs has been linked to the development and progression of hematological, metabolic, and cardiovascular diseases and cancer. Perturbation of ribosome biogenesis results in ribosomal stress, which triggers activation of the p53 signaling pathway through RPs-MDM2 interactions, resulting in p53-dependent cell cycle arrest and apoptosis. RPs also regulate cellular functions through p53-independent mechanisms. We herein review the recent advances in several forefronts of RP research, including the understanding of their biological features and roles in regulating cellular functions, maintaining cell homeostasis, and their involvement in the pathogenesis of human diseases. We also highlight the translational potential of this research for the identification of molecular biomarkers, and in the discovery and development of novel treatments for human diseases.
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Affiliation(s)
- Wei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas, 79106; Cancer Biology Center, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas, 79106
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39
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Xiong X, Zhao Y, Tang F, Wei D, Thomas D, Wang X, Liu Y, Zheng P, Sun Y. Ribosomal protein S27-like is a physiological regulator of p53 that suppresses genomic instability and tumorigenesis. eLife 2014; 3:e02236. [PMID: 25144937 PMCID: PMC4163686 DOI: 10.7554/elife.02236] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 08/20/2014] [Indexed: 12/24/2022] Open
Abstract
Cell-based studies showed that several Mdm2-binding ribosomal proteins, upon overexpression, stabilize and activate p53. In contrast, here we show in a mouse knockout study that Mdm2-binding ribosomal protein S27-like (Rps27l), upon disruption, activates p53. Germline inactivation of Rps27l triggers ribosomal stress to stabilize Mdm2, which degrades Mdm4 to reduce Mdm2-Mdm4 E3 ligase towards p53, leading to p53-dependent apoptotic depletion of hematopoietic stem cells and postnatal death, which is rescued by Trp53 deletion. Paradoxically, while increased p53 is expected to inhibit tumorigenesis, Rps27l−/−;Trp53+/− mice develop lymphomas at higher incidence with p53 loss-of-heterozygosity and severe genome aneuploidy, suggesting that Rps27l disruption impose a selection pressure against p53. Thus, Rps27l has dual functions in p53 regulation: under Trp53+/+ background, Rps27l disruption triggers ribosomal stress to induce p53 and apoptosis, whereas under Trp53+/− background, Rps27l disruption triggers genomic instability and Trp53 deletion to promote tumorigenesis. Our study provides a new paradigm of p53 regulation. DOI:http://dx.doi.org/10.7554/eLife.02236.001 There are over a hundred different types of cancer that can affect humans; but, in general, all cancers are caused by mutations that cause cells to grow and divide abnormally. ‘Tumor suppressor genes’ are genes that normally protect a cell from genetic changes that can lead a cell towards becoming cancerous. About half of all cancers in humans have a mutation in one of the two copies of a tumor suppressor gene that encodes a protein called p53, which helps to control how and when cells grow and divide. In normal cells, the p53 protein can be activated in various ways. Damage to a cell's DNA triggers p53 to stop the cell growing, which gives the cell time to repair the DNA damage. However, if the damage is too severe and cannot be repaired, p53 essentially causes the cell to kill itself, via a process called apoptosis. Furthermore, if a cell has problems building new copies of its protein-making machinery, some of the parts (called ribosomal proteins) that make up these molecular machines can also lead to p53 being activated. By deleting the gene for a protein called Rps27l that is a newly characterized ribosomal protein, Xiong et al. have discovered that, in mice, Rps27I regulates the p53 protein in two different ways. In normal cells, Rps27l appears to inhibit p53, which is likely to encourage cancer to develop. But, if a cell has already lost a copy of the p53 gene—a situation that would normally encourage the cells to accrue further mutations and become cancerous—Rps27l acts as a tumor suppressor. In these mutated cells, the Rps27l protein helps to maintain the stability of the genome and prevent the loss of the second copy of gene for p53, and so protects the cell from becoming cancerous. Thus Rps27l can either activate or inactivate p53 activity depending on how many copies of the gene for p53 remain intact. The next challenge is to investigate if Rps27l levels determine the early-onset of tumor development in cancer-prone cells seen in patients with Li-Fraumeni syndrome, who are born with a mutated copy of the p53 gene. DOI:http://dx.doi.org/10.7554/eLife.02236.002
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Affiliation(s)
- Xiufang Xiong
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, University of Michigan, Ann Arbor, United States
| | - Yongchao Zhao
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, University of Michigan, Ann Arbor, United States
| | - Fei Tang
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington, United States
| | - Dongping Wei
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, University of Michigan, Ann Arbor, United States
| | - Daffyd Thomas
- Department of Pathology, University of Michigan Medical School, Ann Arbor, United States
| | - Xiang Wang
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, University of Michigan, Ann Arbor, United States
| | - Yang Liu
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington, United States
| | - Pan Zheng
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington, United States
| | - Yi Sun
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, University of Michigan, Ann Arbor, United States
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Bresolin de Souza K, Jutfelt F, Kling P, Förlin L, Sturve J. Effects of increased CO2 on fish gill and plasma proteome. PLoS One 2014; 9:e102901. [PMID: 25058324 PMCID: PMC4109940 DOI: 10.1371/journal.pone.0102901] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 06/25/2014] [Indexed: 11/18/2022] Open
Abstract
Ocean acidification and warming are both primarily caused by increased levels of atmospheric CO2, and marine organisms are exposed to these two stressors simultaneously. Although the effects of temperature on fish have been investigated over the last century, the long-term effects of moderate CO2 exposure and the combination of both stressors are almost entirely unknown. A proteomics approach was used to assess the adverse physiological and biochemical changes that may occur from the exposure to these two environmental stressors. We analysed gills and blood plasma of Atlantic halibut (Hippoglossus hippoglossus) exposed to temperatures of 12°C (control) and 18°C (impaired growth) in combination with control (400 µatm) or high-CO2 water (1000 µatm) for 14 weeks. The proteomic analysis was performed using two-dimensional gel electrophoresis (2DE) followed by Nanoflow LC-MS/MS using a LTQ-Orbitrap. The high-CO2 treatment induced the up-regulation of immune system-related proteins, as indicated by the up-regulation of the plasma proteins complement component C3 and fibrinogen β chain precursor in both temperature treatments. Changes in gill proteome in the high-CO2 (18°C) group were mostly related to increased energy metabolism proteins (ATP synthase, malate dehydrogenase, malate dehydrogenase thermostable, and fructose-1,6-bisphosphate aldolase), possibly coupled to a higher energy demand. Gills from fish exposed to high-CO2 at both temperature treatments showed changes in proteins associated with increased cellular turnover and apoptosis signalling (annexin 5, eukaryotic translation elongation factor 1γ, receptor for protein kinase C, and putative ribosomal protein S27). This study indicates that moderate CO2-driven acidification, alone and combined with high temperature, can elicit biochemical changes that may affect fish health.
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Affiliation(s)
- Karine Bresolin de Souza
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
| | - Fredrik Jutfelt
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Peter Kling
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Lars Förlin
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Joachim Sturve
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
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Wong QWL, Li J, Ng SR, Lim SG, Yang H, Vardy LA. RPL39L is an example of a recently evolved ribosomal protein paralog that shows highly specific tissue expression patterns and is upregulated in ESCs and HCC tumors. RNA Biol 2013; 11:33-41. [PMID: 24452241 DOI: 10.4161/rna.27427] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ribosomal proteins (RPs) have been shown to be able to impart selectivity on the translating ribosome implicating them in gene expression control. Many ribosomal proteins are highly conserved and recently a number of ribosomal protein paralogs have been described in mammals. We examined the expression pattern of RPs in differentiating mouse Embryonic Stem Cells (ESCs), paying particular attention to the RP paralogs. We find the RP paralog Rpl39l is highly expressed in ESC and its expression strongly correlates with hepatocellular carcinoma tumor (HCC) samples with high tumor grading and alpha-fetoprotein level giving it diagnostic potential. We further screen the expression pattern of all RPs and their paralogs across 22 different tissues. We find that the more recently evolved RP paralogs show a much greater level of tissue-specific expression. We propose that these RP paralogs evolved more recently to provide a greater level of gene expression control to higher eukaryotes.
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Affiliation(s)
| | - Jia Li
- Cancer Science Institute; National University of Singapore; Singapore
| | - Sheng Rong Ng
- A*STAR Institute of Medical Biology; 8A Biomedical Grove; Immunos, Singapore
| | - Seng Gee Lim
- Department of Medicine; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
| | - Henry Yang
- Cancer Science Institute; National University of Singapore; Singapore
| | - Leah A Vardy
- A*STAR Institute of Medical Biology; 8A Biomedical Grove; Immunos, Singapore; School of Biological Sciences; Nanyang Technological University; Singapore
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42
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Bai D, Zhang J, Xiao W, Zheng X. Regulation of the HDM2-p53 pathway by ribosomal protein L6 in response to ribosomal stress. Nucleic Acids Res 2013; 42:1799-811. [PMID: 24174547 PMCID: PMC3919599 DOI: 10.1093/nar/gkt971] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The HDM2-p53 loop is crucial for monitoring p53 level and human pathologies. Therefore, identification of novel molecules involved in this regulatory loop is necessary for understanding the dynamic regulation of p53 and treatment of human diseases. Here, we characterized that the ribosomal protein L6 binds to and suppresses the E3 ubiquitin ligase activity of HDM2, and subsequently attenuates HDM2-mediated p53 polyubiquitination and degradation. The enhanced p53 activity further slows down cell cycle progression and leads to cell growth inhibition. Conversely, the level of p53 is dramatically decreased upon the depletion of RPL6, indicating that RPL6 is essential for p53 stabilization. We also found that RPL6 translocalizes from the nucleolus to nucleoplasm under ribosomal stress, which facilitates its binding with HDM2. The interaction of RPL6 and HDM2 drives HDM2-mediated RPL6 polyubiquitination and proteasomal degradation. Longer treatment of actinomycin D increases RPL6 ubiquitination and destabilizes RPL6, and thereby putatively attenuates p53 response until the level of L6 subsides. Therefore, RPL6 and HDM2 form an autoregulatory feedback loop to monitor the level of p53 in response to ribosomal stress. Together, our study identifies the crucial function of RPL6 in regulating HDM2-p53 pathway, which highlights the importance of RPL6 in human genetic diseases and cancers.
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Affiliation(s)
- Dongmei Bai
- State Key Lab of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China and Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China
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Yang M, Sun H, Wang H, Zhang S, Yu X, Zhang L. Down-regulation of ribosomal protein L22 in non-small cell lung cancer. Med Oncol 2013; 30:646. [DOI: 10.1007/s12032-013-0646-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Accepted: 06/14/2013] [Indexed: 11/30/2022]
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Nag S, Qin J, Srivenugopal KS, Wang M, Zhang R. The MDM2-p53 pathway revisited. J Biomed Res 2013; 27:254-71. [PMID: 23885265 PMCID: PMC3721034 DOI: 10.7555/jbr.27.20130030] [Citation(s) in RCA: 208] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 04/12/2013] [Indexed: 12/15/2022] Open
Abstract
The p53 tumor suppressor is a key transcription factor regulating cellular pathways such as DNA repair, cell cycle, apoptosis, angiogenesis, and senescence. It acts as an important defense mechanism against cancer onset and progression, and is negatively regulated by interaction with the oncoprotein MDM2. In human cancers, the TP53 gene is frequently mutated or deleted, or the wild-type p53 function is inhibited by high levels of MDM2, leading to downregulation of tumor suppressive p53 pathways. Thus, the inhibition of MDM2-p53 interaction presents an appealing therapeutic strategy for the treatment of cancer. However, recent studies have revealed the MDM2-p53 interaction to be more complex involving multiple levels of regulation by numerous cellular proteins and epigenetic mechanisms, making it imperative to reexamine this intricate interplay from a holistic viewpoint. This review aims to highlight the multifaceted network of molecules regulating the MDM2-p53 axis to better understand the pathway and exploit it for anticancer therapy.
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Affiliation(s)
- Subhasree Nag
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA
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Wang H, Liu X, Wu J, Wu G, Yu L, He C, Yang H, Xie W, Xia X, He H. Bovine fetal epithelium cells expressing shRNA targeting viral VP1 gene resisted against foot-and-mouth disease virus. Virology 2013; 439:115-21. [PMID: 23481248 DOI: 10.1016/j.virol.2013.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 12/30/2012] [Accepted: 02/08/2013] [Indexed: 11/25/2022]
Abstract
RNAi could protect experimental animals from Foot-and-mouth disease virus (FMDV), but pivotal issue is delivery of RNAi. In this study, shRNA recombinant lentiviral plasmid RNAi-LT6 targeting VP1 of FMDV, which strongly suppressed the transient expression of a FLAG-tagged VP1 protein in 293T cells and significantly inhibited viral replication in BHK-21 cells, was screened and transfected into bovine fetal fibroblast cells. With subsequent somatic cell cloning, three 4-month-old transgenic fetuses were obtained, and integration into chromosome and expression of shRNA in primary transgenic tongue epithelium cells were confirmed by Southern hybridization and Northern assay, respectively. shRNA significantly suppressed viral RNA synthesis and viral replication in primary transgenic tongue epithelium cells after inoculation of 200 TCID50 of FMDV. The results suggested that transgenic cloning may be a useful tool for RNAi delivery and RNAi anti-viral strategy, and RNAi-LT6 could be a candidate shRNA used for preparation of transgenic cattle against FMDV.
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Affiliation(s)
- Hongmei Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, PR China
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Yang ZY, Gu QL. Advances in understanding the role of metallopanstimulin-1 in tumors. Shijie Huaren Xiaohua Zazhi 2012; 20:3558-3563. [DOI: 10.11569/wcjd.v20.i35.3558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Metallopanstimulin-1 (MPS-1), belonging to the ribosomal protein S27E family, is ubiquitously expressed in all normal tissues except the brain and placenta. In addition, MPS-1 is highly expressed in malignant tumors and cells. MPS-1 as a tumor marker or tumor-associated antigen has been extensively studied in head and neck cancer and breast cancer. MPS-1 is highly expressed in gastric cancer. Knockdown of MPS-1 expression inhibits the growth of cancer cells both in vitro and in vivo and induces spontaneous apoptosis of gastric cancer cells by repressing the NF-κB signaling pathway. In addition, MPS-1 is also highly expressed in colonic cancer and has a close relationship with the degree of malignancy and prognosis. Therefore, MPS-1 may be a novel potential therapeutic target for cancers.
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Comparative analysis of differentially expressed genes in Sika deer antler at different stages. Mol Biol Rep 2012; 40:1665-76. [DOI: 10.1007/s11033-012-2216-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 10/09/2012] [Indexed: 10/27/2022]
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An open-label phase 2 study of twice-weekly bortezomib and intermittent pegylated liposomal doxorubicin in patients with ovarian cancer failing platinum-containing regimens. Int J Gynecol Cancer 2012; 22:792-800. [PMID: 22635029 DOI: 10.1097/igc.0b013e318251051a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Pegylated liposomal doxorubicin (PLD) is an established treatment for relapsed ovarian cancer. Preclinical and clinical evidences in other tumor types suggest that the proteasome inhibitor bortezomib can act synergistically with PLD. METHODS Patients with relapsed ovarian cancer (N = 58), previously treated with platinum (100%) and taxane (95%), received bortezomib, 1.3 mg/m intravenous (days 1, 4, 8, and 11), and PLD, 30 mg/m intravenous (day 1), every 3 weeks. Tumor responses were assessed using Response Evaluation Criteria In Solid Tumors and Gynecologic Cancer Intergroup criteria. An optimal 2-stage design was implemented. Gene expression profiling in peripheral blood was characterized before and during treatment in 10 platinum-sensitive patients enrolled in stage 2 of the study. RESULTS Median number of bortezomib-PLD cycles was 3.5. Of 38 patients in the platinum-sensitive group, 9 responses were observed (median duration, 4.8 months). The platinum-resistant group was closed at stage 1 owing to lack of response. Toxicity was moderate and mainly consisted of hematologic, gastrointestinal, and mucositis events. Of the total 58 patients, peripheral neuropathy was reported in 9 patients (none were grade 3). Transcription profiling identified the prevalence of genes associated with ribonucleoprotein complexes, RNA processing, and protein translation. The gene expression changes were more robust in patients who responded or had stable disease compared with patients who had progressive disease. CONCLUSIONS The combination of bortezomib and PLD was well tolerated, but the antitumor activity is insufficient to warrant further investigation in ovarian cancer.
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Holmberg Olausson K, Nistér M, Lindström MS. p53 -Dependent and -Independent Nucleolar Stress Responses. Cells 2012; 1:774-98. [PMID: 24710530 PMCID: PMC3901145 DOI: 10.3390/cells1040774] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 09/28/2012] [Accepted: 10/01/2012] [Indexed: 12/27/2022] Open
Abstract
The nucleolus has emerged as a cellular stress sensor and key regulator of p53-dependent and -independent stress responses. A variety of abnormal metabolic conditions, cytotoxic compounds, and physical insults induce alterations in nucleolar structure and function, a situation known as nucleolar or ribosomal stress. Ribosomal proteins, including RPL11 and RPL5, become increasingly bound to the p53 regulatory protein MDM2 following nucleolar stress. Ribosomal protein binding to MDM2 blocks its E3 ligase function leading to stabilization and activation of p53. In this review we focus on a number of novel regulators of the RPL5/RPL11-MDM2-p53 complex including PICT1 (GLTSCR2), MYBBP1A, PML and NEDD8. p53-independent pathways mediating the nucleolar stress response are also emerging and in particular the negative control that RPL11 exerts on Myc oncoprotein is of importance, given the role of Myc as a master regulator of ribosome biogenesis. We also briefly discuss the potential of chemotherapeutic drugs that specifically target RNA polymerase I to induce nucleolar stress.
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Affiliation(s)
- Karl Holmberg Olausson
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska R8:05, Karolinska University Hospital in Solna, SE-17176, Stockholm, Sweden.
| | - Monica Nistér
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska R8:05, Karolinska University Hospital in Solna, SE-17176, Stockholm, Sweden.
| | - Mikael S Lindström
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska R8:05, Karolinska University Hospital in Solna, SE-17176, Stockholm, Sweden.
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Wang H, Wu J, Liu X, He H, Ding F, Yang H, Cheng L, Liu W, Zhong J, Dai Y, Li G, He C, Yu L, Li J. Identification of short hairpin RNA targeting foot-and-mouth disease virus with transgenic bovine fetal epithelium cells. PLoS One 2012; 7:e42356. [PMID: 22905125 PMCID: PMC3414509 DOI: 10.1371/journal.pone.0042356] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 07/04/2012] [Indexed: 12/28/2022] Open
Abstract
Background Although it is known that RNA interference (RNAi) targeting viral genes protects experimental animals, such as mice, from the challenge of Foot-and-mouth disease virus (FMDV), it has not been previously investigated whether shRNAs targeting FMDV in transgenic dairy cattle or primary transgenic bovine epithelium cells will confer resistance against FMDV challenge. Principal Finding Here we constructed three recombinant lentiviral vectors containing shRNA against VP2 (RNAi-VP2), VP3 (RNAi-VP3), or VP4 (RNAi-VP4) of FMDV, and found that all of them strongly suppressed the transient expression of a FLAG-tagged viral gene fusion protein in 293T cells. In BHK-21 cells, RNAi-VP4 was found to be more potent in inhibition of viral replication than the others with over 98% inhibition of viral replication. Therefore, recombinant lentiviral vector RNAi-VP4 was transfected into bovine fetal fibroblast cells to generate transgenic nuclear donor cells. With subsequent somatic cell cloning, we generated forty transgenic blastocysts, and then transferred them to 20 synchronized recipient cows. Three transgenic bovine fetuses were obtained after pregnant period of 4 months, and integration into chromosome in cloned fetuses was confirmed by Southern hybridization. The primary tongue epithelium cells of transgenic fetuses were isolated and inoculated with 100 TCID50 of FMDV, and it was observed that shRNA significantly suppressed viral RNA synthesis and inhibited over 91% of viral replication after inoculation of FMDV for 48 h. Conclusion RNAi-VP4 targeting viral VP4 gene appears to prevent primary epithelium cells of transgenic bovine fetus from FMDV infection, and it could be a candidate shRNA used for cultivation of transgenic cattle against FMDV.
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Affiliation(s)
- Hongmei Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China
| | - Jianming Wu
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China
| | - Xiao Liu
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China
| | - Hongbin He
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China
- * E-mail: (HH); (GL)
| | - Fangrong Ding
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, People's Republic of China
| | - Hongjun Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China
| | - Lei Cheng
- College of Life Science, Inner Mongolia University, Huhehaote, People's Republic of China
| | - Wenhao Liu
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China
| | - Jifeng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China
| | - Yunping Dai
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, People's Republic of China
| | - Guangpeng Li
- College of Life Science, Inner Mongolia University, Huhehaote, People's Republic of China
- * E-mail: (HH); (GL)
| | - Chengqiang He
- College of Life Science, Shandong Normal University, Jinan, People's Republic of China
| | - Li Yu
- Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Harbin, People's Republic of China
| | - Jianbin Li
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China
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