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Joy J, Fusari E, Milán M. Aneuploidy-induced cellular behaviors: Insights from Drosophila. Dev Cell 2024; 59:295-307. [PMID: 38320484 DOI: 10.1016/j.devcel.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/09/2023] [Accepted: 12/15/2023] [Indexed: 02/08/2024]
Abstract
A balanced gene complement is crucial for proper cell function. Aneuploidy, the condition of having an imbalanced chromosome set, alters the stoichiometry of gene copy numbers and protein complexes and has dramatic consequences at the cellular and organismal levels. In humans, aneuploidy is associated with different pathological conditions including cancer, microcephaly, mental retardation, miscarriages, and aging. Over the last century, Drosophila has provided a valuable system for studying the consequences of systemic aneuploidies. More recently, it has contributed to the identification and molecular dissection of aneuploidy-induced cellular behaviors and their impact at the tissue and organismal levels. In this perspective, we review this active field of research, first by comparing knowledge from yeast, mouse, and human cells, then by highlighting the contributions of Drosophila. The aim of these discussions was to further our understanding of the functional interplay between aneuploidy, cell physiology, and tissue homeostasis in human development and disease.
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Affiliation(s)
- Jery Joy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10-12, 08028 Barcelona, Spain
| | - Elena Fusari
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10-12, 08028 Barcelona, Spain
| | - Marco Milán
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10-12, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys, 23, 08010 Barcelona, Spain.
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2
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Макрецкая НА, Воронцова ИГ, Буянова АА, Коростин ДО, Петряйкина ЕЕ, Тюльпаков АН. [Syndromic growth retardation caused by impaired function of the ribosomal protein eL13]. PROBLEMY ENDOKRINOLOGII 2023; 70:93-97. [PMID: 39069777 PMCID: PMC11334233 DOI: 10.14341/probl13377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 10/23/2023] [Indexed: 07/30/2024]
Abstract
Growth retardation for more than 2 SD below the average population or presumed familial target height is classified as a short stature and may be a clinical manifestation of a large number of disorders. The use of the latest methods of molecular genetic analysis in recent years has allowed for a better understanding of the pathogenesis of inherited forms of a short stature. One of the recently discovered mechanisms of this pathology was monoallelic mutations in RPL13 gene, leading to the development of Isidor-Toutain type spondyloepimetaphyseal dysplasia (SEDM). Characteristic phenotypic features for this form are normal birth length, early postnatal growth deficiency, platyspondyly, proximal femoral epiphyseal changes, coxa vara, genu varum. This study presents the clinical and radiological characteristics of the first patient in the Russian -Federation with SEMD caused by a mutation in RPL13 gene.
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Affiliation(s)
- Н. А. Макрецкая
- Медико-генетический научный центр имени академика Н.П. Бочкова
| | | | - А. А. Буянова
- Центр высокоточного редактирования и генетических технологий для биомедицины ФГАОУ ВО РНИМУ им. Н.И. Пирогова Минздрава России
| | - Д. О. Коростин
- Центр высокоточного редактирования и генетических технологий для биомедицины ФГАОУ ВО РНИМУ им. Н.И. Пирогова Минздрава России
| | | | - А. Н. Тюльпаков
- Медико-генетический научный центр имени академика Н.П. Бочкова; Российская детская клиническая больница
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3
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Li Y, Han L, Li P, Ge J, Xue Y, Chen L. Potential network markers and signaling pathways for B cells of COVID-19 based on single-cell condition-specific networks. BMC Genomics 2023; 24:619. [PMID: 37853311 PMCID: PMC10583333 DOI: 10.1186/s12864-023-09719-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 10/05/2023] [Indexed: 10/20/2023] Open
Abstract
To explore the potential network markers and related signaling pathways of human B cells infected by COVID-19, we performed standardized integration and analysis of single-cell sequencing data to construct conditional cell-specific networks (CCSN) for each cell. Then the peripheral blood cells were clustered and annotated based on the conditional network degree matrix (CNDM) and gene expression matrix (GEM), respectively, and B cells were selected for further analysis. Besides, based on the CNDM of B cells, the hub genes and 'dark' genes (a gene has a significant difference between case and control samples not in a gene expression level but in a conditional network degree level) closely related to COVID-19 were revealed. Interestingly, some of the 'dark' genes and differential degree genes (DDGs) encoded key proteins in the JAK-STAT pathway, which had antiviral effects. The protein p21 encoded by the 'dark' gene CDKN1A was a key regulator for the COVID-19 infection-related signaling pathway. Elevated levels of proteins encoded by some DDGs were directly related to disease severity of patients with COVID-19. In short, the proteins encoded by 'dark' genes complement some missing links in COVID-19 and these signaling pathways played an important role in the growth and activation of B cells.
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Affiliation(s)
- Ying Li
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang, 471023, China
- Longmen Laboratory, Luoyang, 471003, Henan, China
| | - Liqin Han
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang, 471023, China
- Longmen Laboratory, Luoyang, 471003, Henan, China
| | - Peiluan Li
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang, 471023, China.
- Longmen Laboratory, Luoyang, 471003, Henan, China.
| | - Jing Ge
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Yun Xue
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 201100, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310000, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201100, China.
- West China Biomedical Big Data Center, Med-X Center for Informatics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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4
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Miller SC, MacDonald CC, Kellogg MK, Karamysheva ZN, Karamyshev AL. Specialized Ribosomes in Health and Disease. Int J Mol Sci 2023; 24:ijms24076334. [PMID: 37047306 PMCID: PMC10093926 DOI: 10.3390/ijms24076334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
Ribosomal heterogeneity exists within cells and between different cell types, at specific developmental stages, and occurs in response to environmental stimuli. Mounting evidence supports the existence of specialized ribosomes, or specific changes to the ribosome that regulate the translation of a specific group of transcripts. These alterations have been shown to affect the affinity of ribosomes for certain mRNAs or change the cotranslational folding of nascent polypeptides at the exit tunnel. The identification of specialized ribosomes requires evidence of the incorporation of different ribosomal proteins or of modifications to rRNA and/or protein that lead(s) to physiologically relevant changes in translation. In this review, we summarize ribosomal heterogeneity and specialization in mammals and discuss their relevance to several human diseases.
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Affiliation(s)
- Sarah C. Miller
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Clinton C. MacDonald
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Morgana K. Kellogg
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | | | - Andrey L. Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Correspondence: ; Tel.: +1-806-743-4102
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Llavanera M, Delgado-Bermúdez A, Ribas-Maynou J, Salas-Huetos A, Yeste M. A systematic review identifying fertility biomarkers in semen: a clinical approach through Omics to diagnose male infertility. Fertil Steril 2022; 118:291-313. [PMID: 35718545 DOI: 10.1016/j.fertnstert.2022.04.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 02/03/2023]
Abstract
OBJECTIVE To identify the most robust molecular biomarkers in sperm and seminal plasma for the diagnosis of male infertility, and to evaluate their clinical use. DESIGN Systematic review. SETTING Not applicable. PATIENT(S) Accessible studies reporting well-defined (in)fertile populations and semen molecular biomarkers were included in this review. INTERVENTION(S) A systematic search of the literature published in MEDLINE-PubMed and EMBASE databases was performed, following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. MAIN OUTCOME MEASURE(S) The primary outcome was the content, expression, or activity of molecular biomarkers in human semen samples. Only studies reporting a receiver-operating characteristic (ROC) analysis values were included. RESULT(S) Eighty-nine studies were included. Direct evaluation of sperm DNA damage has high potential as a diagnostic biomarker of fertility and assisted reproductive technology outcomes (area under the curve [AUCs] median = 0.67). Regarding strand break-associated chromatin modifications, γH2AX levels show good predictive value for the diagnosis of male infertility (AUCs median = 0.93). Some noncoding ribonucleic acid (RNA) exhibit excellent predictive values; miR-34c-5p in semen is the most well-characterized and robust transcriptomic biomarker (AUCs median = 0.78). While many proteins in semen show fair diagnostic value for sperm quality and fertilizing capacity, the levels of some, such as TEX101, in seminal plasma have an excellent diagnostic potential (AUCs median = 0.69). Although individual metabolites and metabolomic profiles in seminal plasma present good predictive value, the latter seem to be better than the former when inferring sperm quality and fertilizing capacity. CONCLUSION(S) The current review supports that some Omics (e.g., DNA structure and integrity, genomics and epigenomics, transcriptomics, metabolomics, and proteomics) could be considered relevant molecular biomarkers that may help identify infertility etiologies and fertilization prognosis with cost-effective, simple, and accurate diagnosis.
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Affiliation(s)
- Marc Llavanera
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, Spain; Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, Spain
| | - Ariadna Delgado-Bermúdez
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, Spain; Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, Spain
| | - Jordi Ribas-Maynou
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, Spain; Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, Spain
| | - Albert Salas-Huetos
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, Spain; Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, Spain; Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts; Consorcio CIBER, M.P., Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
| | - Marc Yeste
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, Spain; Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, Spain
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Lan T, Xiong W, Chen X, Mo B, Tang G. Plant cytoplasmic ribosomal proteins: an update on classification, nomenclature, evolution and resources. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:292-318. [PMID: 35000252 DOI: 10.1111/tpj.15667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/23/2021] [Accepted: 01/02/2022] [Indexed: 06/14/2023]
Abstract
Standardized naming systems are essential to integrate and unify distinct research fields, and to link multi-species data within and across kingdoms. We conducted a comprehensive survey of cytoplasmic ribosomal proteins (CRPs) in the dicot model Arabidopsis thaliana and the monocot model rice, noting that the standardized naming system has not been widely adopted in the plant community. We generated a database linking the old classical names to their updated and compliant names. We also explored the sequences, molecular evolution, and structural and functional characteristics of all plant CRP families, emphasizing evolutionarily conserved and plant-specific features through cross-kingdom comparisons. Unlike fungal CRP paralogs that were mainly created by whole-genome duplication (WGD) or retroposition under a concerted evolution mode, plant CRP genes evolved primarily through both WGD and tandem duplications in a rapid birth-and-death process. We also provide a web-based resource (http://www.plantcrp.cn/) with the aim of sharing the latest knowledge on plant CRPs and facilitating the continued development of a standardized framework across the entire community.
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Affiliation(s)
- Ting Lan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Wei Xiong
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, 92521, CA, USA
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Guiliang Tang
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, 49931, MI, USA
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7
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Bhattacharya A, Freedman AN, Avula V, Harris R, Liu W, Pan C, Lusis AJ, Joseph RM, Smeester L, Hartwell HJ, Kuban KCK, Marsit CJ, Li Y, O'Shea TM, Fry RC, Santos HP. Placental genomics mediates genetic associations with complex health traits and disease. Nat Commun 2022; 13:706. [PMID: 35121757 PMCID: PMC8817049 DOI: 10.1038/s41467-022-28365-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/15/2021] [Indexed: 01/09/2023] Open
Abstract
As the master regulator in utero, the placenta is core to the Developmental Origins of Health and Disease (DOHaD) hypothesis but is historically understudied. To identify placental gene-trait associations (GTAs) across the life course, we perform distal mediator-enriched transcriptome-wide association studies (TWAS) for 40 traits, integrating placental multi-omics from the Extremely Low Gestational Age Newborn Study. At [Formula: see text], we detect 248 GTAs, mostly for neonatal and metabolic traits, across 176 genes, enriched for cell growth and immunological pathways. In aggregate, genetic effects mediated by placental expression significantly explain 4 early-life traits but no later-in-life traits. 89 GTAs show significant mediation through distal genetic variants, identifying hypotheses for distal regulation of GTAs. Investigation of one hypothesis in human placenta-derived choriocarcinoma cells reveal that knockdown of mediator gene EPS15 upregulates predicted targets SPATA13 and FAM214A, both associated with waist-hip ratio in TWAS, and multiple genes involved in metabolic pathways. These results suggest profound health impacts of placental genomic regulation in developmental programming across the life course.
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Affiliation(s)
- Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
- Institute for Quantitative and Computational Biosciences, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
| | - Anastasia N Freedman
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Vennela Avula
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Rebeca Harris
- Biobehavioral Laboratory, School of Nursing, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Weifang Liu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Calvin Pan
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Aldons J Lusis
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Robert M Joseph
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Lisa Smeester
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Hadley J Hartwell
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Karl C K Kuban
- Department of Pediatrics, Division of Pediatric Neurology, Boston University Medical Center, Boston, MA, 02118, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health Emory University, Atlanta, GA, 30322, USA
| | - Yun Li
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27514, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - T Michael O'Shea
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA.
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA.
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina, Chapel Hill, NC, 27514, USA.
| | - Hudson P Santos
- Biobehavioral Laboratory, School of Nursing, University of North Carolina, Chapel Hill, NC, 27514, USA.
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA.
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8
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Chunduri NK, Menges P, Zhang X, Wieland A, Gotsmann VL, Mardin BR, Buccitelli C, Korbel JO, Willmund F, Kschischo M, Raeschle M, Storchova Z. Systems approaches identify the consequences of monosomy in somatic human cells. Nat Commun 2021; 12:5576. [PMID: 34552071 PMCID: PMC8458293 DOI: 10.1038/s41467-021-25288-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 07/30/2021] [Indexed: 01/22/2023] Open
Abstract
Chromosome loss that results in monosomy is detrimental to viability, yet it is frequently observed in cancers. How cancers survive with monosomy is unknown. Using p53-deficient monosomic cell lines, we find that chromosome loss impairs proliferation and genomic stability. Transcriptome and proteome analysis demonstrates reduced expression of genes encoded on the monosomes, which is partially compensated in some cases. Monosomy also induces global changes in gene expression. Pathway enrichment analysis reveals that genes involved in ribosome biogenesis and translation are downregulated in all monosomic cells analyzed. Consistently, monosomies display defects in protein synthesis and ribosome assembly. We further show that monosomies are incompatible with p53 expression, likely due to defects in ribosome biogenesis. Accordingly, impaired ribosome biogenesis and p53 inactivation are associated with monosomy in cancer. Our systematic study of monosomy in human cells explains why monosomy is so detrimental and reveals the importance of p53 for monosomy occurrence in cancer. The mechanisms that allow cancer cells to survive with monosomies are poorly understood. Here the authors analyse p53-deficient monosomic cell lines using transcriptomics and proteomics, and find that impaired ribosome biogenesis and p53 downregulation are associated with sustained monosomies.
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Affiliation(s)
| | - Paul Menges
- Department of Molecular Genetics, TU Kaiserslautern, Kaiserslautern, Germany
| | - Xiaoxiao Zhang
- University of Applied Sciences Koblenz, Remagen, Germany
| | - Angela Wieland
- Department of Molecular Genetics, TU Kaiserslautern, Kaiserslautern, Germany
| | | | - Balca R Mardin
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Jan O Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Felix Willmund
- Group Genetics of Eukaryotes, TU Kaiserslautern, Kaiserslautern, Germany
| | - Maik Kschischo
- University of Applied Sciences Koblenz, Remagen, Germany
| | - Markus Raeschle
- Department of Molecular Genetics, TU Kaiserslautern, Kaiserslautern, Germany
| | - Zuzana Storchova
- Department of Molecular Genetics, TU Kaiserslautern, Kaiserslautern, Germany.
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9
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Guo YQ, Yang Y, Chai Y, Gao LL, Ma R. Identification and Evaluation of Reference Genes for Quantitative PCR Normalization in Alligator Weed Flea Beetle (Coleoptera: Chrysomelidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2021; 21:6378301. [PMID: 34591086 PMCID: PMC8482964 DOI: 10.1093/jisesa/ieab067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Indexed: 06/13/2023]
Abstract
Stably expressed reference genes are critical internal standards for the quantification of gene transcription levels using quantitative real-time PCR. Housekeeping genes are commonly used as reference genes but their expressions were variable depending on experimental conditions in many insect species studied. Here we report the identification and evaluation of 10 housekeeping genes in alligator weed flea beetle, Agasicles hygrophila Selman & Vogt (Coleoptera: Chrysomelidae), a biocontrol agent of alligator weed. The 10 housekeeping genes are: beta-actin (Actin), ribosomal protein L13A (PRL13a), succinate dehydrogenase complex subunit A (SDHA), ribosomal protein S20 (RPS20), ribosomal protein S13 (RPS13), glyceraldehyde phosphate dehydrogenase (GAPDH), TATA-box-binding protein (TBP), ribosomal protein L32 (RPL32), tubulin alpha-1 chain (TUBULIN), and elongation factor-1 alpha (ELF). Five programs, geNorm, NormFinder, BestKeeper, ΔCt method, and RefFinder, were used to evaluate the expression stability of the 10 genes among various A. hygrophila body parts and with different nutrient types (starvation, diet types). The expression stability analysis showed that RPS32 and RPL13a were reliable reference genes for the study of gene transcription in different body parts; Actin and RPL13a were optimal reference genes for different nutrient types. The selections of reference genes were validated using a CarE gene (GeneBank No: KX353552). The results of this study provide useful bases for studies of gene expression in various aspects relating to A. hygrophila.
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Affiliation(s)
- Yan-Qiong Guo
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Yongchang Yang
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Yanping Chai
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Ling-Ling Gao
- CSIRO Agriculture and Food, Wembley 6014, Western Australia, Australia
| | - Ruiyan Ma
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi 030801, China
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10
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Mullis A, Lu Z, Zhan Y, Wang TY, Rodriguez J, Rajeh A, Chatrath A, Lin Z. Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance. Mol Biol Evol 2020; 37:455-468. [PMID: 31589316 PMCID: PMC6993855 DOI: 10.1093/molbev/msz229] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ribosomal protein (RP) genes encode structural components of ribosomes, the cellular machinery for protein synthesis. A single functional copy has been maintained in most of 78–80 RP families in animals due to evolutionary constraints imposed by gene dosage balance. Some fungal species have maintained duplicate copies in most RP families. The mechanisms by which the RP genes were duplicated and maintained and their functional significance are poorly understood. To address these questions, we identified all RP genes from 295 fungi and inferred the timing and nature of gene duplication events for all RP families. We found that massive duplications of RP genes have independently occurred by different mechanisms in three distantly related lineages: budding yeasts, fission yeasts, and Mucoromycota. The RP gene duplicates in budding yeasts and Mucoromycota were mainly created by whole genome duplication events. However, duplicate RP genes in fission yeasts were likely generated by retroposition, which is unexpected considering their dosage sensitivity. The sequences of most RP paralogs have been homogenized by repeated gene conversion in each species, demonstrating parallel concerted evolution, which might have facilitated the retention of their duplicates. Transcriptomic data suggest that the duplication and retention of RP genes increased their transcript abundance. Physiological data indicate that increased ribosome biogenesis allowed these organisms to rapidly consume sugars through fermentation while maintaining high growth rates, providing selective advantages to these species in sugar-rich environments.
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Affiliation(s)
- Alison Mullis
- Department of Biology, Saint Louis University, St. Louis, MO
| | - Zhaolian Lu
- Department of Biology, Saint Louis University, St. Louis, MO
| | - Yu Zhan
- Department of Biology, Saint Louis University, St. Louis, MO
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Judith Rodriguez
- Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO
| | - Ahmad Rajeh
- Department of Biology, Saint Louis University, St. Louis, MO.,Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO
| | - Ajay Chatrath
- Department of Biology, Saint Louis University, St. Louis, MO
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO
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Vriend J, Rastegar M. Ubiquitin ligases and medulloblastoma: genetic markers of the four consensus subgroups identified through transcriptome datasets. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165839. [PMID: 32445667 DOI: 10.1016/j.bbadis.2020.165839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 04/23/2020] [Accepted: 05/13/2020] [Indexed: 01/05/2023]
Abstract
The ubiquitin proteasome system regulates key cellular processes in normal and in cancer cells. Herein, we review published data on the role of ubiquitin ligases in the four major subgroups of medulloblastoma (MB). While conventional literature serves as an initial source of information on cellular pathways in MB, large publicly available datasets of gene expression can be used to add information not previously identified in the literature. By analysing the publicly available Cavalli dataset, we show that increased expression of ZNRF3 characterizes the WNT subgroup of MB. The ZNRF3 gene codes for an E3 ligase associated with WNT receptors. Loss of a copy of chromosome 6 in a subtype of the WNT group was associated with decreased expression of the gene encoding the E3 ligase RNF146. While the E3 ligase SMURF regulates SHH receptors, increased expression of the gene encoding the Cullin Ring E3 adaptor PPP2R2C was statistically a better genetic marker of the SHH group. Genes whose expression was statistically strongly related to Group 3 included the E3 ligase gene TRIM58, and the gene for the E3 ligase adaptor, PPP2R2B. Group 4 MB was associated with expression of genes encoding several E3 ligases and E3 ligase adaptors involved in ribosome biogenesis. Increased expression of the genes encoding the E3 ligase adaptors and transcription repressors ZBTB18 and ZBTB38 were also noted in subgroup 4. These data suggest that several E3 ligases and their adaptors should be investigated as therapeutic targets for subgroup specific MB brain tumors.
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Affiliation(s)
- Jerry Vriend
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.
| | - Mojgan Rastegar
- Department of Biochemistry and Medical Genetics and Regenerative Medicine Program, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
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12
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Deshpande P, Flinkman D, Hong Y, Goltseva E, Siino V, Sun L, Peltonen S, Elo LL, Kaasinen V, James P, Coffey ET. Protein synthesis is suppressed in sporadic and familial Parkinson's disease by LRRK2. FASEB J 2020; 34:14217-14233. [PMID: 32926469 DOI: 10.1096/fj.202001046r] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/12/2020] [Accepted: 07/29/2020] [Indexed: 12/21/2022]
Abstract
Gain of function LRRK2-G2019S is the most frequent mutation found in familial and sporadic Parkinson's disease. It is expected therefore that understanding the cellular function of LRRK2 will provide insight on the pathological mechanism not only of inherited Parkinson's, but also of sporadic Parkinson's, the more common form. Here, we show that constitutive LRRK2 activity controls nascent protein synthesis in rodent neurons. Specifically, pharmacological inhibition of LRRK2, Lrrk2 knockdown or Lrrk2 knockout, all lead to increased translation. In the rotenone model for sporadic Parkinson's, LRRK2 activity increases, dopaminergic neuron translation decreases, and the neurites atrophy. All are prevented by LRRK2 inhibitors. Moreover, in striatum and substantia nigra of rotenone treated rats, phosphorylation changes are observed on eIF2α-S52(↑), eIF2s2-S2(↓), and eEF2-T57(↑) in directions that signify protein synthesis arrest. Significantly, translation is reduced by 40% in fibroblasts from Parkinson's patients (G2019S and sporadic cases alike) and this is reversed upon LRRK2 inhibitor treatment. In cells from multiple system atrophy patients, translation is unchanged suggesting that repression of translation is specific to Parkinson's disease. These findings indicate that repression of translation is a proximal function of LRRK2 in Parkinson's pathology.
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Affiliation(s)
| | - Dani Flinkman
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland.,Department of Immunotechnology, Lund University, Lund, Sweden
| | - Ye Hong
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
| | - Elena Goltseva
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Valentina Siino
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Lihua Sun
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
| | - Sirkku Peltonen
- Department of Dermatology, University of Turku and Turku University Hospital, Turku, Finland
| | - Laura L Elo
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
| | - Valtteri Kaasinen
- Division of Clinical Neurosciences, Turku University Hospital and University of Turku, Turku, Finland
| | - Peter James
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland.,Department of Immunotechnology, Lund University, Lund, Sweden
| | - Eleanor T Coffey
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
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13
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Housekeeping gene validation for RT-qPCR studies on synovial fibroblasts derived from healthy and osteoarthritic patients with focus on mechanical loading. PLoS One 2019; 14:e0225790. [PMID: 31809510 PMCID: PMC6897414 DOI: 10.1371/journal.pone.0225790] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/12/2019] [Indexed: 12/13/2022] Open
Abstract
Selection of appropriate housekeeping genes is essential for the validity of data normalization in reverse transcription quantitative PCR (RT-qPCR). Synovial fibroblasts (SF) play a mediating role in the development and progression of osteoarthritis (OA) pathogenesis, but there is no information on reliable housekeeping genes available. Therefore the goal of this study was to identify a set of reliable housekeeping genes suitable for studies of mechanical loading on SF from healthy and OA patients. Nine genes were evaluated towards expression stability and ranked according their relative stability determined by four different mathematical procedures (geNorm, NormFinder, BestKeeper and comparative ΔCq). We observed that RPLP0 (ribosomal protein, large, P0) and EEF1A1 (eukaryotic translation elongation factor 1 alpha 1) turned out to be the genes with the most stable expression in SF from non-OA or OA patients treated with or without mechanical loading. According to geNorm two genes are sufficient for normalization throughout. Expression of one tested target gene varied considerably, if normalized to different candidate housekeeping genes. Our study provides a tool for accurate and valid housekeeping gene selection in gene expression experiments on SF from healthy and OA patients with and without mechanical loading in consistent with the MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines and additionally demonstrates the impact of proper housekeeping gene selection on the expression of the gene of interest.
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14
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Kong L, Wei Q, Hu X, Chen L, Li J. Ribosomal protein small subunit 15A (RPS15A) inhibits the apoptosis of breast cancer MDA-MB-231 cells via upregulating phosphorylated ERK1/2, Bad, and Chk1. J Cell Biochem 2019; 121:587-595. [PMID: 31535410 DOI: 10.1002/jcb.29304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 06/18/2019] [Indexed: 12/14/2022]
Abstract
AIM To detect the expression and identify the role of Ribosomal protein S15A (RPS15A) in human breast cancer (BC). METHODS Immunohistochemistry (IHC) was carried out for detecting the levels of RPS15A protein. Quantitative PCR was used to evaluate the mRNA level of RPS15A in one normal breast and three BC cell lines. Lentivirus-mediated shRNA targeting RPS15A was designed to investigate the impact of silencing RPS15A in MDA-MB-231 cell. RESULTS Higher RPS15A expression was detected in tumor tissues than in para-cancer tissues, and higher RPS15A expression was related to larger tumor size and higher TNM stage. Also, RPS15A mRNA expression in all three BC cell lines was higher than that in normal breast cell (all P < .005). Further, RPS15A knockdown significantly suppressed MDA-MB-231 cell proliferation and induced apoptosis. Moreover, RPS15A knockdown increased the caspase-3/-7 activity, and suppressed the phosphorylated levels of ERK1/2, Bad, and Chk1 (all P < .01). CONCLUSION RPS15A inhibits apoptosis via upregulating phosphorylated ERK1/2, Bad, and Chk1 in MDA-MB-231 cell line.
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Affiliation(s)
- Lingsuo Kong
- Department of Anesthesiology, Division of life Sciences and Medicine, West district of The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, Hefei, Anhui, China
| | - Qing Wei
- Department of Anesthesiology, Division of life Sciences and Medicine, West district of The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, Hefei, Anhui, China
| | - Xianwen Hu
- Department of Anesthesiology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lanren Chen
- Department of Anesthesiology, Division of life Sciences and Medicine, West district of The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, Hefei, Anhui, China
| | - Juan Li
- Department of Anesthesia, Qilu Medical College of Shandong University, Jinan, China
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Cao D, Luo Y, Qin S, Yu M, Mu Y, Ye G, Yang N, Cong Z, Chen J, Qin J, Cui R, Jing R, Cao H, Zhong M. Metallopanstimulin-1 (MPS-1) mediates the promotion effect of leptin on colorectal cancer through activation of JNK/c-Jun signaling pathway. Cell Death Dis 2019; 10:655. [PMID: 31506433 PMCID: PMC6736844 DOI: 10.1038/s41419-019-1911-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/24/2019] [Accepted: 08/26/2019] [Indexed: 01/11/2023]
Abstract
Obesity is a major epigenetic cause for colorectal cancer (CRC). Leptin is implicated in obesity-associated CRC, but the underlying mechanism remains unclear. The current study identified over-expression of metallopanstimulin-1 (MPS-1) in CRC patients through microarray and histological analysis, especially in obese CRC patients. MPS-1 was correlated with advanced tumor stage, suggesting its association with CRC progression. In addition, MPS-1 over-expression was associated with poor overall survival (OS) in obese CRC patients, but not in their non-obese counterparts, suggesting its potential as a prognostic marker of obese CRC patients. MPS-1 expression was positively associated with circulating leptin levels in CRC patients, especially in obese cases. Functional experiments demonstrated that MPS-1 silencing inhibited tumor proliferation and colony formation, and induced apoptosis of CRC cells in vitro. Converse results were obtained from the experiments with MPS-1 over-expression. Mechanistically, MPS-1 executed its action through induction of c-Jun N-terminal kinase (JNK)/c-Jun pathway. Moreover, the promotion effect of MPS-1 on CRC progression was modulated by leptin. In vivo studies demonstrated that MPS-1 silencing suppressed tumor growth of CRC via inhibiting JNK/c-Jun signaling. Collectively, this study indicates that MPS-1 promotes leptin-induced CRC via activating JNK/c-Jun pathway. MPS-1 might represent a potent candidate for the treatment and prognostic prediction of obesity-associated CRC.
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Affiliation(s)
- Dongxing Cao
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Yang Luo
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Shaolan Qin
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Minhao Yu
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Yifei Mu
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Guangyao Ye
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Nailin Yang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Zhijie Cong
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Jianjun Chen
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Jun Qin
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Ran Cui
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Ran Jing
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Hui Cao
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Ming Zhong
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
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16
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Integration analysis of a miRNA-mRNA expression in A549 cells infected with a novel H3N2 swine influenza virus and the 2009 H1N1 pandemic influenza virus. INFECTION GENETICS AND EVOLUTION 2019; 74:103922. [PMID: 31207403 DOI: 10.1016/j.meegid.2019.103922] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/29/2019] [Accepted: 06/13/2019] [Indexed: 01/08/2023]
Abstract
Swine are reservoirs for anthropogenic/zoonotic influenza viruses, and the prevalence and repeated introduction of the 2009 H1N1 pandemic influenza virus (pdm/09) into pigs raises the possibility of generating novel swine influenza viruses with the potential to infect humans. However, studies aiming to identify miRNAs involved in the transfer of novel swine influenza virus infection to human cells are rare. In this investigation, from the view of small RNA, microarrays and high-throughput sequencing were used to detect differentially expressed miRNAs and mRNAs after human lung epithelial cells were infected with the following three stains of influenza viruses: a novel H3N2 swine influenza virus reassorted with pdm/09 fragments, pdm/09 and classical swine influenza virus. A miRNA-mRNA interaction map was generated to show the correlation between miRNAs related to infection by the viruses with human infective potential/capability. The expression of 4 miRNAs (hsa-miR-96-5p, hsa-miR-140-5p, hsa-miR-30a-3p and hsa-miR-582-5p) and 5 relevant mRNAs (RCC1, ERVFRD-1, RANBP1, SCARB2 and RPS29) was determined. The integration analysis indicated that these candidates have rarely been reported to be associated with influenza virus. Focusing on miRNA expression changes could reveal novel reassortant viruses with human infective potential that may provide insight into future pandemics.
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17
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Raval NP, Shah TM, George LB, Joshi CG. Insight into bovine (Bos indicus) spermatozoal whole transcriptome profile. Theriogenology 2019; 129:8-13. [PMID: 30784792 DOI: 10.1016/j.theriogenology.2019.01.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 12/25/2018] [Accepted: 01/31/2019] [Indexed: 01/26/2023]
Abstract
Mature spermatozoa harbor both coding and non-coding type of RNAs which regulates spermatogenesis, fertilization and early development. Characterization of bovine sperm transcriptome can provide more insight into the molecular mechanisms involved in these processes. Here, we have analyzed whole transcriptome profile of Bos indicus spermatozoa to access the global RNA expression. RNA-Seq analysis identified 14,306 genes expressed with FPKM >0, while 405 genes expressed when threshold increased to FPKM >5. Functional annotations showed that sperm transcripts were associated with molecular processes (translation, ribosomal small and large subunit assembly) and cellular components (cytosolic small and large ribosomal subunit and membranes) related to known sperm functions at fertilization and spermatogenesis. The RNA-Seq data was validated using droplet digital PCR where both highly abundant gene viz. RN7SL1 and less abundant gene viz. ZFP280B were validated. This study may provide future directions in reproductive biology of Bos indicus.
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Affiliation(s)
- Nidhi P Raval
- Department of Zoology, Biomedical Technology and Human Genetics, University School of Sciences, Gujarat University, Ahmedabad, 380009, India
| | - Tejas M Shah
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Linz-Buoy George
- Department of Zoology, Biomedical Technology and Human Genetics, University School of Sciences, Gujarat University, Ahmedabad, 380009, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India.
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18
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Yuan F, Wang W, Cheng H. Co-expression network analysis of gene expression profiles of HER2 + breast cancer-associated brain metastasis. Oncol Lett 2018; 16:7008-7019. [PMID: 30546434 PMCID: PMC6256326 DOI: 10.3892/ol.2018.9562] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 07/30/2018] [Indexed: 12/13/2022] Open
Abstract
Brain metastasis occurs in ~30% of patients with breast cancer, and patients with human epidermal growth factor receptor 2 (HER2)+ breast cancer have a particularly high frequency of brain metastasis. Weighted gene co-expression network analysis was conducted to identify the hub differentially expressed genes from patients with HER2+ breast cancer between brain metastases and primary tumors. The potential candidate genes were investigated in another set of patient samples to confirm their relevance. The results indicated that a number of pathways altered significantly when breast cancer metastasized to the brain. Cyclophilin A (CypA) and ribosomal protein L17 (RPL17) were overexpressed in breast cancer-associated brain metastases, whereas tumor protein 63 (TP63) and von Willebrand factor A domain-containing 8 (VWA8) were significantly downregulated in breast cancer brain metastases. Furthermore, the expression of CypA and RPL17 in brain metastases were significantly increased compared with that in primary breast tumors, and the expression of TP63 and VWA8 in brain metastases were significantly decreased. This result indicated that the significant differences in expression observed between primary breast tumors and brain metastases were derived from significantly altered systems, including gene modules rather than single genes.
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Affiliation(s)
- Feng Yuan
- Department of Breast Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430079, P.R. China
| | - Wei Wang
- Department of Breast Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430079, P.R. China
| | - Hongtao Cheng
- Department of Breast Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430079, P.R. China
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19
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Yan TT, Fu XL, Li J, Bian YN, Liu DJ, Hua R, Ren LL, Li CT, Sun YW, Chen HY, Fang JY, Hong J. Downregulation of RPL15 may predict poor survival and associate with tumor progression in pancreatic ductal adenocarcinoma. Oncotarget 2016; 6:37028-42. [PMID: 26498693 PMCID: PMC4741913 DOI: 10.18632/oncotarget.5939] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/17/2015] [Indexed: 12/29/2022] Open
Abstract
Early diagnosis and treatment in pancreatic ductal adenocarcinoma (PDAC) is still a challenge worldwide. The poor survival of PDAC patients mainly due to early metastasis when first diagnosed and lack of prognostic biomarker. Ribosomal protein L15 (RPL15), an RNA-binding protein, is a component of ribosomal 60S subunit. It was reported that RPL15 is dysregulated in various type of cancers. However, little is known about the role of RPL15 in PDAC carcinogenesis and progression. Herein, we clarified RPL15 expression status may serve as an independent prognostic biomarker in three independent PDAC patient cohorts. We found that RPL15 was dramatically decreased in PDAC tissues and cell lines. The high expression of RPL15 was inversely correlated with TNM stage, histological differentiation, T classification and vascular invasion. Low expression of RPL15 was significantly associated with poor overall survival of PDAC patients. Furthermore, we demonstrated that the reduction of RPL15 may promote invasion ability of pancreatic cell by inducing EMT process. In conclusion, decreased RPL15 expression is associated with invasiveness of PDAC cells, and RPL15 expression status may serve as a reliable prognostic biomarker in PDAC patients.
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Affiliation(s)
- Ting-Ting Yan
- Division of Gastroenterology and Hepatology, Renji Hospital, Shanghai Institution of Digestive Disease, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory of Oncogene and Related Genes, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Xue-Liang Fu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Jiao Li
- Department of Biliary-Pancreatic Surgery, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Ying-Nan Bian
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - D Jun Liu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Rong Hua
- Department of Biliary-Pancreatic Surgery, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Lin-Lin Ren
- Division of Gastroenterology and Hepatology, Renji Hospital, Shanghai Institution of Digestive Disease, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory of Oncogene and Related Genes, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Cheng-Tao Li
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Yong-Wei Sun
- Department of Biliary-Pancreatic Surgery, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Hao-Yan Chen
- Division of Gastroenterology and Hepatology, Renji Hospital, Shanghai Institution of Digestive Disease, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory of Oncogene and Related Genes, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Renji Hospital, Shanghai Institution of Digestive Disease, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory of Oncogene and Related Genes, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Jie Hong
- Division of Gastroenterology and Hepatology, Renji Hospital, Shanghai Institution of Digestive Disease, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory of Oncogene and Related Genes, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
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20
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Friedenberg SG, Meurs KM, Mackay TFC. Evaluation of artificial selection in Standard Poodles using whole-genome sequencing. Mamm Genome 2016; 27:599-609. [PMID: 27510710 DOI: 10.1007/s00335-016-9660-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 07/28/2016] [Indexed: 12/11/2022]
Abstract
Identifying regions of artificial selection within dog breeds may provide insights into genetic variation that underlies breed-specific traits or diseases-particularly if these traits or disease predispositions are fixed within a breed. In this study, we searched for runs of homozygosity (ROH) and calculated the d i statistic (which is based upon F ST) to identify regions of artificial selection in Standard Poodles using high-coverage, whole-genome sequencing data of 15 Standard Poodles and 49 dogs across seven other breeds. We identified consensus ROH regions ≥1 Mb in length and common to at least ten Standard Poodles covering 0.6 % of the genome, and d i regions that most distinguish Standard Poodles from other breeds covering 3.7 % of the genome. Within these regions, we identified enriched gene pathways related to olfaction, digestion, and taste, as well as pathways related to adrenal hormone biosynthesis, T cell function, and protein ubiquitination that could contribute to the pathogenesis of some Poodle-prevalent autoimmune diseases. We also validated variants related to hair coat and skull morphology that have previously been identified as being under selective pressure in Poodles, and flagged additional polymorphisms in genes such as ITGA2B, CBX4, and TNXB that may represent strong candidates for other common Poodle disorders.
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Affiliation(s)
- Steven G Friedenberg
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA.
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, 27607, USA.
| | - Kathryn M Meurs
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, 27607, USA
| | - Trudy F C Mackay
- Department of Biological Sciences, College of Sciences, North Carolina State University, 3510 Thomas Hall, Raleigh, NC, 27695, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, 27607, USA
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21
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Integrative analyses shed new light on human ribosomal protein gene regulation. Sci Rep 2016; 6:28619. [PMID: 27346035 PMCID: PMC4921865 DOI: 10.1038/srep28619] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/06/2016] [Indexed: 12/05/2022] Open
Abstract
Ribosomal protein genes (RPGs) are important house-keeping genes that are well-known for their coordinated expression. Previous studies on RPGs are largely limited to their promoter regions. Recent high-throughput studies provide an unprecedented opportunity to study how human RPGs are transcriptionally modulated and how such transcriptional regulation may contribute to the coordinate gene expression in various tissues and cell types. By analyzing the DNase I hypersensitive sites under 349 experimental conditions, we predicted 217 RPG regulatory regions in the human genome. More than 86.6% of these computationally predicted regulatory regions were partially corroborated by independent experimental measurements. Motif analyses on these predicted regulatory regions identified 31 DNA motifs, including 57.1% of experimentally validated motifs in literature that regulate RPGs. Interestingly, we observed that the majority of the predicted motifs were shared by the predicted distal and proximal regulatory regions of the same RPGs, a likely general mechanism for enhancer-promoter interactions. We also found that RPGs may be differently regulated in different cells, indicating that condition-specific RPG regulatory regions still need to be discovered and investigated. Our study advances the understanding of how RPGs are coordinately modulated, which sheds light to the general principles of gene transcriptional regulation in mammals.
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22
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Zhang C, Fu J, Xue F, Ryu B, Zhang T, Zhang S, Sun J, Xu X, Shen Z, Zheng L, Chen X. Knockdown of ribosomal protein S15A induces human glioblastoma cell apoptosis. World J Surg Oncol 2016; 14:129. [PMID: 27130037 PMCID: PMC4850639 DOI: 10.1186/s12957-016-0891-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 04/21/2016] [Indexed: 11/11/2022] Open
Abstract
Background RPS15A is a ribosome protein that is highly conserved in many organisms from yeast to human. A number of studies implied its role in promoting cancer cell growth. Methods Here, we firstly conducted RPS15A gene expression analysis in brain cancer using Oncomine database and found RPS15A was remarkably overexpressed in glioblastoma (GBM) compared with that in normal tissues. Then, the expression of RPS15A was specifically silenced in GBM cell line U251 using lentiviral-mediated RNA interference technique. We further investigated the effect of RPS15A knockdown in U251 cells using MTT assay, colony formation test, and flow cytometry analysis. We detected the protein level of Bcl-2 and poly (ADP-ribose) polymerase (PARP) as well as activation of caspase-3. Results Our results showed that the knockdown of RPS15A could inhibit cancer cell growth and colony formation in vitro, as well as induced cell cycle arrest at G0/G1 phase and cell apoptosis. In addition, Western blot analysis indicated that the knockdown of RPS15A could significantly inhibit bcl-2 and activate caspase-3 and PARP. Conclusions Our findings suggest RPS15A may play an important role in the progression of GBM and lentiviral-mediated silencing of RPS15A could be an effective tool in GBM treatment.
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Affiliation(s)
- Chen Zhang
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, 301 Yanchang Road, Shanghai, 200072, China
| | - Jiqiang Fu
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, 301 Yanchang Road, Shanghai, 200072, China
| | - Fei Xue
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, 301 Yanchang Road, Shanghai, 200072, China
| | - Bomi Ryu
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 274 Middle Zhijiang Road, Shanghai, 200071, China
| | - Ting Zhang
- College of Medical Technology, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Shuili Zhang
- College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jingyu Sun
- Sports and Health Research Center, Tongji University Department of Physical Education, Shanghai, 200092, China
| | - Xinxin Xu
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, 301 Yanchang Road, Shanghai, 200072, China
| | - Zhaoli Shen
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, 301 Yanchang Road, Shanghai, 200072, China
| | - Longpo Zheng
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, 301 Yanchang Road, Shanghai, 200072, China.
| | - Xianzhen Chen
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, 301 Yanchang Road, Shanghai, 200072, China.
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Ali-Rahmani F, FitzGerald DJ, Martin S, Patel P, Prunotto M, Ormanoglu P, Thomas C, Pastan I. Anticancer Effects of Mesothelin-Targeted Immunotoxin Therapy Are Regulated by Tyrosine Kinase DDR1. Cancer Res 2016; 76:1560-8. [PMID: 26719540 PMCID: PMC4794364 DOI: 10.1158/0008-5472.can-15-2401] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/22/2015] [Indexed: 02/04/2023]
Abstract
Recombinant immunotoxins (RIT) have been highly successful in cancer therapy due, in part, to the high cancer-specific expression of cell surface antigens such as mesothelin, which is overexpressed in mesothelioma, ovarian, lung, breast, and pancreatic cancers, but is limited in normal cells. RG7787 is a clinically optimized RIT consisting of a humanized anti-mesothelin Fab fused to domain III of Pseudomonas exotoxin A, in which immunogenic B-cell epitopes are silenced. To enhance the therapeutic efficacy of RITs, we conducted a kinome RNAi sensitization screen, which identified discoidin domain receptor 1 (DDR1), a collagen-activated tyrosine kinase, as a potential target. The collagen/DDR1 axis is implicated in tumor-stromal interactions and potentially affects tumor response to therapy. Therefore, we investigated the effects of DDR1 on RIT. Knockdown of DDR1 by siRNA or treatment with inhibitor, 7rh, greatly enhanced the cytotoxic activity of RG7787 in several cancer cell lines. Investigation into the mechanism of action showed DDR1 silencing was associated with decreased expression of several ribosomal proteins and enhanced inhibition of protein synthesis. Conversely, induction of DDR1 expression or collagen-stimulated DDR1 activity protected cancer cells from RG7787 killing. Moreover, the combination of RG7787 and DDR1 inhibitor caused greater shrinkage of tumor xenografts than either agent alone. These data demonstrate that DDR1 is a key modulator of RIT activity and represents a novel therapeutic strategy to improve targeting of mesothelin-expressing cancers.
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Affiliation(s)
- Fatima Ali-Rahmani
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland
| | - David J FitzGerald
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Scott Martin
- National Center for Advancing Translational Sciences, NIH, Rockville, Maryland
| | - Paresma Patel
- National Center for Advancing Translational Sciences, NIH, Rockville, Maryland
| | - Marco Prunotto
- Discovery Technologies, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Pinar Ormanoglu
- National Center for Advancing Translational Sciences, NIH, Rockville, Maryland
| | - Craig Thomas
- National Center for Advancing Translational Sciences, NIH, Rockville, Maryland
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland.
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24
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Goudarzi KM, Lindström MS. Role of ribosomal protein mutations in tumor development (Review). Int J Oncol 2016; 48:1313-24. [PMID: 26892688 PMCID: PMC4777597 DOI: 10.3892/ijo.2016.3387] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/07/2016] [Indexed: 12/16/2022] Open
Abstract
Ribosomes are cellular machines essential for protein synthesis. The biogenesis of ribosomes is a highly complex and energy consuming process that initiates in the nucleolus. Recently, a series of studies applying whole-exome or whole-genome sequencing techniques have led to the discovery of ribosomal protein gene mutations in different cancer types. Mutations in ribosomal protein genes have for example been found in endometrial cancer (RPL22), T-cell acute lymphoblastic leukemia (RPL10, RPL5 and RPL11), chronic lymphocytic leukemia (RPS15), colorectal cancer (RPS20), and glioma (RPL5). Moreover, patients suffering from Diamond-Blackfan anemia, a bone marrow failure syndrome caused by mutant ribosomal proteins are also at higher risk for developing leukemia, or solid tumors. Different experimental models indicate potential mechanisms whereby ribosomal proteins may initiate cancer development. In particular, deregulation of the p53 tumor suppressor network and altered mRNA translation are mechanisms likely to be involved. We envisage that changes in expression and the occurrence of ribosomal protein gene mutations play important roles in cancer development. Ribosome biology constitutes a re-emerging vital area of basic and translational cancer research.
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Affiliation(s)
- Kaveh M Goudarzi
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, CCK R8:05, Karolinska University Hospital in Solna, Stockholm, Sweden
| | - Mikael S Lindström
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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25
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Yao Y, Liu Y, Lv X, Dong B, Wang F, Li J, Zhang Q, Xu R, Xu Y. Down-regulation of ribosomal protein S15A inhibits proliferation of human glioblastoma cells in vivo and in vitro via AKT pathway. Tumour Biol 2015; 37:4979-90. [PMID: 26537582 DOI: 10.1007/s13277-015-4323-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/26/2015] [Indexed: 01/13/2023] Open
Abstract
Ribosomal protein s15a (RPS15A), a highly conserved cytoplasmic protein, promotes mRNA/ribosome interaction in translation. Recent evidence showed that RPS15A is essential for tumor growth. RPS15A expression level was measured in glioblastoma tissue samples and normal brain (NB) tissue samples. RPS15A RNAi stable cell line U87 and U251 was generated by the pLVTHM-GFP lentiviral RNAi expression system. The knockdown efficiency was confirmed by quantitative real-time PCR and western blot. Molecular mechanisms and the effect of RPS15A on cell growth and migration were investigated by using western blot, MTT assay, wound healing assay, transwell migration assay, and tumorigenesis in nude mice. Here, we report that RPS15A is overexpressed in human glioblastoma tumor tissues. RPS15A knockdown inhibits proliferation and migration of glioblastoma cells in vitro. Knocking down RPS15A leads to the level of p-Akt decrease and cell cycle arrested in G0/G1 phase in U87 and U251 cells. Furthermore, the growth of glioblastoma cell-transplanted tumors in nude mice is inhibited by transduction with Lv-shRPS15A. Our findings indicate that RPS15A promotes cell proliferation and migration in glioblastoma for the first time. RPS15A might play a distinct role in glioblastoma and serve as a potential target for therapy.
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Affiliation(s)
- Yiqun Yao
- Department of Neurosurgery, First Affiliated Hospital, Dalian Medical University, 222 Zhong Shan Road, Dalian, 116011, People's Republic of China
| | - Yongjian Liu
- Department of interventional therapy, First Affiliated Hospital, Dalian Medical University, Dalian, People's Republic of China
| | - Xiupeng Lv
- Department of Neurosurgery, First Affiliated Hospital, Dalian Medical University, 222 Zhong Shan Road, Dalian, 116011, People's Republic of China
| | - Bin Dong
- Department of Neurosurgery, First Affiliated Hospital, Dalian Medical University, 222 Zhong Shan Road, Dalian, 116011, People's Republic of China
| | - Feng Wang
- Department of interventional therapy, First Affiliated Hospital, Dalian Medical University, Dalian, People's Republic of China
| | - Jun Li
- Department of Neurosurgery, First Affiliated Hospital, Dalian Medical University, 222 Zhong Shan Road, Dalian, 116011, People's Republic of China
| | - Qiuping Zhang
- Department of Pathology, First Affiliated Hospital, Dalian Medical University, Dalian, People's Republic of China
| | - Ruixue Xu
- Department of Neurosurgery, First Affiliated Hospital, Dalian Medical University, 222 Zhong Shan Road, Dalian, 116011, People's Republic of China
| | - Yinghui Xu
- Department of Neurosurgery, First Affiliated Hospital, Dalian Medical University, 222 Zhong Shan Road, Dalian, 116011, People's Republic of China.
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26
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Zhang C, Zhang T, Song E, Himaya SWA, Chen X, Zheng L. Ribosomal protein S15A augments human osteosarcoma cell proliferation in vitro. Cancer Biother Radiopharm 2015; 29:451-6. [PMID: 25409460 DOI: 10.1089/cbr.2014.1698] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
As a highly conserved housekeeping gene, the biological implications of ribosomal protein S15A (RPS15A) during various processes, including carcinogenesis, remain elusive. Herein, the authors reported that knockdown of RPS15A expression significantly inhibited human osteosarcoma U2OS cell proliferation and colony formation in vitro by using a lentivirus-mediated RNA interference (RNAi) system. Moreover, an excess accumulation of cells in the G0/G1 phase was observed in U2OS cells transduced with lentivirus targeting RPS15A, suggesting that the growth inhibition mediated by RPS15A knockdown in osteosarcoma cells was probably due to the induction of cell cycle arrest. Taken together, this study highlights the crucial role of RPS15A in promoting osteosarcoma cell proliferation, and provides a foundation for further study into the clinical potential of inhibition of RPS15A for the treatment of osteosarcoma.
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Affiliation(s)
- Chen Zhang
- 1 Shanghai Tenth People's Hospital, Tongji University School of Medicine , Shanghai, China
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27
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Kim TH, Leslie P, Zhang Y. Ribosomal proteins as unrevealed caretakers for cellular stress and genomic instability. Oncotarget 2015; 5:860-71. [PMID: 24658219 PMCID: PMC4011588 DOI: 10.18632/oncotarget.1784] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Ribosomal proteins (RPs) have gained much attention for their extraribosomal functions particularly with respect to p53 regulation. To date, about fourteen RPs have shown to bind to MDM2 and regulate p53. Upon binding to MDM2, the RPs suppress MDM2 E3 ubiquitin ligase activity resulting in the stabilization and activation of p53. Of the RPs that bind to MDM2, RPL5 and RPL11 are the most studied and RPL11 appears to have the most significant role in p53 regulation. Considering that more than 17% of RP species have been shown to interact with MDM2, one of the questions remains unresolved is why so many RPs bind MDM2 and modulate p53. Genes encoding RPs are widely dispersed on different chromosomes in both mice and humans. As components of ribosome, RP expression is tightly regulated to meet the appropriate stoichiometric ratio between RPs and rRNAs. Once genomic instability (e.g. aneuploidy) occurs, transcriptional and translational changes due to change of DNA copy number can result in an imbalance in the expression of RPs including those that bind to MDM2. Such an imbalance in RP expression could lead to failure to assemble functional ribosomes resulting in ribosomal stress. We propose that RPs have evolved ability to regulate MDM2 in response to genomic instability as an additional layer of p53 regulation. Full understanding of the biological roles of RPs could potentially establish RPs as a novel class of therapeutic targets in human diseases such as cancer.
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Affiliation(s)
- Tae-Hyung Kim
- Department of Radiation Oncology, University of North Carolina, Chapel Hill, NC, USA
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28
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Dharia AP, Obla A, Gajdosik MD, Simon A, Nelson CE. Tempo and mode of gene duplication in mammalian ribosomal protein evolution. PLoS One 2014; 9:e111721. [PMID: 25369106 PMCID: PMC4219774 DOI: 10.1371/journal.pone.0111721] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/06/2014] [Indexed: 12/17/2022] Open
Abstract
Gene duplication has been widely recognized as a major driver of evolutionary change and organismal complexity through the generation of multi-gene families. Therefore, understanding the forces that govern the evolution of gene families through the retention or loss of duplicated genes is fundamentally important in our efforts to study genome evolution. Previous work from our lab has shown that ribosomal protein (RP) genes constitute one of the largest classes of conserved duplicated genes in mammals. This result was surprising due to the fact that ribosomal protein genes evolve slowly and transcript levels are very tightly regulated. In our present study, we identified and characterized all RP duplicates in eight mammalian genomes in order to investigate the tempo and mode of ribosomal protein family evolution. We show that a sizable number of duplicates are transcriptionally active and are very highly conserved. Furthermore, we conclude that existing gene duplication models do not readily account for the preservation of a very large number of intact retroduplicated ribosomal protein (RT-RP) genes observed in mammalian genomes. We suggest that selection against dominant-negative mutations may underlie the unexpected retention and conservation of duplicated RP genes, and may shape the fate of newly duplicated genes, regardless of duplication mechanism.
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Affiliation(s)
- Asav P. Dharia
- University of Connecticut Department of Molecular and Cell Biology, Storrs, Connecticut, United States of America
| | - Ajay Obla
- University of Connecticut Department of Molecular and Cell Biology, Storrs, Connecticut, United States of America
| | - Matthew D. Gajdosik
- University of Connecticut Department of Molecular and Cell Biology, Storrs, Connecticut, United States of America
| | - Amanda Simon
- University of Connecticut Department of Molecular and Cell Biology, Storrs, Connecticut, United States of America
| | - Craig E. Nelson
- University of Connecticut Department of Molecular and Cell Biology, Storrs, Connecticut, United States of America
- * E-mail:
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29
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Spice EK, Whyard S, Docker MF. Gene expression during ovarian differentiation in parasitic and non-parasitic lampreys: implications for fecundity and life history types. Gen Comp Endocrinol 2014; 208:116-25. [PMID: 25218130 DOI: 10.1016/j.ygcen.2014.08.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 08/14/2014] [Accepted: 08/30/2014] [Indexed: 12/12/2022]
Abstract
Lampreys diverged from the jawed vertebrate lineage approximately 500million years ago. Lampreys undergo sex differentiation much later than most other vertebrates, and ovarian differentiation occurs several years before testicular differentiation. The genetic basis of lamprey sex differentiation is of particular interest both because of the phylogenetic importance of lampreys and because of their unusual pattern of sex differentiation. As well, differences between parasitic and non-parasitic lampreys may first become evident at ovarian differentiation. However, nothing is known about the genetic basis of ovarian differentiation in lampreys. This study examined potential differences in gene expression before, during, and after ovarian differentiation in parasitic chestnut lamprey Ichthyomyzon castaneus and non-parasitic northern brook lamprey Ichthyomyzonfossor. Eight target genes (17β-hydroxysteroid dehydrogenase, germ cell-less, estrogen receptor β, insulin-like growth factor 1 receptor, daz-associated protein 1, cytochrome c oxidase subunit III, Wilms' tumour suppressor protein 1, and dehydrocholesterol reductase 7) were examined. Northern brook lamprey displayed higher expression of cytochrome c oxidase subunit III, whereas chestnut lamprey displayed higher expression of insulin-like growth factor 1 receptor; these genes may be involved in apoptosis and oocyte growth, respectively. Presumptive male larvae had higher expression of Wilms' tumour suppressor protein 1, which may be involved in the undifferentiated gonad and/or later testicular development. Differentiated females had higher expression of 17β hydroxysteroid dehydrogenase and daz-associated protein 1, which may be involved in female development. This study is the first to identify genes that may be involved in ovarian differentiation and fecundity in lampreys.
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Affiliation(s)
- Erin K Spice
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.
| | - Steven Whyard
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.
| | - Margaret F Docker
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.
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30
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Lan X, Li D, Zhong B, Ren J, Wang X, Sun Q, Li Y, Liu L, Liu L, Lu S. Identification of differentially expressed genes related to metabolic syndrome induced with high-fat diet in E3 rats. Exp Biol Med (Maywood) 2014; 240:235-41. [PMID: 25294893 DOI: 10.1177/1535370214554531] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Understanding the genes differentially expressing in aberrant organs of metabolic syndrome (MetS) facilitates the uncovering of molecular mechanisms and the identification of novel therapeutic targets for the disease. This study aimed to identify differentially expressed genes related to MetS in livers of E3 rats with high-fat-diet-induced metabolic syndrome (HFD-MetS). E3 rats were fed with high-fat diet for 24 weeks to induce MetS. Then, suppression subtractive hybridization (SSH) technology was used to identify the genes differentially expressed between HFD-MetS and control E3 rat livers. Twenty positive recombinant clones were chosen randomly from forward subtractive library and sent to sequence. BLAST analysis in GenBank database was used to determine the property of each cDNA fragment. In total, 11 annotated genes, 3 ESTs, and 2 novel gene fragments were identified by SSH technology. The expression of four genes (Alb, Pip4k2a, Scd1, and Tf) known to be associated with MetS and other five genes (Eif1, Rnase4, Rps12, Rup2, and Tmsb4) unknown to be relevant to MetS was significantly up-regulated in the livers of HFD-MetS E3 rats compared with control rats using real-time quantitative PCR (RT-qPCR). By analyzing the correlations between the expression of these nine genes and serum concentrations of TG, Tch, HDL-C, and LDL-C, we found that there were significant positive correlations between TG and the expression of five genes (Alb, Eif1, Pip4k2a, Rps12, and Tmsb4x), Tch and three genes (Rnase4, Scd1, and Tmsb4x), and LDL-C and two genes (Rnase4 and Scd1), as well there were significant negative correlations between HDL-C and the expression of three genes (Rup2, Scd1, and Tf). This study provides important clues for unraveling the molecular mechanisms of MetS.
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Affiliation(s)
- Xi Lan
- Department of Genetics and Molecular Biology, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi 710061, PR China Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi 710061, PR China
| | - Dongmin Li
- Department of Genetics and Molecular Biology, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi 710061, PR China Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi 710061, PR China
| | - Bo Zhong
- Department of Genetics and Molecular Biology, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi 710061, PR China Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi 710061, PR China
| | - Juan Ren
- Department of Genetics and Molecular Biology, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi 710061, PR China Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi 710061, PR China
| | - Xuan Wang
- Department of Genetics and Molecular Biology, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi 710061, PR China Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi 710061, PR China
| | - Qingzhu Sun
- Department of Genetics and Molecular Biology, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi 710061, PR China Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi 710061, PR China
| | - Yue Li
- Department of Genetics and Molecular Biology, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi 710061, PR China Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi 710061, PR China
| | - Lee Liu
- Department of Genetics and Molecular Biology, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi 710061, PR China Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi 710061, PR China
| | - Li Liu
- Department of Genetics and Molecular Biology, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi 710061, PR China Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi 710061, PR China
| | - Shemin Lu
- Department of Genetics and Molecular Biology, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi 710061, PR China Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi 710061, PR China
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Abstract
Meningiomas represent one-third of all primary brain tumors and cause 35,000 new cases each year. Because of this high incidence, we sought to determine if there are proteomic differences between meningiomas and neighboring tissues. Two-dimensional gel electrophoresis and mass spectrometry were used to detect differentially expressed proteins in tumor samples, using arachnoid tissue as a control. Western blot analysis was used to validate the identified candidate proteins. We obtained quantitative data on 112 proteins, 17 of which were down-regulated and 26 of which were up-regulated in meningiomas relative to normal arachnoid tissue. Our analysis showed that the expression of galectin-3, vimentin, and endoplasmin was decreased significantly in meningiomas. The expression of 40S ribosomal protein S12, glutathione S-transferase P, and hypoxia up-regulated protein 1 was increased significantly (P < 0.05). The six above-mentioned differentially expressed proteins might be closely involved with the development of meningiomas. The results of this study provide basic insights into the proteome of meningiomas and provide a preliminary database for further research to enhance understanding of meningioma development.
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32
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Fuentes EN, Zuloaga R, Valdes JA, Molina A, Alvarez M. Skeletal muscle plasticity induced by seasonal acclimatization involves IGF1 signaling: implications in ribosomal biogenesis and protein synthesis. Comp Biochem Physiol B Biochem Mol Biol 2014; 176:48-57. [PMID: 25088252 DOI: 10.1016/j.cbpb.2014.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/11/2014] [Accepted: 07/22/2014] [Indexed: 12/15/2022]
Abstract
One of the most fundamental biological processes in living organisms that are affected by environmental fluctuations is growth. In fish, skeletal muscle accounts for the largest proportion of body mass, and the growth of this tissue is mainly controlled by the insulin-like growth factor (IGF) system. By using the carp (Cyprinus carpio), a fish that inhabits extreme conditions during winter and summer, we assessed the skeletal muscle plasticity induced by seasonal acclimatization and the relation of IGF signaling with protein synthesis and ribosomal biogenesis. The expression of igf1 in muscle decreased during winter in comparison with summer, whereas the expression for both paralogues of igf2 did not change significantly between seasons. The expression of igf1 receptor a (igf1ra), but not of igf1rb, was down-regulated in muscle during the winter as compared to the summer. A decrease in protein contents and protein phosphorylation for IGF signaling molecules in muscle was observed in winter-acclimatized carp. This was related with a decreased expression in muscle for markers of myogenesis (myoblast determination factor (myod), myogenic factor 5 (myf5), and myogenin (myog)); protein synthesis (myosin heavy chain (mhc) and myosin light chain (mlc3 and mlc1b)); and ribosomal biogenesis (pre-rRNA and ribosomal proteins). IGF signaling, and key markers of ribosomal biogenesis, protein synthesis, and myogenesis were affected by seasonal acclimatization, with differential regulation in gene expression and signaling pathway activation observed in muscle between both seasons. This suggests that these molecules are responsible for the muscle plasticity induced by seasonal acclimatization in carp.
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Affiliation(s)
- Eduardo N Fuentes
- Laboratorio de Biotecnología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Av. Republica 217, Santiago, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile.
| | - Rodrigo Zuloaga
- Laboratorio de Biotecnología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Av. Republica 217, Santiago, Chile
| | - Juan Antonio Valdes
- Laboratorio de Biotecnología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Av. Republica 217, Santiago, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile
| | - Alfredo Molina
- Laboratorio de Biotecnología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Av. Republica 217, Santiago, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile
| | - Marco Alvarez
- Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile; Laboratorio de Biología Celular y Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Quillota 980, Viña del Mar, Chile.
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Vossaert L, O'Leary T, Van Neste C, Heindryckx B, Vandesompele J, De Sutter P, Deforce D. Reference loci for RT-qPCR analysis of differentiating human embryonic stem cells. BMC Mol Biol 2013; 14:21. [PMID: 24028740 PMCID: PMC3848990 DOI: 10.1186/1471-2199-14-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 09/11/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Selecting stably expressed reference genes is essential for proper reverse transcription quantitative polymerase chain reaction gene expression analysis. However, this choice is not always straightforward. In the case of differentiating human embryonic stem (hES) cells, differentiation itself introduces changes whereby reference gene stability may be influenced. RESULTS In this study, we evaluated the stability of various references during retinoic acid-induced (2 microM) differentiation of hES cells. Out of 12 candidate references, beta-2-microglobulin, ribosomal protein L13A and Alu repeats are found to be the most stable for this experimental set-up. CONCLUSIONS Our results show that some of the commonly used reference genes are actually not amongst the most stable loci during hES cell differentiation promoted by retinoic acid. Moreover, a novel normalization strategy based on expressed Alu repeats is validated for use in hES cell experiments.
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Affiliation(s)
- Liesbeth Vossaert
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Harelbekestraat 72, Ghent 9000, Belgium.
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Jacobi A, Rauh J, Bernstein P, Liebers C, Zou X, Stiehler M. Comparative analysis of reference gene stability in human mesenchymal stromal cells during osteogenic differentiation. Biotechnol Prog 2013; 29:1034-42. [PMID: 23674393 DOI: 10.1002/btpr.1747] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 03/27/2013] [Indexed: 01/07/2023]
Abstract
Mesenchymal stromal cells (MSCs) are one of the most frequently used cell sources for tissue engineering strategies. Cultivation of osteogenic MSCs is a prerequisite for cell-based concepts that aim at bone regeneration. Quantitative real time reverse transcription polymerase chain reaction (qRT-PCR) analysis is a commonly used method for the examination of mRNA expression levels. However, data on suitable reference genes for osteogenically cultivated MSCs is scarce. Hence, the aim of the study was to compare the regulation of different potential reference genes in osteogenically stimulated MSCs. Human MSCs were isolated from bone marrow aspirates of N = 6 hematologically healthy individuals, expanded by polystyrene-adherence, and maintained with and without osteogenic supplements for 14 days. Cellular proliferation and osteogenic differentiation were assessed by total DNA quantification, cell-specific alkaline phosphatase (ALP) activity and by qualitative staining for ALP and alizarin red, respectively. mRNA expression levels of N = 32 potential reference genes were quantified using the human Endogenous Control TaqMan® assays. mRNA expression stability was calculated using geNorm. The combined use of the most stable reference genes and DNA-damage-inducible alpha, Pumilio homolog 1, and large ribosomal protein P0 significantly improved gene expression accuracy as compared to the use of the commonly used reference genes beta actin and glyceraldehyde-3-phosphate dehydrogenase during qRT-PCR-based target gene expression analysis of osteogenically stimulated MSCs.
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Affiliation(s)
- Angela Jacobi
- Dept. of Orthopaedics and Centre for Translational Bone, Joint and Soft Tissue Research, University Hospital Carl Gustav Carus, 01307, Dresden, Germany
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Yang ZY, Qu Y, Zhang Q, Wei M, Liu CX, Chen XH, Yan M, Zhu ZG, Liu BY, Chen GQ, Wu YL, Gu QL. Knockdown of metallopanstimulin-1 inhibits NF-κB signaling at different levels: the role of apoptosis induction of gastric cancer cells. Int J Cancer 2011; 130:2761-70. [PMID: 21796632 DOI: 10.1002/ijc.26331] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 07/15/2011] [Indexed: 01/23/2023]
Abstract
The ribosomal protein S27 (metallopanstimulin-1, MPS-1) has been reported to be a multifunctional protein, with increased expression in a number of cancers. We reported previously that MPS-1 was highly expressed in human gastric cancer. Knockdown of MPS-1 led to spontaneous apoptosis and repressed proliferation of human gastric cancer cells in vitro and in vivo. However, how does MPS-1 regulate these processes is unclear. Here we performed microarray and pathway analyses to investigate possible pathways involved in MPS-1 knockdown-induced apoptosis in gastric cancer cells. Our results showed that knockdown of MPS-1 inhibited NF-κB activity by reducing phosphorylation of p65 at Ser536 and IκBα at Ser32, inhibiting NF-κB nuclear translocation, and down-regulating its DNA binding activity. Furthermore, data-mining the Gene-Regulatory-Network revealed that growth arrest DNA damage inducible gene 45β (Gadd45β), a direct NF-κB target gene, played a critical role in MPS-1 knockdown-induced apoptosis. Over-expression of Gadd45β inhibited MPS-1 knockdown-induced apoptosis via inhibition of JNK phosphorylation. Taken together, these data revealed a novel pathway, the MPS-1/NF-κB/Gadd45β signal pathway, played an important role in MPS-1 knockdown-induced apoptosis of gastric cancer cells. This study sheds new light on the role of MPS-1/NF-κB in apoptosis and the possible use of MPS-1 targeting strategy in the treatment of gastric cancer.
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Affiliation(s)
- Zhong-Yin Yang
- Department of General Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Clarke C, Doolan P, Barron N, Meleady P, O'Sullivan F, Gammell P, Melville M, Leonard M, Clynes M. Large scale microarray profiling and coexpression network analysis of CHO cells identifies transcriptional modules associated with growth and productivity. J Biotechnol 2011; 155:350-9. [DOI: 10.1016/j.jbiotec.2011.07.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Revised: 07/07/2011] [Accepted: 07/08/2011] [Indexed: 12/31/2022]
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Gonçalves KDA, Bressan GC, Saito A, Morello LG, Zanchin NIT, Kobarg J. Evidence for the association of the human regulatory protein Ki-1/57 with the translational machinery. FEBS Lett 2011; 585:2556-60. [PMID: 21771594 DOI: 10.1016/j.febslet.2011.07.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Revised: 07/04/2011] [Accepted: 07/04/2011] [Indexed: 02/06/2023]
Abstract
Ki-1/57 is a cytoplasmic and nuclear protein of 57 kDa first identified in malignant cells from Hodgkin's lymphoma. Based on yeast-two hybrid protein interaction we found out that Ki-1/57 interacts with adaptor protein RACK1 (receptor of activated kinase 1), CIRP (cold-inducible RNA-binding protein), RPL38 (ribosomal protein L38) and FXR1 (fragile X mental retardation-related protein 1). Since these proteins are involved in the regulation of translation we suspected that Ki-1/57 may have a role in it. We show by immunoprecipitation the association of Ki-1/57 with FMRP. Confocal microscopy revealed that Ki-1/57 colocalizes with FMRP/FXR1/2 to stress granules. Furthermore Ki-1/57 cosediments with free ribosomal particles and enhances translation, when tethered to a reporter mRNA, suggesting that Ki-1/57 may be involved in translational regulation.
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Affiliation(s)
- Kaliandra de Almeida Gonçalves
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
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Barthel SR, Antonopoulos A, Cedeno-Laurent F, Schaffer L, Hernandez G, Patil SA, North SJ, Dell A, Matta KL, Neelamegham S, Haslam SM, Dimitroff CJ. Peracetylated 4-fluoro-glucosamine reduces the content and repertoire of N- and O-glycans without direct incorporation. J Biol Chem 2011; 286:21717-31. [PMID: 21493714 PMCID: PMC3122228 DOI: 10.1074/jbc.m110.194597] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 04/12/2011] [Indexed: 12/21/2022] Open
Abstract
Prior studies have shown that treatment with the peracetylated 4-fluorinated analog of glucosamine (4-F-GlcNAc) elicits anti-skin inflammatory activity by ablating N-acetyllactosamine (LacNAc), sialyl Lewis X (sLe(X)), and related lectin ligands on effector leukocytes. Based on anti-sLe(X) antibody and lectin probing experiments on 4-F-GlcNAc-treated leukocytes, it was hypothesized that 4-F-GlcNAc inhibited sLe(X) formation by incorporating into LacNAc and blocking the addition of galactose or fucose at the carbon 4-position of 4-F-GlcNAc. To test this hypothesis, we determined whether 4-F-GlcNAc is directly incorporated into N- and O-glycans released from 4-F-GlcNAc-treated human sLe(X) (+) T cells and leukemic KG1a cells. At concentrations that abrogated galectin-1 (Gal-1) ligand and E-selectin ligand expression and related LacNAc and sLe(X) structures, MALDI-TOF and MALDI-TOF/TOF mass spectrometry analyses showed that 4-F-GlcNAc 1) reduced content and structural diversity of tri- and tetra-antennary N-glycans and of O-glycans, 2) increased biantennary N-glycans, and 3) reduced LacNAc and sLe(X) on N-glycans and on core 2 O-glycans. Moreover, MALDI-TOF MS did not reveal any m/z ratios relating to the presence of fluorine atoms, indicating that 4-F-GlcNAc did not incorporate into glycans. Further analysis showed that 4-F-GlcNAc treatment had minimal effect on expression of 1200 glycome-related genes and did not alter the activity of LacNAc-synthesizing enzymes. However, 4-F-GlcNAc dramatically reduced intracellular levels of uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc), a key precursor of LacNAc synthesis. These data show that Gal-1 and E-selectin ligand reduction by 4-F-GlcNAc is not caused by direct 4-F-GlcNAc glycan incorporation and consequent chain termination but rather by interference with UDP-GlcNAc synthesis.
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Affiliation(s)
- Steven R. Barthel
- From the Harvard Skin Disease Research Center, Department of Dermatology, and
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Aristotelis Antonopoulos
- the Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Filiberto Cedeno-Laurent
- From the Harvard Skin Disease Research Center, Department of Dermatology, and
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Lana Schaffer
- Scripps Research Institute, La Jolla, California 92037
| | | | - Shilpa A. Patil
- the Department of Chemical and Biological Engineering, State University of New York, Buffalo, New York 14260, and
| | - Simon J. North
- the Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Anne Dell
- the Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Khushi L. Matta
- the Department of Cancer Biology, Roswell Park Cancer Institute, Buffalo, New York 14263
| | - Sriram Neelamegham
- the Department of Chemical and Biological Engineering, State University of New York, Buffalo, New York 14260, and
| | - Stuart M. Haslam
- the Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Charles J. Dimitroff
- From the Harvard Skin Disease Research Center, Department of Dermatology, and
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
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Woo S, Yum S. Transcriptional response of marine medaka (Oryzias javanicus) on exposure to toxaphene. Comp Biochem Physiol C Toxicol Pharmacol 2011; 153:355-61. [PMID: 21220043 DOI: 10.1016/j.cbpc.2010.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Revised: 12/20/2010] [Accepted: 12/27/2010] [Indexed: 10/18/2022]
Abstract
Differential gene expression profiles were established from the head and liver tissues of the marine medaka fish (Oryzias javanicus) after its exposure to toxaphene, a persistent organic pollutant and insecticide, using differential display polymerase chain reaction. Twenty-seven differentially expressed genes were identified, which were associated with the cytoskeleton, development, metabolism, nucleic acid/protein binding, and signal transduction. Among these genes, those encoding molecular biomarkers known to be involved in metabolism, ATP hydrolysis, and protein regulation were strongly induced at the transcription level, and genes encoding one structural protein subunit or involved in lipid metabolism were strongly downregulated. The same trends in gene expression changes were observed with real-time PCR analysis of 12 selected clones. The genes identified could be used as molecular biomarkers of biological responses to polychlorinated camphene contamination in aquatic environments.
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Affiliation(s)
- Seonock Woo
- South Sea Environment Research Department, Korea Ocean Research and Development Institute, Geoje 656-830, Republic of Korea
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O'Donohue MF, Choesmel V, Faubladier M, Fichant G, Gleizes PE. Functional dichotomy of ribosomal proteins during the synthesis of mammalian 40S ribosomal subunits. ACTA ACUST UNITED AC 2010; 190:853-66. [PMID: 20819938 PMCID: PMC2935573 DOI: 10.1083/jcb.201005117] [Citation(s) in RCA: 157] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Subsets of 40S ribosomal subunits are required for initiating rRNA processing, rRNA maturation, and nuclear export. Our knowledge of the functions of metazoan ribosomal proteins in ribosome synthesis remains fragmentary. Using siRNAs, we show that knockdown of 31 of the 32 ribosomal proteins of the human 40S subunit (ribosomal protein of the small subunit [RPS]) strongly affects pre–ribosomal RNA (rRNA) processing, which often correlates with nucleolar chromatin disorganization. 16 RPSs are strictly required for initiating processing of the sequences flanking the 18S rRNA in the pre-rRNA except at the metazoan-specific early cleavage site. The remaining 16 proteins are necessary for progression of the nuclear and cytoplasmic maturation steps and for nuclear export. Distribution of these two subsets of RPSs in the 40S subunit structure argues for a tight dependence of pre-rRNA processing initiation on the folding of both the body and the head of the forming subunit. Interestingly, the functional dichotomy of RPS proteins reported in this study is correlated with the mutation frequency of RPS genes in Diamond-Blackfan anemia.
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Affiliation(s)
- Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire des Eucaryotes, Université de Toulouse-UPS and Centre National de La Recherche Scientifique, F-31000 Toulouse, France
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Chen SM, Ma KY, Zeng J. Pseudogene: lessons from PCR bias, identification and resurrection. Mol Biol Rep 2010; 38:3709-15. [PMID: 21116863 DOI: 10.1007/s11033-010-0485-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 11/09/2010] [Indexed: 11/26/2022]
Abstract
Pseudogenes are fragments of non-functional genomic DNA with high sequences similarity to normal functional genes. They are a kind of non-coding DNA produced by gene duplications or retrotranspositions. Pseudogenes exist in human genome at a large quantity which is nearly as much as that of normal functional genes. They could cause PCR bias in molecular biology experiments and confuse related analysis. On the other hand, pesudogenes are important elements in genomics study for getting an integral picture of genome annotation. They give diverse information of evolutionary history and are regarded as genome fossils. Worldwide research project "encyclopedia of DNA elements"(ENCODE) founded in recent years have enhanced our understanding of pseudogenes. Approaches established to identify pseudogenes include PseudoPipe, HAVANA method, PseudoFinder, RetroFinder, GIS-PET method and consensus method. This paper discuss pseudogenes with respect to the formation mechanisms, distribution, and problems for PCR, importance and identification of pseudogenes. Furthermore, potential resurrection of pseudogenes and their potential function are discussed.
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Affiliation(s)
- Shan-Min Chen
- School of Life Science and Food Engineering, Yibin University, Yibin, Sichuan, China
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42
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Meyer A, Witek A, Lieb B. Selecting ribosomal protein genes for invertebrate phylogenetic inferences: how many genes to resolve the Mollusca? Methods Ecol Evol 2010. [DOI: 10.1111/j.2041-210x.2010.00052.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Normalization with genes encoding ribosomal proteins but not GAPDH provides an accurate quantification of gene expressions in neuronal differentiation of PC12 cells. BMC Genomics 2010; 11:75. [PMID: 20113474 PMCID: PMC2831847 DOI: 10.1186/1471-2164-11-75] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 01/29/2010] [Indexed: 12/14/2022] Open
Abstract
Background Gene regulation at transcript level can provide a good indication of the complex signaling mechanisms underlying physiological and pathological processes. Transcriptomic methods such as microarray and quantitative real-time PCR require stable reference genes for accurate normalization of gene expression. Some but not all studies have shown that housekeeping genes (HGKs), β-actin (ACTB) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which are routinely used for normalization, may vary significantly depending on the cell/tissue type and experimental conditions. It is currently unclear if these genes are stably expressed in cells undergoing drastic morphological changes during neuronal differentiation. Recent meta-analysis of microarray datasets showed that some but not all of the ribosomal protein genes are stably expressed. To test the hypothesis that some ribosomal protein genes can serve as reference genes for neuronal differentiation, a genome-wide analysis was performed and putative reference genes were identified based on stability of expressions. The stabilities of these potential reference genes were then analyzed by reverse transcription quantitative real-time PCR in six differentiation conditions. Results Twenty stably expressed genes, including thirteen ribosomal protein genes, were selected from microarray analysis of the gene expression profiles of GDNF and NGF induced differentiation of PC12 cells. The expression levels of these candidate genes as well as ACTB and GAPDH were further analyzed by reverse transcription quantitative real-time PCR in PC12 cells differentiated with a variety of stimuli including NGF, GDNF, Forskolin, KCl and ROCK inhibitor, Y27632. The performances of these candidate genes as stable reference genes were evaluated with two independent statistical approaches, geNorm and NormFinder. Conclusions The ribosomal protein genes, RPL19 and RPL29, were identified as suitable reference genes during neuronal differentiation of PC12 cells, regardless of the type of differentiation conditions. The combination of these two novel reference genes, but not the commonly used HKG, GAPDH, allows robust and accurate normalization of differentially expressed genes during PC12 differentiation.
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Balasubramanian S, Zheng D, Liu YJ, Fang G, Frankish A, Carriero N, Robilotto R, Cayting P, Gerstein M. Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes. Genome Biol 2009; 10:R2. [PMID: 19123937 PMCID: PMC2687790 DOI: 10.1186/gb-2009-10-1-r2] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Accepted: 01/05/2009] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The availability of genome sequences of numerous organisms allows comparative study of pseudogenes in syntenic regions. Conservation of pseudogenes suggests that they might have a functional role in some instances. RESULTS We report the first large-scale comparative analysis of ribosomal protein pseudogenes in four mammalian genomes (human, chimpanzee, mouse and rat). To this end, we have assigned these pseudogenes in the four organisms using an automated pipeline and make the results available online. Each organism has a large number of ribosomal protein pseudogenes (approximately 1,400 to 2,800). The majority of them are processed (generated by retrotransposition). However, we do not see a correlation between the number of pseudogenes associated with a ribosomal protein gene and its mRNA abundance. Analysis of pseudogenes in syntenic regions between species shows that most are conserved between human and chimpanzee, but very few are conserved between primates and rodents. Interestingly, syntenic pseudogenes have a lower rate of nucleotide substitution than their surrounding intergenic DNA. Moreover, evidence from expressed sequence tags indicates that two pseudogenes conserved between human and mouse are transcribed. Detailed analysis shows that one of them, the pseudogene of RPS27, is likely to be a protein-coding gene. This is significant as previous reports indicated there are exactly 80 ribosomal protein genes encoded by the human genome. CONCLUSIONS Our analysis indicates that processed ribosomal protein pseudogenes abound in mammalian genomes, but few of these are conserved between primates and rodents. This highlights the large amount of recent retrotranspositional activity in mammals and a relatively larger amount of it in the rodent lineage.
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Hou YL, Hou WR, Ren ZL, Hao YZ, Zhang T. cDNA Cloning and Overexpression of Ribosomal Protein S19 Gene (RPS19) from the Giant Panda. DNA Cell Biol 2009; 28:41-7. [PMID: 19072723 DOI: 10.1089/dna.2008.0799] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yi-Ling Hou
- College of Agriculture, Sichuan Agricultural University, Ya-an, China
- College of Life Science, China West Normal University, Nanchong, China
| | - Wan-Ru Hou
- College of Life Science, China West Normal University, Nanchong, China
| | - Zheng-Long Ren
- College of Agriculture, Sichuan Agricultural University, Ya-an, China
| | - Yan-Zhe Hao
- College of Life Science, China West Normal University, Nanchong, China
| | - Tian Zhang
- College of Life Science, China West Normal University, Nanchong, China
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46
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Shapshak P, Rodriguez HE, Kayathri R, Levine A, Chiappelli F, Minagar A. Alzheimer's disease and HIV associated dementia related genes: I. location and function. Bioinformation 2008; 2:348-57. [PMID: 18685724 PMCID: PMC2478736 DOI: 10.6026/97320630002348] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 05/06/2008] [Indexed: 11/23/2022] Open
Abstract
Alzheimer's disease (AD), the most common cause of dementia, has few clinical similarities to HIV-1-associated dementia (HAD). However, genes were identified related among these dementias. Discovering correlations between gene function, expression, and structure in the human genome continues to aid in understanding the similarities between pathogenesis of these two dementing disorders. The current work attempts to identify relationships between these dementias in spite of their clinical differences, based on genomic structure, function, and expression. In this comparative study, the NCBI Entrez Genome Database is used to detect these relationships. This approach serves as a model for future diagnosis and treatment in the clinical arena as well as suggesting parallel pathways of disease mechanisms. Identifying a correlation among expression, structure, and function of genes involved in pathogenesis of these dementing disorders, may assist to understand better their interaction with each other and the human genome.
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Affiliation(s)
- Paul Shapshak
- Division of Infectious Diseases, Department of Internal Medicine, of South Florida, College of Medicine, Tampa, FL 33613, USA.
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47
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Marygold SJ, Roote J, Reuter G, Lambertsson A, Ashburner M, Millburn GH, Harrison PM, Yu Z, Kenmochi N, Kaufman TC, Leevers SJ, Cook KR. The ribosomal protein genes and Minute loci of Drosophila melanogaster. Genome Biol 2008; 8:R216. [PMID: 17927810 PMCID: PMC2246290 DOI: 10.1186/gb-2007-8-10-r216] [Citation(s) in RCA: 280] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2007] [Revised: 10/10/2007] [Accepted: 10/10/2007] [Indexed: 02/07/2023] Open
Abstract
A combined bioinformatic and genetic approach was used to conduct a systematic analysis of the relationship between ribosomal protein genes and Minute loci in Drosophila melanogaster, allowing the identification of 64 Minute loci corresponding to ribosomal genes. Background Mutations in genes encoding ribosomal proteins (RPs) have been shown to cause an array of cellular and developmental defects in a variety of organisms. In Drosophila melanogaster, disruption of RP genes can result in the 'Minute' syndrome of dominant, haploinsufficient phenotypes, which include prolonged development, short and thin bristles, and poor fertility and viability. While more than 50 Minute loci have been defined genetically, only 15 have so far been characterized molecularly and shown to correspond to RP genes. Results We combined bioinformatic and genetic approaches to conduct a systematic analysis of the relationship between RP genes and Minute loci. First, we identified 88 genes encoding 79 different cytoplasmic RPs (CRPs) and 75 genes encoding distinct mitochondrial RPs (MRPs). Interestingly, nine CRP genes are present as duplicates and, while all appear to be functional, one member of each gene pair has relatively limited expression. Next, we defined 65 discrete Minute loci by genetic criteria. Of these, 64 correspond to, or very likely correspond to, CRP genes; the single non-CRP-encoding Minute gene encodes a translation initiation factor subunit. Significantly, MRP genes and more than 20 CRP genes do not correspond to Minute loci. Conclusion This work answers a longstanding question about the molecular nature of Minute loci and suggests that Minute phenotypes arise from suboptimal protein synthesis resulting from reduced levels of cytoribosomes. Furthermore, by identifying the majority of haplolethal and haplosterile loci at the molecular level, our data will directly benefit efforts to attain complete deletion coverage of the D. melanogaster genome.
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Affiliation(s)
- Steven J Marygold
- Growth Regulation Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields, London WC2A 3PX, UK.
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Timmermans MJTN, Roelofs D, Mariën J, van Straalen NM. Revealing pancrustacean relationships: phylogenetic analysis of ribosomal protein genes places Collembola (springtails) in a monophyletic Hexapoda and reinforces the discrepancy between mitochondrial and nuclear DNA markers. BMC Evol Biol 2008; 8:83. [PMID: 18366624 PMCID: PMC2315649 DOI: 10.1186/1471-2148-8-83] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 03/12/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In recent years, several new hypotheses on phylogenetic relations among arthropods have been proposed on the basis of DNA sequences. One of the challenged hypotheses is the monophyly of hexapods. This discussion originated from analyses based on mitochondrial DNA datasets that, due to an unusual positioning of Collembola, suggested that the hexapod body plan evolved at least twice. Here, we re-evaluate the position of Collembola using ribosomal protein gene sequences. RESULTS In total 48 ribosomal proteins were obtained for the collembolan Folsomia candida. These 48 sequences were aligned with sequence data on 35 other ecdysozoans. Each ribosomal protein gene was available for 25% to 86% of the taxa. However, the total sequence information was unequally distributed over the taxa and ranged between 4% and 100%. A concatenated dataset was constructed (5034 inferred amino acids in length), of which ~66% of the positions were filled. Phylogenetic tree reconstructions, using Maximum Likelihood, Maximum Parsimony, and Bayesian methods, resulted in a topology that supports monophyly of Hexapoda. CONCLUSION Although ribosomal proteins in general may not evolve independently, they once more appear highly valuable for phylogenetic reconstruction. Our analyses clearly suggest that Hexapoda is monophyletic. This underpins the inconsistency between nuclear and mitochondrial datasets when analyzing pancrustacean relationships. Caution is needed when applying mitochondrial markers in deep phylogeny.
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Affiliation(s)
- MJTN Timmermans
- Department of Animal Ecology, VU University Amsterdam, Amsterdam, The Netherlands
| | - D Roelofs
- Department of Animal Ecology, VU University Amsterdam, Amsterdam, The Netherlands
| | - J Mariën
- Department of Animal Ecology, VU University Amsterdam, Amsterdam, The Netherlands
| | - NM van Straalen
- Department of Animal Ecology, VU University Amsterdam, Amsterdam, The Netherlands
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49
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Hu H, Li X. Transcriptional regulation in eukaryotic ribosomal protein genes. Genomics 2007; 90:421-3. [PMID: 17707610 DOI: 10.1016/j.ygeno.2007.07.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 05/20/2007] [Accepted: 07/03/2007] [Indexed: 11/23/2022]
Abstract
Understanding ribosomal protein gene regulation provides a good avenue for understanding gene regulatory networks. Even after 5 decades of research on ribosomal protein gene regulation, little is known about how higher eukaryotic ribosomal protein genes are coordinately regulated at the transcriptional level. However, a few recent papers shed some light on this complicated problem.
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Affiliation(s)
- Haiyan Hu
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, 410 W. 10th Street, Indianapolis, IN 46202, USA
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50
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Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigó R, Harrow J, Gerstein MB. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res 2007; 17:839-51. [PMID: 17568002 PMCID: PMC1891343 DOI: 10.1101/gr.5586307] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are "genomic fossils" valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome's structure and function. However, no consensus computational scheme for defining and detecting pseudogenes has been developed thus far. As part of the ENCyclopedia Of DNA Elements (ENCODE) project, we have compared several distinct pseudogene annotation strategies and found that different approaches and parameters often resulted in rather distinct sets of pseudogenes. We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction ( approximately 80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates. Analysis of sequence conservation and variation also demonstrated that most pseudogenes evolve neutrally, and processed pseudogenes appear to have lost their coding potential immediately or soon after their emergence. In order to explore the functional implication of pseudogene prevalence, we have extensively examined the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues.
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Affiliation(s)
- Deyou Zheng
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
- Corresponding authors.E-mail ; fax (360) 838-7861.E-mail ; fax (360) 838-7861
| | - Adam Frankish
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1HH, United Kingdom
| | - Robert Baertsch
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | | | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Siew Woh Choo
- Genome Institute of Singapore, Singapore 138672, Singapore
| | - Yontao Lu
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - France Denoeud
- Grup de Recerca en Informática Biomèdica, Institut Municipal d’Investigació Mèdica/Universitat Pompeu Fabra, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Catalonia, Spain
| | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Michael Snyder
- Molecular, Cellular & Developmental Biology Department, Yale University, New Haven, Connecticut 06520, USA
| | - Yijun Ruan
- Genome Institute of Singapore, Singapore 138672, Singapore
| | - Chia-Lin Wei
- Genome Institute of Singapore, Singapore 138672, Singapore
| | | | - Roderic Guigó
- Grup de Recerca en Informática Biomèdica, Institut Municipal d’Investigació Mèdica/Universitat Pompeu Fabra, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Catalonia, Spain
- Center for Genomic Regulation, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Catalonia, Spain
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1HH, United Kingdom
| | - Mark B. Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
- Department of Computer Science, Yale University, New Haven, Connecticut 06520, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
- Corresponding authors.E-mail ; fax (360) 838-7861.E-mail ; fax (360) 838-7861
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