A Distinct P53 Target Gene Set Predicts for Response to the Selective P53
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The Ribosomal Protein Rpl22 Controls Ribosome Composition by Directly Repressing Expression of Its Own Paralog, Rpl22l1
The Ribosomal Protein Rpl22 Controls Ribosome Composition by Directly Repressing Expression of Its Own Paralog, Rpl22l1 Monique N. O’Leary1,2, Katherine H. Schreiber1,2, Yong Zhang3, Anne-Ce´cile E. Duc3, Shuyun Rao3,J. Scott Hale4¤, Emmeline C. Academia2, Shreya R. Shah1, John F. Morton5, Carly A. Holstein6, Dan B. Martin6, Matt Kaeberlein7, Warren C. Ladiges5, Pamela J. Fink4, Vivian L. MacKay1, David L. Wiest3, Brian K. Kennedy1,2* 1 Department of Biochemistry, University of Washington, Seattle, Washington, United States of America, 2 Buck Institute for Research on Aging, Novato, California, United States of America, 3 Blood Cell Development and Cancer Keystone, Immune Cell Development and Host Defense Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America, 4 Department of Immunology, University of Washington, Seattle, Washington, United States of America, 5 Department of Comparative Medicine, University of Washington, Seattle, Washington, United States of America, 6 Institute for Systems Biology, Seattle, Washington, United States of America, 7 Department of Pathology, University of Washington, Seattle, Washington, United States of America Abstract Most yeast ribosomal protein genes are duplicated and their characterization has led to hypotheses regarding the existence of specialized ribosomes with different subunit composition or specifically-tailored functions. In yeast, ribosomal protein genes are generally duplicated and evidence has emerged that paralogs might have specific roles. Unlike yeast, most mammalian ribosomal proteins are thought to be encoded by a single gene copy, raising the possibility that heterogenous populations of ribosomes are unique to yeast. Here, we examine the roles of the mammalian Rpl22, finding that Rpl222/2 mice have only subtle phenotypes with no significant translation defects. -
Assessment of Hematopoietic Failure Due to Rpl11 Deficiency in a Zebrafish Model of Diamond-Blackfan Anemia by Deep Sequencing
Zhang et al. BMC Genomics 2013, 14:896 http://www.biomedcentral.com/1471-2164/14/896 RESEARCH ARTICLE Open Access Assessment of hematopoietic failure due to Rpl11 deficiency in a zebrafish model of Diamond- Blackfan anemia by deep sequencing Zhaojun Zhang1†, Haibo Jia2†, Qian Zhang1, Yang Wan3, Yang Zhou2, Qiong Jia2, Wanguang Zhang4, Weiping Yuan3, Tao Cheng3, Xiaofan Zhu3* and Xiangdong Fang1* Abstract Background: Diamond–Blackfan anemia is a rare congenital red blood cell dysplasia that develops soon after birth. RPL11 mutations account for approximately 4.8% of human DBA cases with defective hematopoietic phenotypes. However, the mechanisms by which RPL11 regulates hematopoiesis in DBA remain elusive. In this study, we analyzed the transcriptome using deep sequencing data from an Rpl11-deficient zebrafish model to identify Rpl11-mediated hematopoietic failure and investigate the underlying mechanisms. Results: We characterized hematological defects in Rpl11-deficient zebrafish embryos by identifying affected hematological genes, hematopoiesis-associated pathways, and regulatory networks. We found that hemoglobin biosynthetic and hematological defects in Rpl11-deficient zebrafish were related to dysregulation of iron metabolism-related genes, including tfa, tfr1b, alas2 and slc25a37, which are involved in heme and hemoglobin biosynthesis. In addition, we found reduced expression of the hematopoietic stem cells (HSC) marker cmyb and HSC transcription factors tal1 and hoxb4a in Rpl11-deficient zebrafish embryos, indicating that the hematopoietic defects may be related to impaired HSC formation, differentiation, and proliferation. However, Rpl11 deficiency did not affect the development of other blood cell lineages such as granulocytes and myelocytes. Conclusion: We identified hematopoietic failure of Rpl11-deficient zebrafish embryos using transcriptome deep sequencing and elucidated potential underlying mechanisms. -
Identification of the Key Genes and Pathways in Prostate Cancer
ONCOLOGY LETTERS 16: 6663-6669, 2018 Identification of the key genes and pathways in prostate cancer SHUTONG FAN1*, ZUMU LIANG1*, ZHIQIN GAO1, ZHIWEI PAN2, SHAOJIE HAN3, XIAOYING LIU1, CHUNLING ZHAO1, WEIWEI YANG1, ZHIFANG PAN1 and WEIGUO FENG1 1College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong 261053; 2Department of Internal Medicine, Laizhou Development Zone Hospital, Yantai, Shandong 261400; 3Animal Epidemic Prevention and Epidemic Control Center, Changle County Bureau of Animal Health and Production, Weifang, Shandong 262400, P.R. China Received March 5, 2018; Accepted September 17, 2018 DOI: 10.3892/ol.2018.9491 Abstract. Prostate cancer (PCa) is one of the most common Introduction malignancies in men globally. The aim of the present study was to identify the key genes and pathways involved in the Prostate cancer (PCa) is one of the most common malignancies occurrence of PCa. Gene expression profile (GSE55945) in men globally and the second leading cause of cancer was downloaded from Gene Expression Omnibus, and associated mortality in developed countries (1,2). Like other the differentially expressed genes (DEGs) were identified. cancers, PCa is considered to be a disease which caused by Subsequently, Gene ontology analysis, KEGG pathway age, diet and gene aberrations (3). Accumulating evidences analysis and protein-protein interaction (PPI) analysis of have demonstrated that a series of genes and pathways involved DEGs were performed. Finally, the identified key genes were in the occurrence, progression and metastasis of PCa (4). At confirmed by immunohistochemistry. The GO analysis results present, the underlying mechanism of PCa occurrence is still showed that the DEGs were mainly participated in cell cycle, unclear, which limits the diagnosis and therapy. -
(P -Value<0.05, Fold Change≥1.4), 4 Vs. 0 Gy Irradiation
Table S1: Significant differentially expressed genes (P -Value<0.05, Fold Change≥1.4), 4 vs. 0 Gy irradiation Genbank Fold Change P -Value Gene Symbol Description Accession Q9F8M7_CARHY (Q9F8M7) DTDP-glucose 4,6-dehydratase (Fragment), partial (9%) 6.70 0.017399678 THC2699065 [THC2719287] 5.53 0.003379195 BC013657 BC013657 Homo sapiens cDNA clone IMAGE:4152983, partial cds. [BC013657] 5.10 0.024641735 THC2750781 Ciliary dynein heavy chain 5 (Axonemal beta dynein heavy chain 5) (HL1). 4.07 0.04353262 DNAH5 [Source:Uniprot/SWISSPROT;Acc:Q8TE73] [ENST00000382416] 3.81 0.002855909 NM_145263 SPATA18 Homo sapiens spermatogenesis associated 18 homolog (rat) (SPATA18), mRNA [NM_145263] AA418814 zw01a02.s1 Soares_NhHMPu_S1 Homo sapiens cDNA clone IMAGE:767978 3', 3.69 0.03203913 AA418814 AA418814 mRNA sequence [AA418814] AL356953 leucine-rich repeat-containing G protein-coupled receptor 6 {Homo sapiens} (exp=0; 3.63 0.0277936 THC2705989 wgp=1; cg=0), partial (4%) [THC2752981] AA484677 ne64a07.s1 NCI_CGAP_Alv1 Homo sapiens cDNA clone IMAGE:909012, mRNA 3.63 0.027098073 AA484677 AA484677 sequence [AA484677] oe06h09.s1 NCI_CGAP_Ov2 Homo sapiens cDNA clone IMAGE:1385153, mRNA sequence 3.48 0.04468495 AA837799 AA837799 [AA837799] Homo sapiens hypothetical protein LOC340109, mRNA (cDNA clone IMAGE:5578073), partial 3.27 0.031178378 BC039509 LOC643401 cds. [BC039509] Homo sapiens Fas (TNF receptor superfamily, member 6) (FAS), transcript variant 1, mRNA 3.24 0.022156298 NM_000043 FAS [NM_000043] 3.20 0.021043295 A_32_P125056 BF803942 CM2-CI0135-021100-477-g08 CI0135 Homo sapiens cDNA, mRNA sequence 3.04 0.043389246 BF803942 BF803942 [BF803942] 3.03 0.002430239 NM_015920 RPS27L Homo sapiens ribosomal protein S27-like (RPS27L), mRNA [NM_015920] Homo sapiens tumor necrosis factor receptor superfamily, member 10c, decoy without an 2.98 0.021202829 NM_003841 TNFRSF10C intracellular domain (TNFRSF10C), mRNA [NM_003841] 2.97 0.03243901 AB002384 C6orf32 Homo sapiens mRNA for KIAA0386 gene, partial cds. -
Early-Life Exposure to the Antidepressant Fluoxetine Induces A
Early-life exposure to the antidepressant fluoxetine induces a male-specific transgenerational disruption of the stress axis and exploratory behavior in adult zebrafish, Danio rerio Marilyn Nohely Vera Chang Thesis submitted to the Faculty of Graduate and Postdoctoral Studies in partial fulfillment of the requirements for the Doctorate in Philosophy degree in Biology with specialization in Chemical and Environmental Toxicology Department of Biology Faculty of Science University of Ottawa © Marilyn Nohely Vera Chang, Ottawa, Canada, 2018 ACKNOWLEDGMENTS Finishing this thesis has been both a challenging and gratifying experience. There are many people whom I must express my sincere gratitude toward as the work presented in this thesis would not have been possible without their contributions and never-ending support. First and foremost, I would like to acknowledge my supervisors, Dr. Vance Trudeau and Dr. Thomas Moon. I want to say how grateful I am for providing me with the opportunity to purse my academic and professional interests. I was first accepted by Tom and I will be forever thankful that he took a shot on me. Also, thanks to you Vance for adopting me when I was lab-less and for believing in my abilities as a scientist. Thank you to both of you for your outstanding guidance, patience and friendship which have given me an amazing experience in these past 6 years, you have been excellent mentors. Your concerns for your student’s well-being and mental health were bonus that I will not soon forget. I don’t think there are enough words to describe how thankful and fortunate I am to have benefit from your supervision not only at the academic and scientific level but also at the personal level, for all my accomplishments during this doctorate, I will forever be indebted to both of you. -
105.Full.Pdf
CANCER GENOMICS & PROTEOMICS 8: 105-126 (2011) Conservation of Multifunctional Ribosomal Protein Metallopanstimulin-1 (RPS27) through Complex Evolution Demonstrates its Key Role in Growth Regulation in Archaea, Eukaryotic Cells, DNA Repair, Translation and Viral Replication J. ALBERTO FERNANDEZ-POL Antagoras Agrobusiness, LLC., Biotechnology, Chesterfield, MO, U.S.A. Abstract. Background: When the functions of a protein serve determined by NMR. Results: The data presented here a useful survival and unique purpose, the selective pressures of indicates that anti-ZFP agents can potentially be used to evolutionary laws of nature conserve the DNA sequences prevent and control viral infections by disrupting viral ZFP encoding such proteins. In many instances, the conservation motifs. Different DNA/RNA virus-infected cells exposed to the of these sequences has occurred since the inception of life on antivirals resulted in distruption of both RPMPS-1/S27 and earth to the present in phylogenetically related species. The essential viral ZFPs. Picolinic acid (PA) and fusaric acid (FU) unique function(s) of metallopanstimulin (MPS-1/RPS27) were tested and have been shown to have both antiviral and ribosomal protein (RP) and a limited number of other RPs, in preventive antiviral activities which have been consistently growth regulation, and viral infection is further documented shown to be mediated, at least in part, via interacting with here. Based on the correlation of information concerning RPMPS-1/S27. The same antiviral agents simultaneously Genome Context Analysis, and new information presented disrupt essential viral ZFPs. Both antiviral events on ZFPs here, the author proposes that neutralization or elimination of render the pathogenic virus inactive. -
Patterns of Ribosomal Protein Expression Specify Normal and Malignant Human Cells Joao C
Guimaraes and Zavolan Genome Biology (2016) 17:236 DOI 10.1186/s13059-016-1104-z RESEARCH Open Access Patterns of ribosomal protein expression specify normal and malignant human cells Joao C. Guimaraes* and Mihaela Zavolan* Abstract Background: Ribosomes are highly conserved molecular machines whose core composition has traditionally been regarded as invariant. However, recent studies have reported intriguing differences in the expression of some ribosomal proteins (RPs) across tissues and highly specific effects on the translation of individual mRNAs. Results: To determine whether RPs are more generally linked to cell identity, we analyze the heterogeneity of RP expression in a large set of human tissues, primary cells, and tumors. We find that about a quarter of human RPs exhibit tissue-specific expression and that primary hematopoietic cells display the most complex patterns of RP expression, likely shaped by context-restricted transcriptional regulators. Strikingly, we uncover patterns of dysregulated expression of individual RPs across cancer types that arise through copy number variations and are predictive for disease progression. Conclusions: Our study reveals an unanticipated plasticity of RP expression across normal and malignant human cell types and provides a foundation for future characterization of cellular behaviors that are orchestrated by specific RPs. Keywords: Ribosomal proteins, Ribosome heterogeneity, Translation, Hematopoiesis, Cancer Background Indeed, many feedback mechanisms have been discov- Protein synthesis is at the core of cellular life. It is car- ered that link the production of different ribosomal ried out by the ribosome, a highly conserved molecular components to maintain an appropriate stoichiometry machine with the same basic architecture in all free- [7]; a number of RPs act in negative feedback loops to living organisms [1–3]. -
CD29 Identifies IFN-Γ–Producing Human CD8+ T Cells with an Increased Cytotoxic Potential
+ CD29 identifies IFN-γ–producing human CD8 T cells with an increased cytotoxic potential Benoît P. Nicoleta,b, Aurélie Guislaina,b, Floris P. J. van Alphenc, Raquel Gomez-Eerlandd, Ton N. M. Schumacherd, Maartje van den Biggelaarc,e, and Monika C. Wolkersa,b,1 aDepartment of Hematopoiesis, Sanquin Research, 1066 CX Amsterdam, The Netherlands; bLandsteiner Laboratory, Oncode Institute, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; cDepartment of Research Facilities, Sanquin Research, 1066 CX Amsterdam, The Netherlands; dDivision of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; and eDepartment of Molecular and Cellular Haemostasis, Sanquin Research, 1066 CX Amsterdam, The Netherlands Edited by Anjana Rao, La Jolla Institute for Allergy and Immunology, La Jolla, CA, and approved February 12, 2020 (received for review August 12, 2019) Cytotoxic CD8+ T cells can effectively kill target cells by producing therefore developed a protocol that allowed for efficient iso- cytokines, chemokines, and granzymes. Expression of these effector lation of RNA and protein from fluorescence-activated cell molecules is however highly divergent, and tools that identify and sorting (FACS)-sorted fixed T cells after intracellular cytokine + preselect CD8 T cells with a cytotoxic expression profile are lacking. staining. With this top-down approach, we performed an un- + Human CD8 T cells can be divided into IFN-γ– and IL-2–producing biased RNA-sequencing (RNA-seq) and mass spectrometry cells. Unbiased transcriptomics and proteomics analysis on cytokine- γ– – + + (MS) analyses on IFN- and IL-2 producing primary human producing fixed CD8 T cells revealed that IL-2 cells produce helper + + + CD8 Tcells. -
Sex-Specific Transcriptome Differences in Human Adipose
G C A T T A C G G C A T genes Article Sex-Specific Transcriptome Differences in Human Adipose Mesenchymal Stem Cells 1, 2, 3 1,3 Eva Bianconi y, Raffaella Casadei y , Flavia Frabetti , Carlo Ventura , Federica Facchin 1,3,* and Silvia Canaider 1,3 1 National Laboratory of Molecular Biology and Stem Cell Bioengineering of the National Institute of Biostructures and Biosystems (NIBB)—Eldor Lab, at the Innovation Accelerator, CNR, Via Piero Gobetti 101, 40129 Bologna, Italy; [email protected] (E.B.); [email protected] (C.V.); [email protected] (S.C.) 2 Department for Life Quality Studies (QuVi), University of Bologna, Corso D’Augusto 237, 47921 Rimini, Italy; [email protected] 3 Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy; fl[email protected] * Correspondence: [email protected]; Tel.: +39-051-2094114 These authors contributed equally to this work. y Received: 1 July 2020; Accepted: 6 August 2020; Published: 8 August 2020 Abstract: In humans, sexual dimorphism can manifest in many ways and it is widely studied in several knowledge fields. It is increasing the evidence that also cells differ according to sex, a correlation still little studied and poorly considered when cells are used in scientific research. Specifically, our interest is on the sex-related dimorphism on the human mesenchymal stem cells (hMSCs) transcriptome. A systematic meta-analysis of hMSC microarrays was performed by using the Transcriptome Mapper (TRAM) software. This bioinformatic tool was used to integrate and normalize datasets from multiple sources and allowed us to highlight chromosomal segments and genes differently expressed in hMSCs derived from adipose tissue (hADSCs) of male and female donors. -
The Ribosomal Protein Rpl22 Controls Ribosome Composition by Directly Repressing Expression of Its Own Paralog, Rpl22l1
The Ribosomal Protein Rpl22 Controls Ribosome Composition by Directly Repressing Expression of Its Own Paralog, Rpl22l1 Monique N. O’Leary1,2, Katherine H. Schreiber1,2, Yong Zhang3, Anne-Ce´cile E. Duc3, Shuyun Rao3,J. Scott Hale4¤, Emmeline C. Academia2, Shreya R. Shah1, John F. Morton5, Carly A. Holstein6, Dan B. Martin6, Matt Kaeberlein7, Warren C. Ladiges5, Pamela J. Fink4, Vivian L. MacKay1, David L. Wiest3, Brian K. Kennedy1,2* 1 Department of Biochemistry, University of Washington, Seattle, Washington, United States of America, 2 Buck Institute for Research on Aging, Novato, California, United States of America, 3 Blood Cell Development and Cancer Keystone, Immune Cell Development and Host Defense Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America, 4 Department of Immunology, University of Washington, Seattle, Washington, United States of America, 5 Department of Comparative Medicine, University of Washington, Seattle, Washington, United States of America, 6 Institute for Systems Biology, Seattle, Washington, United States of America, 7 Department of Pathology, University of Washington, Seattle, Washington, United States of America Abstract Most yeast ribosomal protein genes are duplicated and their characterization has led to hypotheses regarding the existence of specialized ribosomes with different subunit composition or specifically-tailored functions. In yeast, ribosomal protein genes are generally duplicated and evidence has emerged that paralogs might have specific roles. Unlike yeast, most mammalian ribosomal proteins are thought to be encoded by a single gene copy, raising the possibility that heterogenous populations of ribosomes are unique to yeast. Here, we examine the roles of the mammalian Rpl22, finding that Rpl222/2 mice have only subtle phenotypes with no significant translation defects. -
Downloaded from Ftp://Ftp.Uniprot.Org/ on July 3, 2019) Using Maxquant (V1.6.10.43) Search Algorithm
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.385096; this version posted November 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. The proteomic landscape of resting and activated CD4+ T cells reveal insights into cell differentiation and function Yashwanth Subbannayya1, Markus Haug1, Sneha M. Pinto1, Varshasnata Mohanty2, Hany Zakaria Meås1, Trude Helen Flo1, T.S. Keshava Prasad2 and Richard K. Kandasamy1,* 1Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491 Trondheim, Norway 2Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India *Correspondence to: Professor Richard Kumaran Kandasamy Norwegian University of Science and Technology (NTNU) Centre of Molecular Inflammation Research (CEMIR) PO Box 8905 MTFS Trondheim 7491 Norway E-mail: [email protected] (Kandasamy R K) Tel.: +47-7282-4511 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.385096; this version posted November 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Abstract CD4+ T cells (T helper cells) are cytokine-producing adaptive immune cells that activate or regulate the responses of various immune cells. -
Systematic Interrogation of 3Q26 Identifies TLOC1 and SKIL As Cancer Drivers
Published OnlineFirst June 13, 2013; DOI: 10.1158/2159-8290.CD-12-0592 RESEARCH ARTICLE Systematic Interrogation of 3q26 Identifi es TLOC1 and SKIL as Cancer Drivers Daniel Hagerstrand 1 , Alexander Tong 1 , Steven E. Schumacher 2 , 5 , Nina Ilic 1 , Rhine R. Shen 1 , Hiu Wing Cheung 1 , 5 , Francisca Vazquez 1 , 5 , Yashaswi Shrestha 1 , 5 , So Young Kim 1 , 6 , Andrew O. Giacomelli 1 , Joseph Rosenbluh 1 , 5 , Anna C. Schinzel 1 , Nicole A. Spardy 1 , David A. Barbie 1 , 5 , Craig H. Mermel 1 , 5 , Barbara A. Weir 5 , Levi A. Garraway 1 , 3 , 5 , Pablo Tamayo 5 , Jill P. Mesirov 5 , Rameen Beroukhim 1 , 2 , 3 , 5 , and William C. Hahn 1 , 3 , 4 , 5 Downloaded from cancerdiscovery.aacrjournals.org on September 29, 2021. © 2013 American Association for Cancer Research. Published OnlineFirst June 13, 2013; DOI: 10.1158/2159-8290.CD-12-0592 ABSTRACT 3q26 is frequently amplifi ed in several cancer types with a common amplifi ed region containing 20 genes. To identify cancer driver genes in this region, we inter- rogated the function of each of these genes by loss- and gain-of-function genetic screens. Specifi cally, we found that TLOC1 (SEC62 ) was selectively required for the proliferation of cell lines with 3q26 amplifi cation. Increased TLOC1 expression induced anchorage-independent growth, and a second 3q26 gene, SKIL (SNON ), facilitated cell invasion in immortalized human mammary epithelial cells. Expres- sion of both TLOC1 and SKIL induced subcutaneous tumor growth. Proteomic studies showed that TLOC1 binds to DDX3X, which is essential for TLOC1-induced transformation and affected protein translation.