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Genome-Wide Analysis of Differentially Expressed Lncrna in Sporadic Parathyroid Tumors
Osteoporosis International (2019) 30:1511–1519 https://doi.org/10.1007/s00198-019-04959-y ORIGINAL ARTICLE Genome-wide analysis of differentially expressed lncRNA in sporadic parathyroid tumors T. Jiang1 & B. J. Wei2,3 & D. X. Zhang1 & L. Li4 & G. L. Qiao5 & X. A. Yao1 & Z. W. Chen6 & X. Liu6 & X. Y. Du6 Received: 4 December 2018 /Accepted: 25 March 2019 /Published online: 10 April 2019 # International Osteoporosis Foundation and National Osteoporosis Foundation 2019 Abstract Summary Diagnosis of parathyroid carcinoma on histological examination is challenging. Thousands of differentially expressed lncRNAs were identified on the microarray data between parathyroid cancer and adenoma samples. Four lncRNAs were signif- icantly dysregulated in further validation. The BlncRNA score^ calculated from these lncRNAs differentiated parathyroid carcino- mas from adenomas. LncRNAs serve as biomarkers for parathyroid cancer diagnosis. Introduction Diagnosis of parathyroid carcinoma (PC) on histological examination is challenging. LncRNA profile study was conducted to find diagnostic biomarkers for PC. Methods LncRNA arrays containing 91,007 lncRNAs as well as 29,857 mRNAs were used to assess parathyroid specimen (5 carcinomas and 6 adenomas). Bioinformatics analyses were also conducted to compare the microarray results between parathyroid carcinomas and adenomas (PAs). Differentially expressed lncRNAs of 11 PCs and 31 PAs were validated by real-time quantitative PCR. Results On the microarray data between PC and PA samples (fold change ≥ 2, P < 0.05), 1809 differentially expressed lncRNAs and 1349 mRNAs also were identified. All carcinomas were clustered in the same group by clustering analysis using dysregulated lncRNAs or mRNAs. Four lncRNAs (LINC00959, lnc-FLT3-2:2, lnc-FEZF2-9:2, and lnc-RP11-1035H13.3.1-2:1) identified were significantly dysregulated in further RT-PCR validation. -
Analysis of Gene Expression Data for Gene Ontology
ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION A Thesis Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Robert Daniel Macholan May 2011 ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION Robert Daniel Macholan Thesis Approved: Accepted: _______________________________ _______________________________ Advisor Department Chair Dr. Zhong-Hui Duan Dr. Chien-Chung Chan _______________________________ _______________________________ Committee Member Dean of the College Dr. Chien-Chung Chan Dr. Chand K. Midha _______________________________ _______________________________ Committee Member Dean of the Graduate School Dr. Yingcai Xiao Dr. George R. Newkome _______________________________ Date ii ABSTRACT A tremendous increase in genomic data has encouraged biologists to turn to bioinformatics in order to assist in its interpretation and processing. One of the present challenges that need to be overcome in order to understand this data more completely is the development of a reliable method to accurately predict the function of a protein from its genomic information. This study focuses on developing an effective algorithm for protein function prediction. The algorithm is based on proteins that have similar expression patterns. The similarity of the expression data is determined using a novel measure, the slope matrix. The slope matrix introduces a normalized method for the comparison of expression levels throughout a proteome. The algorithm is tested using real microarray gene expression data. Their functions are characterized using gene ontology annotations. The results of the case study indicate the protein function prediction algorithm developed is comparable to the prediction algorithms that are based on the annotations of homologous proteins. -
Identification of the Binding Partners for Hspb2 and Cryab Reveals
Brigham Young University BYU ScholarsArchive Theses and Dissertations 2013-12-12 Identification of the Binding arP tners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non- Redundant Roles for Small Heat Shock Proteins Kelsey Murphey Langston Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Microbiology Commons BYU ScholarsArchive Citation Langston, Kelsey Murphey, "Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins" (2013). Theses and Dissertations. 3822. https://scholarsarchive.byu.edu/etd/3822 This Thesis is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins Kelsey Langston A thesis submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Master of Science Julianne H. Grose, Chair William R. McCleary Brian Poole Department of Microbiology and Molecular Biology Brigham Young University December 2013 Copyright © 2013 Kelsey Langston All Rights Reserved ABSTRACT Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactors and Non-Redundant Roles for Small Heat Shock Proteins Kelsey Langston Department of Microbiology and Molecular Biology, BYU Master of Science Small Heat Shock Proteins (sHSP) are molecular chaperones that play protective roles in cell survival and have been shown to possess chaperone activity. -
Cytoplasmic Parafibromin/Hcdc73 Targets and Destabilizes P53 Mrna
ARTICLE Received 4 Apr 2014 | Accepted 1 Oct 2014 | Published 12 Nov 2014 DOI: 10.1038/ncomms6433 Cytoplasmic parafibromin/hCdc73 targets and destabilizes p53 mRNA to control p53-mediated apoptosis Jay-Hyun Jo1, Tae-Moon Chung2, Hyewon Youn2,3 & Joo-Yeon Yoo1 The parafibromin/hCdc73 is a component of the PAFc, which controls RNA polymerase II-mediated general transcription. In parathyroid carcinoma and familial autosomal dominant hyperparathyroidism-jaw tumour (HPT-JT), hCdc73 mutations are heavily implicated, yet the underlying mechanism of its carcinogenic action is poorly understood. Here we demonstrate that hCdc73 specifically controls messenger RNA stability of p53 and p53-mediated apoptosis. hCdc73 is associated with mature p53 mRNA in the cytoplasm and facilitates its degradation. Cytoplasmic hCdc73 physically interacts with eEF1Bg and hSki8, and this interaction is required to bind and destabilize p53 mRNA. Furthermore, enhanced association of p53 mRNA with a cancer-driven hCdc73(K34Q) mutant was also observed. As a result, reduced p53 expression as well as enhanced cell proliferation was acquired in the hCdc73 (K34Q)-overexpressed cells. Altogether, our findings indicate that hCdc73 directly targets p53 mRNA to repress p53 expression, and aberrant regulation of this interaction may lead to tumour progression. 1 Department of Life Sciences, Pohang University of Science and Technology, Life Science Building 208, POSTECH, Nam-Gu, Pohang, Gyungbuk 790-784, Korea. 2 Department of Nuclear Medicine, Cancer Imaging Center, Seoul National University Cancer Hospital, Seoul 110-744, Korea. 3 Tumor Microenvironment Global Core Research Center, Cancer Research Institute, Seoul National University, Seoul 110-799, Korea. Correspondence and requests for materials should be addressed to J.-Y.Y. -
Insights Into the Non-Coding Genome of Parathyroid Tumors
UNIVERSITÀ DEGLI STUDI DI MILANO SCUOLA di DOTTORATO IN MEDICINA MOLECOLARE E TRASLAZIONALE Dipartimento di Fisiopatologia Chirurgica e dei Trapianti CICLO XXXI Anno Accademico 2017/2018 TESI DI DOTTORATO DI RICERCA Settore Scientifico Disciplinare MED/08 INSIGHTS INTO THE NON-CODING GENOME OF PARATHYROID TUMORS Dottorando: Annamaria MOROTTI Matricola N° R11312 Tutor: Dott.ssa Valentina VAIRA Co-Tutor: Prof.ssa Monica MIOZZO Coordinatore del Corso di Dottorato: Prof. Riccardo GHIDONI ABSTRACT ABSTRACT Recently, long non-coding RNAs (lncRNAs) have been implicated in the regulation of several physiological processes such as cell growth, differentiation and proliferation. Although lncRNAs functions in human diseases have not been completely disclosed, some lncRNAs have already been identified as prognostic and diagnostic biomarkers in different tumors. LncRNAs have also a crucial role in normal development of endocrine organs and their role in endocrine cancer pathogenesis is emerging. Parathyroid tumors are rare and heterogeneous diseases characterized by genetic and epigenetic alterations resulting in aberrant expression of both protein coding and non-coding genes. Tumors of the parathyroid glands show a great variability in clinical features such as parathormone (PTH) secretion, in the pattern of cell proliferation and in the genetic background. Mutations in the oncosuppressor CDC73 are key events in most carcinomas whereas alterations in the tumor suppressor Multiple Endocrine Neoplasia 1 (MEN1, located at 11q13.1) occur in up to a third of sporadic adenomas. Although lncRNAs play a regulatory role in endocrine cancer pathogenesis, a lncRNAs profiling in human parathyroid tumors is missing. Therefore, we investigated known lncRNAs expression in a series of normal (PaN) and pathological (adenomatous, PAd, and carcinomatous, PCa) parathyroid glands and correlated their expression with cytogenetic aberration, CDC73 status and MEN1 level. -
Atlas Journal
Atlas of Genetics and Cytogenetics in Oncology and Haematology Home Genes Leukemias Tumors Cancer prone Deep Insight Case Reports Portal Journals Teaching X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA Atlas Journal Atlas Journal versus Atlas Database: the accumulation of the issues of the Journal constitutes the body of the Database/Text-Book. TABLE OF CONTENTS Volume 13, Number 7, July 2009 Previous Issue / Next Issue Genes ABL1 (v-abl Abelson murine leukemia viral oncogene homolog 1) (9q34.1) - updated. Ali G Turhan. Atlas Genet Cytogenet Oncol Haematol 2009; 13 (7): 757-766. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/ABL.html BCL2L12 (BCL2-like 12 (proline-rich)) (19q13.3). Christos Kontos, Hellinida Thomadaki, Andreas Scorilas. Atlas Genet Cytogenet Oncol Haematol 2009; 13 (7): 767-771. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/BCL2L12ID773ch19q13.html BCR (Breakpoint cluster region) (22q11.2) - updated. Ali G Turhan. Atlas Genet Cytogenet Oncol Haematol 2009; 13 (7): 772-779. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/BCR.html ENAH (enabled homolog (Drosophila)) (1q42.12). Paola Nisticò, Francesca Di Modugno. Atlas Genet Cytogenet Oncol Haematol 2009; 13 (7): 780-785. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/ENAHID44148ch1q42.html FGFR2 (fibroblast growth factor receptor 2) (10q26.13). Masaru Katoh. Atlas Genet Cytogenet Oncol Haematol 2009; 13 (7): 786-799. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/FGFR2ID40570ch10q26.html MAPK6 (mitogen-activated protein kinase 6) (15q21.2). Sylvain Meloche. Atlas Genet Cytogenet Oncol Haematol 2009; 13 (7): 800-804. -
Interactome Analyses Revealed That the U1 Snrnp Machinery Overlaps Extensively with the RNAP II Machinery and Contains Multiple
www.nature.com/scientificreports OPEN Interactome analyses revealed that the U1 snRNP machinery overlaps extensively with the RNAP II Received: 12 April 2018 Accepted: 24 May 2018 machinery and contains multiple Published: xx xx xxxx ALS/SMA-causative proteins Binkai Chi1, Jeremy D. O’Connell1,2, Tomohiro Yamazaki1, Jaya Gangopadhyay1, Steven P. Gygi1 & Robin Reed1 Mutations in multiple RNA/DNA binding proteins cause Amyotrophic Lateral Sclerosis (ALS). Included among these are the three members of the FET family (FUS, EWSR1 and TAF15) and the structurally similar MATR3. Here, we characterized the interactomes of these four proteins, revealing that they largely have unique interactors, but share in common an association with U1 snRNP. The latter observation led us to analyze the interactome of the U1 snRNP machinery. Surprisingly, this analysis revealed the interactome contains ~220 components, and of these, >200 are shared with the RNA polymerase II (RNAP II) machinery. Among the shared components are multiple ALS and Spinal muscular Atrophy (SMA)-causative proteins and numerous discrete complexes, including the SMN complex, transcription factor complexes, and RNA processing complexes. Together, our data indicate that the RNAP II/U1 snRNP machinery functions in a wide variety of molecular pathways, and these pathways are candidates for playing roles in ALS/SMA pathogenesis. Te neurodegenerative disease Amyotrophic Lateral Sclerosis (ALS) has no known treatment, and elucidation of disease mechanisms is urgently needed. Tis problem has been especially daunting, as mutations in greater than 30 genes are ALS-causative, and these genes function in numerous cellular pathways1. Tese include mitophagy, autophagy, cytoskeletal dynamics, vesicle transport, DNA damage repair, RNA dysfunction, apoptosis, and pro- tein aggregation2–6. -
Using Long Nanopore Reads to Delineate Structural Variants (Svs)
Using long nanopore reads to delineate structural variants (SVs) in the human genome SVs, including large deletions, duplications, inversions, translocations and copy-number changes are abundant in large genomes, and require long reads for precise characterisation Contact: [email protected] More information at: www.nanoporetech.com and publications.nanoporetech.com Unique Repeat Unique Repeat Unique a) b) a) b) sequence 1 1 sequence 2 2 sequence 3 1,000 60 Short reads Insertions Long A B C D E Reference chromosome 1 40 reads 800 Deletions > 50 bp Short-read assembly 20 Collapsed repeat consensus Unique contig 1 Long-read Bases sequenced (Mb) assembly 600 0 Unique contig 1 Unique contig 3 0 10 20 30 40 V W X Y Z Reference chromosome 2 Single, fully-resolved contig Count Read length (kb) c) > 50 bp 400 chr7 (q33) 7p21.3 15.321.1 15.3 7p14.3 7p14.1 13 11.2 11.21 11.22 11.23 7q21.11 q21.3 7q22.1 7q31.1 7q33 7q34 7q35 36.1 36.3 Scale 50 kb hg38 chr7: 134,550,000 134,600,000 134,650,000 134,700,000 Inversion A D C B E GENCODE v24 comprehensive transcript set (only Basic displayed by default) 200 AKR1B10 AKR1B15 BGPM CALD1 AKR1B15 BGPM Deletion BGPM A B C E AC009276.4 Duplication A B C C C D E 0 1,000 10,000 20,000 30,000 Translocation V W C D E + A B X Y Z Event size (bp) Adapted from Huddleston, J. et al. Discovery and genotyping of structural variation from long-read haploid genome sequence data. -
A Yeast Phenomic Model for the Influence of Warburg Metabolism on Genetic Buffering of Doxorubicin Sean M
Santos and Hartman Cancer & Metabolism (2019) 7:9 https://doi.org/10.1186/s40170-019-0201-3 RESEARCH Open Access A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Sean M. Santos and John L. Hartman IV* Abstract Background: The influence of the Warburg phenomenon on chemotherapy response is unknown. Saccharomyces cerevisiae mimics the Warburg effect, repressing respiration in the presence of adequate glucose. Yeast phenomic experiments were conducted to assess potential influences of Warburg metabolism on gene-drug interaction underlying the cellular response to doxorubicin. Homologous genes from yeast phenomic and cancer pharmacogenomics data were analyzed to infer evolutionary conservation of gene-drug interaction and predict therapeutic relevance. Methods: Cell proliferation phenotypes (CPPs) of the yeast gene knockout/knockdown library were measured by quantitative high-throughput cell array phenotyping (Q-HTCP), treating with escalating doxorubicin concentrations under conditions of respiratory or glycolytic metabolism. Doxorubicin-gene interaction was quantified by departure of CPPs observed for the doxorubicin-treated mutant strain from that expected based on an interaction model. Recursive expectation-maximization clustering (REMc) and Gene Ontology (GO)-based analyses of interactions identified functional biological modules that differentially buffer or promote doxorubicin cytotoxicity with respect to Warburg metabolism. Yeast phenomic and cancer pharmacogenomics data were integrated to predict differential gene expression causally influencing doxorubicin anti-tumor efficacy. Results: Yeast compromised for genes functioning in chromatin organization, and several other cellular processes are more resistant to doxorubicin under glycolytic conditions. Thus, the Warburg transition appears to alleviate requirements for cellular functions that buffer doxorubicin cytotoxicity in a respiratory context. -
Association Analyses Based on False Discovery Rate Implicate Many New Loci for Coronary Artery Disease
1 Association analyses based on false discovery rate implicate many new loci 2 for coronary artery disease 3 Christopher P. Nelson1,2,61, Anuj Goel3,4,61, Adam S Butterworth5,6,61, Stavroula Kanoni7,8,61, 4 Tom R. Webb1,2, Eirini Marouli7,8, Lingyao Zeng9, Ioanna Ntalla7,8, Florence Y. Lai1,2, Jemma C. 5 Hopewell10, Olga Giannakopoulou7,8, Tao Jiang5, Stephen E. Hamby1,2, Emanuele Di 6 Angelantonio5,6, Themistocles L. Assimes11, Erwin P. Bottinger12, John C. Chambers13,14,15, 7 Robert Clarke10, Colin NA Palmer16,17, Richard M. Cubbon18, Patrick Ellinor19, Raili Ermel20, 8 Evangelos Evangelou21,22, Paul W. Franks23,24,25, Christopher Grace3,4, Dongfeng Gu26, Aroon 9 D. Hingorani27, Joanna M. M. Howson5, Erik Ingelsson28, Adnan Kastrati9, Thorsten Kessler9, 10 Theodosios Kyriakou3,4, Terho Lehtimäki29, Xiangfeng Lu26, Yingchang Lu12,30, Winfried 11 März31,32,33, Ruth McPherson34, Andres Metspalu35, Mar Pujades-Rodriguez36, Arno 12 Ruusalepp20,37, Eric E. Schadt38, Amand F. Schmidt39, Michael J. Sweeting5, Pierre A. 13 Zalloua40,41, Kamal AIGhalayini42, Bernard D. Keavney43,44, Jaspal S. Kooner14,15,45, Ruth J. F. 14 Loos12,46, Riyaz S. Patel47,48, Martin K. Rutter49,50, Maciej Tomaszewski51,52, Ioanna Tzoulaki21,22, 15 Eleftheria Zeggini53, Jeanette Erdmann54,55,56, George Dedoussis57, Johan L. M. 16 Björkegren37,38,58, EPIC-CVD Consortium, CARDIoGRAMplusC4D, The UK Biobank 17 CardioMetabolic Consortium CHD working group, Heribert Schunkert9,61, Martin Farrall3,4,61, 18 John Danesh5,6,59,61, Nilesh J. Samani1,2,61, Hugh Watkins3,4,61, Panos Deloukas7,8,60,61 19 1. Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK 20 2. -
Atlas Journal
Atlas of Genetics and Cytogenetics in Oncology and Haematology Home Genes Leukemias Solid Tumours Cancer-Prone Deep Insight Portal Teaching X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA Atlas Journal Atlas Journal versus Atlas Database: the accumulation of the issues of the Journal constitutes the body of the Database/Text-Book. TABLE OF CONTENTS Volume 12, Number 6, Nov-Dec 2008 Previous Issue / Next Issue Genes BCL8 (B-cell CLL/lymphoma 8) (15q11). Silvia Rasi, Gianluca Gaidano. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (6): 781-784. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/BCL8ID781ch15q11.html CDC25A (Cell division cycle 25A) (3p21). Dipankar Ray, Hiroaki Kiyokawa. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (6): 785-791. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/CDC25AID40004ch3p21.html CDC73 (cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)) (1q31.2). Leslie Farber, Bin Tean Teh. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (6): 792-797. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/CDC73D181ch1q31.html EIF3C (eukaryotic translation initiation factor 3, subunit C) (16p11.2). Daniel R Scoles. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (6): 798-802. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/EIF3CID44187ch16p11.html ELAC2 (elaC homolog 2 (E. coli)) (17p11.2). Yang Chen, Sean Tavtigian, Donna Shattuck. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (6): 803-806. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/ELAC2ID40437ch17p11.html FOXM1 (forkhead box M1) (12p13). Jamila Laoukili, Monica Alvarez Fernandez, René H Medema. -
12619 CTR9 (D1Z4F) Rabbit Mab
Revision 1 C 0 2 - t CTR9 (D1Z4F) Rabbit mAb a e r o t S Orders: 877-616-CELL (2355) [email protected] 9 Support: 877-678-TECH (8324) 1 6 Web: [email protected] 2 www.cellsignal.com 1 # 3 Trask Lane Danvers Massachusetts 01923 USA For Research Use Only. Not For Use In Diagnostic Procedures. Applications: Reactivity: Sensitivity: MW (kDa): Source/Isotype: UniProt ID: Entrez-Gene Id: WB, IP H M R Endogenous 140 Rabbit IgG Q6PD62 9646 Product Usage Information 7. Farber, L.J. et al. (2010) Mol Carcinog 49, 215-23. Application Dilution Western Blotting 1:1000 Immunoprecipitation 1:50 Storage Supplied in 10 mM sodium HEPES (pH 7.5), 150 mM NaCl, 100 µg/ml BSA, 50% glycerol and less than 0.02% sodium azide. Store at –20°C. Do not aliquot the antibody. Specificity / Sensitivity CTR9 (D1Z4F) Rabbit mAb recognizes endogenous levels of total CTR9 protein. Species Reactivity: Human, Mouse, Rat Species predicted to react based on 100% sequence homology: Hamster, Chicken, Xenopus, Zebrafish, Bovine, Dog, Pig Source / Purification Monoclonal antibody is produced by immunizing animals with a synthetic peptide corresponding to residues near the amino terminus of human CTR9 protein. Background The PAF (RNA polymerase II (RNAPII) associated factor) complex was initially identified in yeast and is comprised of subunits PAF1, Leo1, Ctr9, Cdc73, RTF1 and Ski8 (1,2). The PAF complex plays an important role in transcription initiation and elongation by RNAPII by regulating the establishment of proper histone modifications such as histone H2B ubiquitination and the recruitment of the histone chaperone FACT (facilitates chromatin transcription) (3-5).