A Cluster of Noncoding Rnas Activates the ESR1 Locus During Breast Cancer Adaptation
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Increased Expression of Dedicator-Cytokinesis-10, Caspase
Agirrezabal et al. Multiple Sclerosis and Demyelinating Disorders (2016) 1:7 Multiple Sclerosis and DOI 10.1186/s40893-016-0009-8 Demyelinating Disorders RESEARCH ARTICLE Open Access Increased expression of dedicator- cytokinesis-10, caspase-2 and Synaptotagmin-like 2 is associated with clinical disease activity in multiple sclerosis Ion Agirrezabal1, Ricardo Palacios1, Beatriz Moreno1, Jorge Sepulcre2, Alice Abernathy1, Albert Saiz1, Sara Llufriu1, Manuel Comabella3, Xavier Montalban3, Antonio Martinez4, David Arteta4 and Pablo Villoslada1,5* Abstract Background: We aim to identify differentially expressed genes (DEGs) and its pathways associated with clinical activity of relapsing–remitting Multiple Sclerosis (RRMS). Methods: We screened DEG in blood samples from patients with clinically stable or active RRMS (≥2 relapses or increase in ≥1 point in the EDSS (due to relapses) in 2 years follow-up), and healthy controls using DNA arrays. The DEGs identified were validated by RT-PCR in a prospective cohort of MS patients. We used Gene Ontology (GO) analysis for identifying the associated pathways and Jaspar database for identifying the associated transcriptions factors. Results: We identified 45 DEG between the three groups (stable RRMS, active RRMS and control), being 14 of them significantly different between stable and active RRMS. We validated 14 out of the 45 DEG in the second cohort, eight out of the 14 being differentially expressed between active and stable patients (ARHGEF7, CASP2, DOCK10, DSP, ITPR1, KLDHC5, RBBP4, SYTL2). We found an overrepresentation of several pathways associated with lymphocyte activation. The analysis of regulatory networks identified the gene triplet of Dedicator of Cytokinesis-10 (DOCK10) – Caspase-2 (CASP2) - Synaptotagmin-like 2 (SYTL2) as being co-regulated by common transcription factors, pointing to lymphocyte activation pathways associated with disease activity. -
Genomic Correlates of Relationship QTL Involved in Fore- Versus Hind Limb Divergence in Mice
Loyola University Chicago Loyola eCommons Biology: Faculty Publications and Other Works Faculty Publications 2013 Genomic Correlates of Relationship QTL Involved in Fore- Versus Hind Limb Divergence in Mice Mihaela Palicev Gunter P. Wagner James P. Noonan Benedikt Hallgrimsson James M. Cheverud Loyola University Chicago, [email protected] Follow this and additional works at: https://ecommons.luc.edu/biology_facpubs Part of the Biology Commons Recommended Citation Palicev, M, GP Wagner, JP Noonan, B Hallgrimsson, and JM Cheverud. "Genomic Correlates of Relationship QTL Involved in Fore- Versus Hind Limb Divergence in Mice." Genome Biology and Evolution 5(10), 2013. This Article is brought to you for free and open access by the Faculty Publications at Loyola eCommons. It has been accepted for inclusion in Biology: Faculty Publications and Other Works by an authorized administrator of Loyola eCommons. For more information, please contact [email protected]. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License. © Palicev et al., 2013. GBE Genomic Correlates of Relationship QTL Involved in Fore- versus Hind Limb Divergence in Mice Mihaela Pavlicev1,2,*, Gu¨ nter P. Wagner3, James P. Noonan4, Benedikt Hallgrı´msson5,and James M. Cheverud6 1Konrad Lorenz Institute for Evolution and Cognition Research, Altenberg, Austria 2Department of Pediatrics, Cincinnati Children‘s Hospital Medical Center, Cincinnati, Ohio 3Yale Systems Biology Institute and Department of Ecology and Evolutionary Biology, Yale University 4Department of Genetics, Yale University School of Medicine 5Department of Cell Biology and Anatomy, The McCaig Institute for Bone and Joint Health and the Alberta Children’s Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Canada 6Department of Anatomy and Neurobiology, Washington University *Corresponding author: E-mail: [email protected]. -
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. -
The N-Cadherin Interactome in Primary Cardiomyocytes As Defined Using Quantitative Proximity Proteomics Yang Li1,*, Chelsea D
© 2019. Published by The Company of Biologists Ltd | Journal of Cell Science (2019) 132, jcs221606. doi:10.1242/jcs.221606 TOOLS AND RESOURCES The N-cadherin interactome in primary cardiomyocytes as defined using quantitative proximity proteomics Yang Li1,*, Chelsea D. Merkel1,*, Xuemei Zeng2, Jonathon A. Heier1, Pamela S. Cantrell2, Mai Sun2, Donna B. Stolz1, Simon C. Watkins1, Nathan A. Yates1,2,3 and Adam V. Kwiatkowski1,‡ ABSTRACT requires multiple adhesion, cytoskeletal and signaling proteins, The junctional complexes that couple cardiomyocytes must transmit and mutations in these proteins can cause cardiomyopathies (Ehler, the mechanical forces of contraction while maintaining adhesive 2018). However, the molecular composition of ICD junctional homeostasis. The adherens junction (AJ) connects the actomyosin complexes remains poorly defined. – networks of neighboring cardiomyocytes and is required for proper The core of the AJ is the cadherin catenin complex (Halbleib and heart function. Yet little is known about the molecular composition of the Nelson, 2006; Ratheesh and Yap, 2012). Classical cadherins are cardiomyocyte AJ or how it is organized to function under mechanical single-pass transmembrane proteins with an extracellular domain that load. Here, we define the architecture, dynamics and proteome of mediates calcium-dependent homotypic interactions. The adhesive the cardiomyocyte AJ. Mouse neonatal cardiomyocytes assemble properties of classical cadherins are driven by the recruitment of stable AJs along intercellular contacts with organizational and cytosolic catenin proteins to the cadherin tail, with p120-catenin β structural hallmarks similar to mature contacts. We combine (CTNND1) binding to the juxta-membrane domain and -catenin β quantitative mass spectrometry with proximity labeling to identify the (CTNNB1) binding to the distal part of the tail. -
Ahnaks Are a Class of Giant Propeller-Like Proteins That Associate with Calcium Channel Proteins of Cardiomyocytes and Other Cells
The AHNAKs are a class of giant propeller-like proteins that associate with calcium channel proteins of cardiomyocytes and other cells Akihiko Komuro*, Yutaka Masuda*, Koichi Kobayashi, Roger Babbitt, Murat Gunel, Richard A. Flavell, and Vincent T. Marchesi† Departments of Pathology and Immunobiology, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, CT 06510 Contributed by Vincent T. Marchesi, December 31, 2003 To explore the function of the giant AHNAK molecule, first de- mechanisms, one operating at the cell surface in collaboration with scribed in 1992 [Shtivelman, E., Cohen, F. E. & Bishop, J. M. (1992) calcium channels, and the second, PLC activation, which is a process Proc. Natl. Acad. Sci. USA 89, 5472–5476], we created AHNAK null that could potentially take place at multiple points throughout the mice by homologous recombination. Homozygous knockouts cell. showed no obvious phenotype, but revealed instead a second The arrangement of channel proteins at the cell surface is AHNAK-like molecule, provisionally designated AHNAK2. Like the believed to be controlled by multidomain polypeptides known as original AHNAK, AHNAK2 is a 600-kDa protein composed of a large scaffolding proteins that link together activated channels at specific number of highly conserved repeat segments. Structural predic- points on the membrane surface. Scaffolding proteins also coordi- tions suggest that the repeat segments of both AHNAKs may have nate the activities of multienzyme complexes by physically linking as their basic framework a series of linked, antiparallel -strands them together, and as in the case with AHNAK, they are often similar to those found in -propeller proteins. -
The Endocytic Membrane Trafficking Pathway Plays a Major Role
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Liverpool Repository RESEARCH ARTICLE The Endocytic Membrane Trafficking Pathway Plays a Major Role in the Risk of Parkinson’s Disease Sara Bandres-Ciga, PhD,1,2 Sara Saez-Atienzar, PhD,3 Luis Bonet-Ponce, PhD,4 Kimberley Billingsley, MSc,1,5,6 Dan Vitale, MSc,7 Cornelis Blauwendraat, PhD,1 Jesse Raphael Gibbs, PhD,7 Lasse Pihlstrøm, MD, PhD,8 Ziv Gan-Or, MD, PhD,9,10 The International Parkinson’s Disease Genomics Consortium (IPDGC), Mark R. Cookson, PhD,4 Mike A. Nalls, PhD,1,11 and Andrew B. Singleton, PhD1* 1Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain 3Transgenics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 4Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 5Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom 6Department of Pathophysiology, University of Tartu, Tartu, Estonia 7Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 8Department of Neurology, Oslo University Hospital, Oslo, Norway 9Department of Neurology and Neurosurgery, Department of Human Genetics, McGill University, Montréal, Quebec, Canada 10Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada 11Data Tecnica International, Glen Echo, Maryland, USA ABSTRACT studies, summary-data based Mendelian randomization Background: PD is a complex polygenic disorder. -
Distinguishing Pleiotropy from Linked QTL Between Milk Production Traits
Cai et al. Genet Sel Evol (2020) 52:19 https://doi.org/10.1186/s12711-020-00538-6 Genetics Selection Evolution RESEARCH ARTICLE Open Access Distinguishing pleiotropy from linked QTL between milk production traits and mastitis resistance in Nordic Holstein cattle Zexi Cai1*†, Magdalena Dusza2†, Bernt Guldbrandtsen1, Mogens Sandø Lund1 and Goutam Sahana1 Abstract Background: Production and health traits are central in cattle breeding. Advances in next-generation sequencing technologies and genotype imputation have increased the resolution of gene mapping based on genome-wide association studies (GWAS). Thus, numerous candidate genes that afect milk yield, milk composition, and mastitis resistance in dairy cattle are reported in the literature. Efect-bearing variants often afect multiple traits. Because the detection of overlapping quantitative trait loci (QTL) regions from single-trait GWAS is too inaccurate and subjective, multi-trait analysis is a better approach to detect pleiotropic efects of variants in candidate genes. However, large sample sizes are required to achieve sufcient power. Multi-trait meta-analysis is one approach to deal with this prob- lem. Thus, we performed two multi-trait meta-analyses, one for three milk production traits (milk yield, protein yield and fat yield), and one for milk yield and mastitis resistance. Results: For highly correlated traits, the power to detect pleiotropy was increased by multi-trait meta-analysis com- pared with the subjective assessment of overlapping of single-trait QTL confdence intervals. Pleiotropic efects of lead single nucleotide polymorphisms (SNPs) that were detected from the multi-trait meta-analysis were confrmed by bivariate association analysis. The previously reported pleiotropic efects of variants within the DGAT1 and MGST1 genes on three milk production traits, and pleiotropic efects of variants in GHR on milk yield and fat yield were con- frmed. -
Essential Genes and Their Role in Autism Spectrum Disorder
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2017 Essential Genes And Their Role In Autism Spectrum Disorder Xiao Ji University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Bioinformatics Commons, and the Genetics Commons Recommended Citation Ji, Xiao, "Essential Genes And Their Role In Autism Spectrum Disorder" (2017). Publicly Accessible Penn Dissertations. 2369. https://repository.upenn.edu/edissertations/2369 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/2369 For more information, please contact [email protected]. Essential Genes And Their Role In Autism Spectrum Disorder Abstract Essential genes (EGs) play central roles in fundamental cellular processes and are required for the survival of an organism. EGs are enriched for human disease genes and are under strong purifying selection. This intolerance to deleterious mutations, commonly observed haploinsufficiency and the importance of EGs in pre- and postnatal development suggests a possible cumulative effect of deleterious variants in EGs on complex neurodevelopmental disorders. Autism spectrum disorder (ASD) is a heterogeneous, highly heritable neurodevelopmental syndrome characterized by impaired social interaction, communication and repetitive behavior. More and more genetic evidence points to a polygenic model of ASD and it is estimated that hundreds of genes contribute to ASD. The central question addressed in this dissertation is whether genes with a strong effect on survival and fitness (i.e. EGs) play a specific oler in ASD risk. I compiled a comprehensive catalog of 3,915 mammalian EGs by combining human orthologs of lethal genes in knockout mice and genes responsible for cell-based essentiality. -
Stemmacs™ Cebpb Mrna
StemMACS™ Cebpb mRNA human Order no. 130-104-377 Contents 1.3 Applications 1. Description ● Differentiation of pluripotent stem cells into adipose tissue. 1.1 Principle 1.2 Background information 2. Protocol: Reconstitution of lyophilizate 1.2 Applications ▲ RNA is susceptible to degradation by exogenous ribonucleases. 2. Protocol: Dissolving of lyophilizate Wear gloves, use RNase-free reagents, tubes, and pipette tips. 1. Dissolve StemMACS Cebpb mRNA in 200 µL of Double- 1. Description distilled Water. Vortex thoroughly. The final concentration will be 0.1 µg/µL. Components 20 µg StemMACS™ Cebpb mRNA encoding the transcription factor C/EBP-beta (CEBPB, 2. Briefly centrifuge to collect the content at the bottom of the LAP, CRP2, TCF5; Entrez Gene ID 1051). tube. 1 mL Double-distilled Water, RNase-free 3. Prepare aliquots and store at –70 °C to –80 °C. Do not subject Specifications In vitro transcribed, polyadenylated and aliquots to more than two freeze-thaw cycles. capped mRNA that has been modified with pseudouridine and 5-methyl-cytidine to reduce For satisfactory transfection results, use a protocol that is the innate antiviral response to single-stranded optimized for your specific cell type. StemMACS™ eGFP mRNA RNA. or StemMACS™ Nuclear eGFP mRNA allow easy evaluation of Formulation Lyophilized from a filtered (0.2 µm) solution. transfection efficiency and are recommended as positive controls. Storage Store the lyophilized product at –20 °C. The Refer to www.miltenyibiotec.com for all data sheets and protocols. expiration date is indicated on the label. After Miltenyi Biotec provides technical support worldwide. Visit reconstitution, the product can be stored at www.miltenyibiotec.com/local to find your nearest Miltenyi Biotec –70°C for up to 3 month. -
Analysis of the Indacaterol-Regulated Transcriptome in Human Airway
Supplemental material to this article can be found at: http://jpet.aspetjournals.org/content/suppl/2018/04/13/jpet.118.249292.DC1 1521-0103/366/1/220–236$35.00 https://doi.org/10.1124/jpet.118.249292 THE JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS J Pharmacol Exp Ther 366:220–236, July 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Analysis of the Indacaterol-Regulated Transcriptome in Human Airway Epithelial Cells Implicates Gene Expression Changes in the s Adverse and Therapeutic Effects of b2-Adrenoceptor Agonists Dong Yan, Omar Hamed, Taruna Joshi,1 Mahmoud M. Mostafa, Kyla C. Jamieson, Radhika Joshi, Robert Newton, and Mark A. Giembycz Departments of Physiology and Pharmacology (D.Y., O.H., T.J., K.C.J., R.J., M.A.G.) and Cell Biology and Anatomy (M.M.M., R.N.), Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada Received March 22, 2018; accepted April 11, 2018 Downloaded from ABSTRACT The contribution of gene expression changes to the adverse and activity, and positive regulation of neutrophil chemotaxis. The therapeutic effects of b2-adrenoceptor agonists in asthma was general enriched GO term extracellular space was also associ- investigated using human airway epithelial cells as a therapeu- ated with indacaterol-induced genes, and many of those, in- tically relevant target. Operational model-fitting established that cluding CRISPLD2, DMBT1, GAS1, and SOCS3, have putative jpet.aspetjournals.org the long-acting b2-adrenoceptor agonists (LABA) indacaterol, anti-inflammatory, antibacterial, and/or antiviral activity. Numer- salmeterol, formoterol, and picumeterol were full agonists on ous indacaterol-regulated genes were also induced or repressed BEAS-2B cells transfected with a cAMP-response element in BEAS-2B cells and human primary bronchial epithelial cells by reporter but differed in efficacy (indacaterol $ formoterol . -
Temporal Mapping of CEBPA and CEBPB Binding
Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries Janus Schou Jakobsen1,2,3,*, Johannes Waage1,2,3,4, Nicolas Rapin1,2,3,4, Hanne Cathrine Bisgaard5, Fin Stolze Larsen6, Bo Torben Porse1,2,3,* 1 The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, DK2200 Copenhagen, Denmark; 2 Biotech Research and Innovation Centre (BRIC), University of Copenhagen, DK-2200 Copenhagen, Denmark; 3 The Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, DK2200 Copenhagen Denmark; 4 The Bioinformatics Centre, University of Copenhagen, DK2200, Copenhagen, Denmark; 5 Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, DK- 2100 Copenhagen, Denmark; 6 Department of Hepatology, Rigshospitalet, DK2200 Copenhagen, Denmark. JW: [email protected]; NR: [email protected]; HCB: [email protected]; FSL: [email protected] * Corresponding authors: BTP: [email protected]; JSJ: [email protected], The Finsen Laboratory, Ole Maaløesvej 5, Copenhagen Biocenter, University of Copenhagen, DK2200 Copenhagen, Denmark. Telephone: +45 3545 6023 Running title: Regulation of liver regeneration Keywords: Temporal ChIP-seq, dynamic binding, liver regeneration, C/EBPalpha, C/EBPbeta, transcriptional networks 1 Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract Dynamic shifts in transcription factor binding are central to the regulation of biological processes by allowing rapid changes in gene transcription. -
Overexpression of RNF38 Facilitates TGF-Β Signaling by Ubiquitinating
Peng et al. Journal of Experimental & Clinical Cancer Research (2019) 38:113 https://doi.org/10.1186/s13046-019-1113-3 RESEARCH Open Access Overexpression of RNF38 facilitates TGF-β signaling by Ubiquitinating and degrading AHNAK in hepatocellular carcinoma Rui Peng1,2†, Peng-Fei Zhang1,3†, Xuan Yang1†, Chuan-Yuan Wei1†, Xiao-Yong Huang1, Jia-Bin Cai1, Jia-Cheng Lu1, Chao Gao1, Hai-Xiang Sun1, Qiang Gao1, Dou-Sheng Bai2, Guo-Ming Shi1*, Ai-Wu Ke1* and Jia Fan1,4* Abstract Background: RING finger protein 38 (RNF38), a member of the RNF protein family, has just emerged as a vital driver of cancer progression. However, the oncogenic mechanisms of RNF38 remain unexplored. Methods: Using frozen tumor tissue and tissue microarray from hepatocellular carcinoma (HCC) patients, we tried to probe the expression of RNF38 in HCC and its clinical value. Then the biological functions of RNF38 were analyzed in vivo and vitro. Stable isotope labeling with amino acids (SILAC) in cell culture and co-immunoprecipitation proteomic analyses were combined to reveal the potential mechanism of RNF38 in HCC progression. Results: We report that RNF38 expression was markedly higher in HCC tissues than in peritumor tissues. Correspondingly, RNF38 overexpression promoted the HCC cell migration and invasion and inhibited apoptosis both in vitro and in vivo. And elevated RNF38 expression induced HCC cell epithelial-mesenchymal transition by facilitating transforming growth factor-β (TGF-β) signaling via ubiquitinating and degrading neuroblast differentiation-associated protein (AHNAK), a well-established inhibitor of TGF-β signaling. Furthermore, AHNAK interference restored the HCC cell invasion and metastasis deprived by RNF38 downregulation.