Improved Estimation of Cancer Dependencies from Large-Scale Rnai Screens Using Model-Based Normalization and Data Integration
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Characterization of Genomic Copy Number Variation in Mus Musculus Associated with the Germline of Inbred and Wild Mouse Populations, Normal Development, and Cancer
Western University Scholarship@Western Electronic Thesis and Dissertation Repository 4-18-2019 2:00 PM Characterization of genomic copy number variation in Mus musculus associated with the germline of inbred and wild mouse populations, normal development, and cancer Maja Milojevic The University of Western Ontario Supervisor Hill, Kathleen A. The University of Western Ontario Graduate Program in Biology A thesis submitted in partial fulfillment of the equirr ements for the degree in Doctor of Philosophy © Maja Milojevic 2019 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Genetics and Genomics Commons Recommended Citation Milojevic, Maja, "Characterization of genomic copy number variation in Mus musculus associated with the germline of inbred and wild mouse populations, normal development, and cancer" (2019). Electronic Thesis and Dissertation Repository. 6146. https://ir.lib.uwo.ca/etd/6146 This Dissertation/Thesis is brought to you for free and open access by Scholarship@Western. It has been accepted for inclusion in Electronic Thesis and Dissertation Repository by an authorized administrator of Scholarship@Western. For more information, please contact [email protected]. Abstract Mus musculus is a human commensal species and an important model of human development and disease with a need for approaches to determine the contribution of copy number variants (CNVs) to genetic variation in laboratory and wild mice, and arising with normal mouse development and disease. Here, the Mouse Diversity Genotyping array (MDGA)-approach to CNV detection is developed to characterize CNV differences between laboratory and wild mice, between multiple normal tissues of the same mouse, and between primary mammary gland tumours and metastatic lung tissue. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
The Cyclin-Dependent Kinase 8 Module Sterically Blocks Mediator Interactions with RNA Polymerase II
The cyclin-dependent kinase 8 module sterically blocks Mediator interactions with RNA polymerase II Hans Elmlund*†, Vera Baraznenok‡, Martin Lindahl†, Camilla O. Samuelsen§, Philip J. B. Koeck*¶, Steen Holmberg§, Hans Hebert*ʈ, and Claes M. Gustafsson‡ʈ *Department of Biosciences and Nutrition, Karolinska Institutet and School of Technology and Health, Royal Institute of Technology, Novum, SE-141 87 Huddinge, Sweden; †Department of Molecular Biophysics, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; ‡Division of Metabolic Diseases, Karolinska Institutet, Novum, SE-141 86 Huddinge, Sweden; §Department of Genetics, Institute of Molecular Biology, Oester Farimagsgade 2A, DK-1353 Copenhagen K, Denmark; and ¶University College of Southern Stockholm, SE-141 57 Huddinge, Sweden Communicated by Roger D. Kornberg, Stanford University School of Medicine, Stanford, CA, August 28, 2006 (received for review February 21, 2006) CDK8 (cyclin-dependent kinase 8), along with CycC, Med12, and Here, we use the S. pombe system to investigate the molecular Med13, form a repressive module (the Cdk8 module) that prevents basis for the distinct functional properties of S and L Mediator. RNA polymerase II (pol II) interactions with Mediator. Here, we We find that the Cdk8 module binds to the pol II-binding cleft report that the ability of the Cdk8 module to prevent pol II of Mediator, where it sterically blocks interactions with the interactions is independent of the Cdk8-dependent kinase activity. polymerase. In contrast to earlier assumptions, the Cdk8 kinase We use electron microscopy and single-particle reconstruction to activity is dispensable for negative regulation of pol II interac- demonstrate that the Cdk8 module forms a distinct structural tions with Mediator. -
Noelia Díaz Blanco
Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr. -
Functional Diversification of the Nleg Effector Family in Enterohemorrhagic Escherichia Coli
Functional diversification of the NleG effector family in enterohemorrhagic Escherichia coli Dylan Valleaua, Dustin J. Littleb, Dominika Borekc,d, Tatiana Skarinaa, Andrew T. Quailea, Rosa Di Leoa, Scott Houlistone,f, Alexander Lemake,f, Cheryl H. Arrowsmithe,f, Brian K. Coombesb, and Alexei Savchenkoa,g,1 aDepartment of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada; bDepartment of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada; cDepartment of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390; dDepartment of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390; ePrincess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; fDepartment of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; and gDepartment of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada Edited by Ralph R. Isberg, Howard Hughes Medical Institute and Tufts University School of Medicine, Boston, MA, and approved August 15, 2018 (receivedfor review November 6, 2017) The pathogenic strategy of Escherichia coli and many other gram- chains. Depending on the length and nature of the polyubiquitin negative pathogens relies on the translocation of a specific set of chain, it posttranslationally regulates the target protein’s locali- proteins, called effectors, into the eukaryotic host cell during in- zation, activation, or degradation. Ubiquitination is a multistep fection. These effectors act in concert to modulate host cell pro- process which begins with the ubiquitin-activating enzyme (E1) cesses in favor of the invading pathogen. Injected by the type III using ATP to “charge” ubiquitin, covalently binding the ubiquitin secretion system (T3SS), the effector arsenal of enterohemorrhagic C terminus by a thioester linkage. -
Supplementary Material
BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Neurol Neurosurg Psychiatry Page 1 / 45 SUPPLEMENTARY MATERIAL Appendix A1: Neuropsychological protocol. Appendix A2: Description of the four cases at the transitional stage. Table A1: Clinical status and center proportion in each batch. Table A2: Complete output from EdgeR. Table A3: List of the putative target genes. Table A4: Complete output from DIANA-miRPath v.3. Table A5: Comparison of studies investigating miRNAs from brain samples. Figure A1: Stratified nested cross-validation. Figure A2: Expression heatmap of miRNA signature. Figure A3: Bootstrapped ROC AUC scores. Figure A4: ROC AUC scores with 100 different fold splits. Figure A5: Presymptomatic subjects probability scores. Figure A6: Heatmap of the level of enrichment in KEGG pathways. Kmetzsch V, et al. J Neurol Neurosurg Psychiatry 2021; 92:485–493. doi: 10.1136/jnnp-2020-324647 BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Neurol Neurosurg Psychiatry Appendix A1. Neuropsychological protocol The PREV-DEMALS cognitive evaluation included standardized neuropsychological tests to investigate all cognitive domains, and in particular frontal lobe functions. The scores were provided previously (Bertrand et al., 2018). Briefly, global cognitive efficiency was evaluated by means of Mini-Mental State Examination (MMSE) and Mattis Dementia Rating Scale (MDRS). Frontal executive functions were assessed with Frontal Assessment Battery (FAB), forward and backward digit spans, Trail Making Test part A and B (TMT-A and TMT-B), Wisconsin Card Sorting Test (WCST), and Symbol-Digit Modalities test. -
Supplementary Materials
Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine -
FBXL19 Recruits CDK-Mediator to Cpg Islands of Developmental Genes Priming Them for Activation During Lineage Commitment
RESEARCH ARTICLE FBXL19 recruits CDK-Mediator to CpG islands of developmental genes priming them for activation during lineage commitment Emilia Dimitrova1, Takashi Kondo2†, Angelika Feldmann1†, Manabu Nakayama3, Yoko Koseki2, Rebecca Konietzny4‡, Benedikt M Kessler4, Haruhiko Koseki2,5, Robert J Klose1* 1Department of Biochemistry, University of Oxford, Oxford, United Kingdom; 2Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; 3Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan; 4Nuffield Department of Medicine, TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of Oxford, Oxford, United Kingdom; 5CREST, Japan Science and Technology Agency, Kawaguchi, Japan Abstract CpG islands are gene regulatory elements associated with the majority of mammalian promoters, yet how they regulate gene expression remains poorly understood. Here, we identify *For correspondence: FBXL19 as a CpG island-binding protein in mouse embryonic stem (ES) cells and show that it [email protected] associates with the CDK-Mediator complex. We discover that FBXL19 recruits CDK-Mediator to †These authors contributed CpG island-associated promoters of non-transcribed developmental genes to prime these genes equally to this work for activation during cell lineage commitment. We further show that recognition of CpG islands by Present address: ‡Agilent FBXL19 is essential for mouse development. Together this reveals a new CpG island-centric Technologies, Waldbronn, mechanism for CDK-Mediator recruitment to developmental gene promoters in ES cells and a Germany requirement for CDK-Mediator in priming these developmental genes for activation during cell lineage commitment. Competing interests: The DOI: https://doi.org/10.7554/eLife.37084.001 authors declare that no competing interests exist. -
MED26 Antibody
Product Datasheet MED26 Antibody Catalog No: #33633 Package Size: #33633-1 50ul #33633-2 100ul Orders: [email protected] Support: [email protected] Description Product Name MED26 Antibody Host Species Rabbit Clonality Polyclonal Purification The antibody was affinity-purified from rabbit antiserum by affinity-chromatography using epitope-specific immunogen. Applications WB Species Reactivity Hu Ms Specificity The antibody detects endogenous levels of total MED26 protein. Immunogen Type Peptide Immunogen Description Synthesized peptide derived from N-terminal of human MED26. Target Name MED26 Other Names ARC70; CRSP complex 7; CRSP70; MED26; activator-recruited cofactor 70 kDa component Accession No. Swiss-Prot: O95402NCBI Gene ID: 9441 SDS-PAGE MW 65kd Concentration 1.0mg/ml Formulation Rabbit IgG in phosphate buffered saline (without Mg2+ and Ca2+), pH 7.4, 150mM NaCl, 0.02% sodium azide and 50% glycerol. Storage Store at -20°C Application Details Western blotting: 1:500~1:3000 Images Western blot analysis of extracts from LOVO cells, using MED26 antibody #33633. Background Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator Address: 8400 Baltimore Ave., Suite 302, College Park, MD 20740, USA http://www.sabbiotech.com 1 functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Ryu S., Nature 397:446-450(1999). Naeaer A.M., Nature 398:828-832(1999). -
Cbx3 Maintains Lineage Specificity During Neural Differentiation
Downloaded from genesdev.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press RESEARCH COMMUNICATION et al. 2013). However, Cbx3 is also enriched at promoters Cbx3 maintains lineage of mouse embryonic fibroblast (MEF)-derived pre-iPSCs specificity during neural (preinduced pluripotent stem cells), where it does not cor- relate with H3K9 methylation (Sridharan et al. 2013). differentiation RNAi knockdown of Cbx3 promotes reprogramming of fi- broblasts to iPSCs (Sridharan et al. 2013). Chengyang Huang,1,2 Trent Su,1 Yong Xue,1 1 3 1 Cbx3 plays important roles in developmental processes Chen Cheng, Fides D. Lay, Robin A. McKee, (Morikawa et al. 2013). In model systems, Cbx3 promotes Meiyang Li,2 Ajay Vashisht,1 James Wohlschlegel,1 neuronal maturation, kidney development, differentia- Bennett G. Novitch,4 Kathrin Plath,1 tion of ESCs to smooth muscle in culture, and embryonic Siavash K. Kurdistani,1 and Michael Carey1 arteriogenesis (Xiao et al. 2011; Dihazi et al. 2015; Oshiro et al. 2015). Little is known of how Cbx3 functions in dif- 1Department of Biological Chemistry, Eli and Edythe Broad ferentiation, but its promoter localization suggested that Center for Regenerative Medicine and Stem Cell Research, David it might directly affect transcription through the preinitia- Geffen School of Medicine, University of California at Los tion complex (PIC) (Grunberg and Hahn 2013; Allen and Angeles, Los Angeles California 90095, USA; 2Department of Taatjes 2015). The PIC is assembled in response to activa- Neurobiology, Shantou University Medical College, Shantou tors and requires the Mediator coactivator complex to re- 515041, China; 3Department of Molecular, Cell, and cruit the general transcription factors and Pol II (Chen Developmental Biology, University of California at Los Angeles, et al. -
Genome-Wide Analyses Identify Transcription Factors Required for Proper Morphogenesis of Drosophila Sensory Neuron Dendrites
Downloaded from genesdev.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Genome-wide analyses identify transcription factors required for proper morphogenesis of Drosophila sensory neuron dendrites Jay Z. Parrish,1 Michael D. Kim,1 Lily Yeh Jan, and Yuh Nung Jan2 Departments of Physiology and Biochemistry, Howard Hughes Medical Institute, University of California, San Francisco, California 94143, USA Dendrite arborization patterns are critical determinants of neuronal function. To explore the basis of transcriptional regulation in dendrite pattern formation, we used RNA interference (RNAi) to screen 730 transcriptional regulators and identified 78 genes involved in patterning the stereotyped dendritic arbors of class I da neurons in Drosophila. Most of these transcriptional regulators affect dendrite morphology without altering the number of class I dendrite arborization (da) neurons and fall primarily into three groups. Group A genes control both primary dendrite extension and lateral branching, hence the overall dendritic field. Nineteen genes within group A act to increase arborization, whereas 20 other genes restrict dendritic coverage. Group B genes appear to balance dendritic outgrowth and branching. Nineteen group B genes function to promote branching rather than outgrowth, and two others have the opposite effects. Finally, 10 group C genes are critical for the routing of the dendritic arbors of individual class I da neurons. Thus, multiple genetic programs operate to calibrate dendritic coverage, to coordinate the elaboration of primary versus secondary branches, and to lay out these dendritic branches in the proper orientation. [Keywords: Transcription; RNAi; Drosophila; neuron; dendrite] Supplemental material is available at http://www.genesdev.org. -
20151014.Nkh Et Al Supplemental
MATERIALS AND METHODS Mice All procedures involving mice were approved by the Fred Hutchinson Cancer Research Center Institutional Animal Care and Use Committee. C57BL/6J mice were obtained from The Jackson Laboratory. Single cell RNA sequencing (RNA-Seq) cDNA libraries were prepared from single olfactory epithelium neurons as previously described (10, 28). In brief, epithelial tissue was isolated from adult or neonatal animals (P2-P6), dissociated cells were plated on coverslips, and single cells transferred to individual tubes using a microcapillary pipet. Oligo dT-primed cDNAs were prepared from mRNAs in each cell using reverse transcriptase, a poly(A) extension was added to the 3’ end of each cDNA using deoxynucleotidyl transferase, and a universal primer then used to amplify the cDNAs. One-third of each cell cDNA mix was used for amplification. For some cells, a duplicate sample was amplified and sequenced starting with a different third of the sample. To assess the cell stages of neurons used for libraries prior to sequencing, aliquots of single cell libraries were used in PCR reactions with primers for genes expressed at different stages. Primers used were: Ascl1, 5’ primer, CCACGGTCTTTGCTTCTGTTTTC , 3’ primer, GTACGCAGAGGTAATCTCATTACATG, Neurog1, 5’ primer, 1 CCCTGAAGACGAGGTGAAAAGTC, 3’ primer, CCAGTGCCTGAATAGCTATGCTAG, Gap43, 5’ primer, CTGAACTTTAAGAAATGGCTTTCCAC , 3’ primer, GTTTAAGCCACACTGTTGGACTTG , Omp, 5’ primer GCATTTGCTGCTCGCTGGTG, 3’ primer, GTGCCACCGTTTTCCTGTCAG. cDNA libraries were prepared for sequencing using the Illumina TruSeq DNA Sample Prep Kit. Briefly, cDNAs were fragmented to ~300 bp, ligated to adaptors, and PCR amplified with adaptor primers. Samples were subjected to multiplexed sequencing using an Illumina HiSeq 2500 instrument and a paired end, 50 bp read-length sequencing strategy.