E-Cadherin Accumulation Within the Lymphovascular Embolus of Inflammatory Breast Cancer Is Due to Altered Trafficking
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MBNL1 Regulates Essential Alternative RNA Splicing Patterns in MLL-Rearranged Leukemia
ARTICLE https://doi.org/10.1038/s41467-020-15733-8 OPEN MBNL1 regulates essential alternative RNA splicing patterns in MLL-rearranged leukemia Svetlana S. Itskovich1,9, Arun Gurunathan 2,9, Jason Clark 1, Matthew Burwinkel1, Mark Wunderlich3, Mikaela R. Berger4, Aishwarya Kulkarni5,6, Kashish Chetal6, Meenakshi Venkatasubramanian5,6, ✉ Nathan Salomonis 6,7, Ashish R. Kumar 1,7 & Lynn H. Lee 7,8 Despite growing awareness of the biologic features underlying MLL-rearranged leukemia, 1234567890():,; targeted therapies for this leukemia have remained elusive and clinical outcomes remain dismal. MBNL1, a protein involved in alternative splicing, is consistently overexpressed in MLL-rearranged leukemias. We found that MBNL1 loss significantly impairs propagation of murine and human MLL-rearranged leukemia in vitro and in vivo. Through transcriptomic profiling of our experimental systems, we show that in leukemic cells, MBNL1 regulates alternative splicing (predominantly intron exclusion) of several genes including those essential for MLL-rearranged leukemogenesis, such as DOT1L and SETD1A.Wefinally show that selective leukemic cell death is achievable with a small molecule inhibitor of MBNL1. These findings provide the basis for a new therapeutic target in MLL-rearranged leukemia and act as further validation of a burgeoning paradigm in targeted therapy, namely the disruption of cancer-specific splicing programs through the targeting of selectively essential RNA binding proteins. 1 Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA. 2 Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA. 3 Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA. -
EFA6A, an Exchange Factor for Arf6, Regulates Early Steps in Ciliogenesis
EFA6A, an exchange factor for Arf6, regulates early steps in ciliogenesis Mariagrazia Partisani, Carole Baron, Rania Ghossoub, Racha Fayad, Sophie Pagnotta, Sophie Abélanet, Eric Macia, Frédéric Brau, Sandra Lacas-Gervais, Alexandre Benmerah, et al. To cite this version: Mariagrazia Partisani, Carole Baron, Rania Ghossoub, Racha Fayad, Sophie Pagnotta, et al.. EFA6A, an exchange factor for Arf6, regulates early steps in ciliogenesis. Journal of Cell Science, Company of Biologists, 2021, 134 (2), pp.jcs249565. 10.1242/jcs.249565. hal-03120586 HAL Id: hal-03120586 https://hal.archives-ouvertes.fr/hal-03120586 Submitted on 19 Apr 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. © 2021. Published by The Company of Biologists Ltd | Journal of Cell Science (2021) 134, jcs249565. doi:10.1242/jcs.249565 RESEARCH ARTICLE EFA6A, an exchange factor for Arf6, regulates early steps in ciliogenesis Mariagrazia Partisani1, Carole L. Baron1, Rania Ghossoub2, Racha Fayad1, Sophie Pagnotta3, Sophie Abélanet1, Eric Macia1,Frédéric Brau1, Sandra Lacas-Gervais3, Alexandre Benmerah4,Frédéric Luton1 and Michel Franco1,* ABSTRACT localized to the PC and which play an important role in its assembly Ciliogenesis is a coordinated process initiated by the recruitment and and/or function. -
Genetic and Genomic Analysis of Hyperlipidemia, Obesity and Diabetes Using (C57BL/6J × TALLYHO/Jngj) F2 Mice
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Nutrition Publications and Other Works Nutrition 12-19-2010 Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P. Stewart Marshall University Hyoung Y. Kim University of Tennessee - Knoxville, [email protected] Arnold M. Saxton University of Tennessee - Knoxville, [email protected] Jung H. Kim Marshall University Follow this and additional works at: https://trace.tennessee.edu/utk_nutrpubs Part of the Animal Sciences Commons, and the Nutrition Commons Recommended Citation BMC Genomics 2010, 11:713 doi:10.1186/1471-2164-11-713 This Article is brought to you for free and open access by the Nutrition at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Nutrition Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Stewart et al. BMC Genomics 2010, 11:713 http://www.biomedcentral.com/1471-2164/11/713 RESEARCH ARTICLE Open Access Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P Stewart1, Hyoung Yon Kim2, Arnold M Saxton3, Jung Han Kim1* Abstract Background: Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution to human T2D and related metabolic disorders is evident, and mostly follows polygenic inheritance. The TALLYHO/ JngJ (TH) mice are a polygenic model for T2D characterized by obesity, hyperinsulinemia, impaired glucose uptake and tolerance, hyperlipidemia, and hyperglycemia. -
Effects of Chronic Stress on Prefrontal Cortex Transcriptome in Mice Displaying Different Genetic Backgrounds
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Springer - Publisher Connector J Mol Neurosci (2013) 50:33–57 DOI 10.1007/s12031-012-9850-1 Effects of Chronic Stress on Prefrontal Cortex Transcriptome in Mice Displaying Different Genetic Backgrounds Pawel Lisowski & Marek Wieczorek & Joanna Goscik & Grzegorz R. Juszczak & Adrian M. Stankiewicz & Lech Zwierzchowski & Artur H. Swiergiel Received: 14 May 2012 /Accepted: 25 June 2012 /Published online: 27 July 2012 # The Author(s) 2012. This article is published with open access at Springerlink.com Abstract There is increasing evidence that depression signaling pathway (Clic6, Drd1a,andPpp1r1b). LA derives from the impact of environmental pressure on transcriptome affected by CMS was associated with genetically susceptible individuals. We analyzed the genes involved in behavioral response to stimulus effects of chronic mild stress (CMS) on prefrontal cor- (Fcer1g, Rasd2, S100a8, S100a9, Crhr1, Grm5,and tex transcriptome of two strains of mice bred for high Prkcc), immune effector processes (Fcer1g, Mpo,and (HA)and low (LA) swim stress-induced analgesia that Igh-VJ558), diacylglycerol binding (Rasgrp1, Dgke, differ in basal transcriptomic profiles and depression- Dgkg,andPrkcc), and long-term depression (Crhr1, like behaviors. We found that CMS affected 96 and 92 Grm5,andPrkcc) and/or coding elements of dendrites genes in HA and LA mice, respectively. Among genes (Crmp1, Cntnap4,andPrkcc) and myelin proteins with the same expression pattern in both strains after (Gpm6a, Mal,andMog). The results indicate significant CMS, we observed robust upregulation of Ttr gene contribution of genetic background to differences in coding transthyretin involved in amyloidosis, seizures, stress response gene expression in the mouse prefrontal stroke-like episodes, or dementia. -
Monoclonal Anti-EXOC7, Clone 70X13F3 Produced in Mouse, Purified Immunoglobulin
Monoclonal Anti-EXOC7, clone 70X13F3 produced in mouse, purified immunoglobulin Catalog Number SAB4200604 Product Description Reagent Monoclonal Anti-EXOC7 (mouse IgG2b isotype) is Supplied as a solution in 0.01 M phosphate buffered derived from the hybridoma 70X13F3 produced by the saline, pH 7.4, containing 15 mM sodium azide as a fusion of mouse myeloma cells and splenocytes from preservative. BALB/c mice immunized with a recombinant full-length Antibody Concentration: ~ 1.0 mg/mL EXOC7 subunit (Gene ID: 64632). The isotype is determined by ELISA using Mouse Monoclonal Precautions and Disclaimer Antibody Isotyping Reagents, Catalog Number ISO2. This product is for R&D use only, not for drug, The antibody is purified from culture supernatant of household, or other uses. Please consult the Material hybridoma cells grown in a bioreactor. Safety Data Sheet for information regarding hazards and safe handling practices. Monoclonal Anti-EXOC7 recognizes human, monkey, chicken, dog, hamster, rat and mouse EXOC7. The Storage/Stability product may be used in several immunochemical For extended storage, freeze at -20 0C in working techniques including immunoblotting (~ 70kDa), aliquots. Repeated freezing and thawing, or storage in immunocytochemistry and flow cytometry. “frost-free” freezers, is not recommended. If slight turbidity occurs upon prolonged storage, clarify the solution by centrifugation before use. Working dilution Exocytosis is an essential membrane traffic event samples should be discarded if not used within 12 mediating the secretion of intracellular protein contents hours. such as hormones and neurotransmitters as well as the incorporation of membrane proteins and lipids to Product Profile specific domains of the plasma membrane. -
Exocyst Components Promote an Incompatible Interaction Between Glycine Max (Soybean) and Heterodera Glycines (The Soybean Cyst Nematode) Keshav Sharma1,7, Prakash M
www.nature.com/scientificreports OPEN Exocyst components promote an incompatible interaction between Glycine max (soybean) and Heterodera glycines (the soybean cyst nematode) Keshav Sharma1,7, Prakash M. Niraula1,8, Hallie A. Troell1, Mandeep Adhikari1, Hamdan Ali Alshehri2, Nadim W. Alkharouf3, Kathy S. Lawrence4 & Vincent P. Klink1,5,6* Vesicle and target membrane fusion involves tethering, docking and fusion. The GTPase SECRETORY4 (SEC4) positions the exocyst complex during vesicle membrane tethering, facilitating docking and fusion. Glycine max (soybean) Sec4 functions in the root during its defense against the parasitic nematode Heterodera glycines as it attempts to develop a multinucleate nurse cell (syncytium) serving to nourish the nematode over its 30-day life cycle. Results indicate that other tethering proteins are also important for defense. The G. max exocyst is encoded by 61 genes: 5 EXOC1 (Sec3), 2 EXOC2 (Sec5), 5 EXOC3 (Sec6), 2 EXOC4 (Sec8), 2 EXOC5 (Sec10) 6 EXOC6 (Sec15), 31 EXOC7 (Exo70) and 8 EXOC8 (Exo84) genes. At least one member of each gene family is expressed within the syncytium during the defense response. Syncytium-expressed exocyst genes function in defense while some are under transcriptional regulation by mitogen-activated protein kinases (MAPKs). The exocyst component EXOC7-H4-1 is not expressed within the syncytium but functions in defense and is under MAPK regulation. The tethering stage of vesicle transport has been demonstrated to play an important role in defense in the G. max-H. glycines pathosystem, with some of the spatially and temporally regulated exocyst components under transcriptional control by MAPKs. Abbreviations DCM Detection call methodology wr Whole root system pg Per gram SAR Systemic acquired resistance During their defense against pathogen infection, plants employ cellular processes to detect and amplify signals derived from the activities of those pathogens. -
Identification of Protein Features Encoded by Alternative Exons Using Exon Ontology
Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Resource Identification of protein features encoded by alternative exons using Exon Ontology Léon-Charles Tranchevent,1 Fabien Aubé,1 Louis Dulaurier,1 Clara Benoit-Pilven,1 Amandine Rey,1 Arnaud Poret,1 Emilie Chautard,2 Hussein Mortada,1 François-Olivier Desmet,1 Fatima Zahra Chakrama,1 Maira Alejandra Moreno-Garcia,1 Evelyne Goillot,3 Stéphane Janczarski,1 Franck Mortreux,1 Cyril F. Bourgeois,1,4 and Didier Auboeuf1,4 1Université Lyon 1, ENS de Lyon, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France; 2Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, UMR CNRS 5558, INRIA Erable, Villeurbanne, F-69622, France; 3Institut NeuroMyoGène, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, F-69007 France Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing var- iation in physiological- or pathological-associated cellular phenotypes. Toward this end, we developed a computational approach, named Exon Ontology, based on terms corresponding to well-characterized protein features organized in an ontology tree. Exon Ontology is conceptually similar to Gene Ontology-based approaches but focuses on exon-encod- ed protein features instead of gene level functional annotations. Exon Ontology describes the protein features encoded by a selected list of exons and looks for potential Exon Ontology term enrichment. By applying this strategy to exons that are differentially spliced between epithelial and mesenchymal cells and after extensive experimental validation, we demonstrate that Exon Ontology provides support to discover specific protein features regulated by alternative splic- ing. -
Supplementary Table S1. List of Differentially Expressed
Supplementary table S1. List of differentially expressed transcripts (FDR adjusted p‐value < 0.05 and −1.4 ≤ FC ≥1.4). 1 ID Symbol Entrez Gene Name Adj. p‐Value Log2 FC 214895_s_at ADAM10 ADAM metallopeptidase domain 10 3,11E‐05 −1,400 205997_at ADAM28 ADAM metallopeptidase domain 28 6,57E‐05 −1,400 220606_s_at ADPRM ADP‐ribose/CDP‐alcohol diphosphatase, manganese dependent 6,50E‐06 −1,430 217410_at AGRN agrin 2,34E‐10 1,420 212980_at AHSA2P activator of HSP90 ATPase homolog 2, pseudogene 6,44E‐06 −1,920 219672_at AHSP alpha hemoglobin stabilizing protein 7,27E‐05 2,330 aminoacyl tRNA synthetase complex interacting multifunctional 202541_at AIMP1 4,91E‐06 −1,830 protein 1 210269_s_at AKAP17A A‐kinase anchoring protein 17A 2,64E‐10 −1,560 211560_s_at ALAS2 5ʹ‐aminolevulinate synthase 2 4,28E‐06 3,560 212224_at ALDH1A1 aldehyde dehydrogenase 1 family member A1 8,93E‐04 −1,400 205583_s_at ALG13 ALG13 UDP‐N‐acetylglucosaminyltransferase subunit 9,50E‐07 −1,430 207206_s_at ALOX12 arachidonate 12‐lipoxygenase, 12S type 4,76E‐05 1,630 AMY1C (includes 208498_s_at amylase alpha 1C 3,83E‐05 −1,700 others) 201043_s_at ANP32A acidic nuclear phosphoprotein 32 family member A 5,61E‐09 −1,760 202888_s_at ANPEP alanyl aminopeptidase, membrane 7,40E‐04 −1,600 221013_s_at APOL2 apolipoprotein L2 6,57E‐11 1,600 219094_at ARMC8 armadillo repeat containing 8 3,47E‐08 −1,710 207798_s_at ATXN2L ataxin 2 like 2,16E‐07 −1,410 215990_s_at BCL6 BCL6 transcription repressor 1,74E‐07 −1,700 200776_s_at BZW1 basic leucine zipper and W2 domains 1 1,09E‐06 −1,570 222309_at -
A Regulator of Innate Immune Responses
(19) TZZ ¥_T (11) EP 2 942 357 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 11.11.2015 Bulletin 2015/46 C07K 14/47 (2006.01) A61K 38/00 (2006.01) C12N 15/113 (2010.01) (21) Application number: 15169327.2 (22) Date of filing: 04.08.2009 (84) Designated Contracting States: (72) Inventor: Barber, Glen N. AT BE BG CH CY CZ DE DK EE ES FI FR GB GR Palmetto Bay, FL 33157 (US) HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL PT RO SE SI SK SM TR (74) Representative: Inspicos A/S Kogle Allé 2 (30) Priority: 04.08.2008 US 129975 P P.O. Box 45 2970 Hørsholm (DK) (62) Document number(s) of the earlier application(s) in accordance with Art. 76 EPC: Remarks: 09805473.7 / 2 324 044 This application was filed on 27-05-2015 as a divisional application to the application mentioned (71) Applicant: Barber, Glen N. under INID code 62. Palmetto Bay, FL 33157 (US) (54) STING (STIMULATOR OF INTEFERON GENES), A REGULATOR OF INNATE IMMUNE RESPONSES (57) Novel molecules termed STING which include STING compositions are useful for the treatment of an nucleic acids, polynucleotides, oligonucleotides, pep- immune-related disorder, including treating and prevent- tides, mutants, variants and active fragments thereof, ing infection by modulating immunity. modulate innate and adaptive immunity in a subject. EP 2 942 357 A1 Printed by Jouve, 75001 PARIS (FR) EP 2 942 357 A1 Description RELATED APPLICATIONS 5 [0001] This application claims priority under 35 USC § 119 to U.S. -
Downloaded Per Proteome Cohort Via the Web- Site Links of Table 1, Also Providing Information on the Deposited Spectral Datasets
www.nature.com/scientificreports OPEN Assessment of a complete and classifed platelet proteome from genome‑wide transcripts of human platelets and megakaryocytes covering platelet functions Jingnan Huang1,2*, Frauke Swieringa1,2,9, Fiorella A. Solari2,9, Isabella Provenzale1, Luigi Grassi3, Ilaria De Simone1, Constance C. F. M. J. Baaten1,4, Rachel Cavill5, Albert Sickmann2,6,7,9, Mattia Frontini3,8,9 & Johan W. M. Heemskerk1,9* Novel platelet and megakaryocyte transcriptome analysis allows prediction of the full or theoretical proteome of a representative human platelet. Here, we integrated the established platelet proteomes from six cohorts of healthy subjects, encompassing 5.2 k proteins, with two novel genome‑wide transcriptomes (57.8 k mRNAs). For 14.8 k protein‑coding transcripts, we assigned the proteins to 21 UniProt‑based classes, based on their preferential intracellular localization and presumed function. This classifed transcriptome‑proteome profle of platelets revealed: (i) Absence of 37.2 k genome‑ wide transcripts. (ii) High quantitative similarity of platelet and megakaryocyte transcriptomes (R = 0.75) for 14.8 k protein‑coding genes, but not for 3.8 k RNA genes or 1.9 k pseudogenes (R = 0.43–0.54), suggesting redistribution of mRNAs upon platelet shedding from megakaryocytes. (iii) Copy numbers of 3.5 k proteins that were restricted in size by the corresponding transcript levels (iv) Near complete coverage of identifed proteins in the relevant transcriptome (log2fpkm > 0.20) except for plasma‑derived secretory proteins, pointing to adhesion and uptake of such proteins. (v) Underrepresentation in the identifed proteome of nuclear‑related, membrane and signaling proteins, as well proteins with low‑level transcripts. -
Regulation of Human Cerebral Cortical Development by EXOC7
ARTICLE Regulation of human cerebral cortical development by EXOC7 and EXOC8, components of the exocyst complex, and roles in neural progenitor cell proliferation and survival Michael E. Coulter, MD, PhD1,2, Damir Musaev, BSc3, Ellen M. DeGennaro, BA1,4, Xiaochang Zhang, PhD1,5, Katrin Henke, PhD6, Kiely N. James, PhD3, Richard S. Smith, PhD1, R. Sean Hill, PhD1, Jennifer N. Partlow, MS1, Muna Al-Saffar, MBChB, MSc1,7, A. Stacy Kamumbu, BA1, Nicole Hatem, BA1, A. James Barkovich, MD8, Jacqueline Aziza, MD9, Nicolas Chassaing, MD, PhD10,11, Maha S. Zaki, MD, PhD12, Tipu Sultan, MD13, Lydie Burglen, MD, PhD14,15, Anna Rajab, MD, PhD16, Lihadh Al-Gazali, MBChB, MSc7, Ganeshwaran H. Mochida, MD, MMSc1,17, Matthew P. Harris, PhD6, Joseph G. Gleeson, MD3 and Christopher A. Walsh, MD, PhD 1 Purpose: The exocyst complex is a conserved protein complex that (LOF) variants in a recessively inherited disorder characterized by mediates fusion of intracellular vesicles to the plasma membrane brain atrophy, seizures, and developmental delay, and in severe and is implicated in processes including cell polarity, cell migration, cases, microcephaly and infantile death. In EXOC8, we found a ciliogenesis, cytokinesis, autophagy, and fusion of secretory vesicles. homozygous truncating variant in a family with a similar clinical The essential role of these genes in human genetic disorders, disorder. We modeled exoc7 deficiency in zebrafish and found the however, is unknown. absence of exoc7 causes microcephaly. Methods: We performed homozygosity mapping and exome Conclusion: Our results highlight the essential role of the exocyst sequencing of consanguineous families with recessively inherited pathway in normal cortical development and how its perturbation brain development disorders. -
Variation in Protein Coding Genes Identifies Information Flow
bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 2019. 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-NC-ND 4.0 International license. Animal complexity and information flow 1 1 2 3 4 5 Variation in protein coding genes identifies information flow as a contributor to 6 animal complexity 7 8 Jack Dean, Daniela Lopes Cardoso and Colin Sharpe* 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Institute of Biological and Biomedical Sciences 25 School of Biological Science 26 University of Portsmouth, 27 Portsmouth, UK 28 PO16 7YH 29 30 * Author for correspondence 31 [email protected] 32 33 Orcid numbers: 34 DLC: 0000-0003-2683-1745 35 CS: 0000-0002-5022-0840 36 37 38 39 40 41 42 43 44 45 46 47 48 49 Abstract bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 2019. 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-NC-ND 4.0 International license. Animal complexity and information flow 2 1 Across the metazoans there is a trend towards greater organismal complexity. How 2 complexity is generated, however, is uncertain. Since C.elegans and humans have 3 approximately the same number of genes, the explanation will depend on how genes are 4 used, rather than their absolute number.