Mechanisms of Impaired Neutrophil Migration by Micrornas in Myelodysplastic Syndromes

Total Page:16

File Type:pdf, Size:1020Kb

Mechanisms of Impaired Neutrophil Migration by Micrornas in Myelodysplastic Syndromes Mechanisms of Impaired Neutrophil Migration by MicroRNAs in Myelodysplastic Syndromes This information is current as Meiwan Cao, Yayoi Shikama, Hideo Kimura, Hideyoshi of September 29, 2021. Noji, Kazuhiko Ikeda, Tomoyuki Ono, Kazuei Ogawa, Yasuchika Takeishi and Junko Kimura J Immunol 2017; 198:1887-1899; Prepublished online 27 January 2017; doi: 10.4049/jimmunol.1600622 Downloaded from http://www.jimmunol.org/content/198/5/1887 Supplementary http://www.jimmunol.org/content/suppl/2017/01/27/jimmunol.160062 Material 2.DCSupplemental http://www.jimmunol.org/ References This article cites 74 articles, 25 of which you can access for free at: http://www.jimmunol.org/content/198/5/1887.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 29, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2017 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Mechanisms of Impaired Neutrophil Migration by MicroRNAs in Myelodysplastic Syndromes Meiwan Cao,* Yayoi Shikama,*,† Hideo Kimura,‡ Hideyoshi Noji,x,{ Kazuhiko Ikeda,x,‖ Tomoyuki Ono,* Kazuei Ogawa,x Yasuchika Takeishi,x and Junko Kimura* In myelodysplastic syndromes (MDS), functional defects of neutrophils result in high mortality because of infections; however, the molecular basis remains unclear. We recently found that miR-34a and miR-155 were significantly increased in MDS neutrophils. To clarify the effects of the aberrant microRNA expression on neutrophil functions, we introduced miR-34a, miR-155, or control micro- RNA into neutrophil-like differentiated HL60 cells. Ectopically introduced miR-34a and miR-155 significantly attenuated migration toward chemoattractants fMLF and IL-8, but enhanced degranulation. To clarify the mechanisms for inhibition of migration, we studied the effects of miR-34a and miR-155 on the migration-regulating Rho family members, Cdc42 and Rac1. The introduced miR-34a and miR-155 decreased the fMLF-induced active form of Cdc42 to 29.0 6 15.9 and 39.7 6 4.8% of that in the control cells, Downloaded from respectively, although Cdc42 protein levels were not altered. miR-34a decreased a Cdc42-specific guanine nucleotide exchange factor (GEF), dedicator of cytokinesis (DOCK) 8, whereas miR-155 reduced another Cdc42-specific GEF, FYVE, RhoGEF, and PH domain-containing (FGD) 4. The knockdown of DOCK8 and FGD4 by small interfering RNA suppressed Cdc42 activation and fMLF/IL-8–induced migration. miR-155, but not miR-34a, decreased Rac1 protein, and introduction of Rac1 small interfering RNA attenuated Rac1 activation and migration. Neutrophils from patients showed significant attenuation in migration compared with healthy cells, and protein levels of DOCK8, FGD4, and Rac1 were well correlated with migration toward fMLF (r = 0.642, 0.686, http://www.jimmunol.org/ and 0.436, respectively) and IL-8 (r = 0.778, 0.659, and 0.606, respectively). Our results indicated that reduction of DOCK8, FGD4, and Rac1 contributes to impaired neutrophil migration in MDS. The Journal of Immunology, 2017, 198: 1887–1899. yelodysplastic syndromes (MDS) are a heterogeneous Neutrophil migration to infection sites is induced by chemo- group of clonal disorders characterized by ineffective attractants, such as fMLF (8, 9) and IL-8 (IL-8/CXCL8) (10, 11). M hematopoiesis resulting in numerical, morphological, Both fMLF- and IL-8/CXCL8–induced migration have been shown and functional abnormalities in blood cells of multiple lineages to be affected in MDS-derived neutrophils (12–14). A previous study (1–4). Most notably, quantitative and qualitative defects of neu- suggested that disturbed activation of the Rac-ERK pathway and by guest on September 29, 2021 trophilic granulocytes reduce bactericidal and fungicidal activities, PI3K is responsible for the aberrant IL-8/CXCL8–induced migration resulting in life-threatening infections (5–7). MDS-derived neutro- in MDS (14). It has been reported that CD18 plays a critical role phils have demonstrated impairment in migration, production of regarding fMLF-induced migration (15), and that expression of the reactive oxygen species, and phagocytosis. However, the molecular CD11b–CD18 complex is decreased in MDS neutrophils (16). When basis of the neutrophil dysfunction has yet to be clearly defined. stimulated with fMLF, activation of ERK1/2 and protein kinase B (PKB/Akt) was also attenuated in MDS (17). Although fMLF has *Department of Pharmacology, School of Medicine, Fukushima Medical University, been shown to activate various Rho family members that play es- Fukushima 960-1295, Japan; †Center for Medical Education and Career Develop- sential roles in regulating cytoskeletal dynamics (18), there have yet ment, Fukushima Medical University, Fukushima 960-1295, Japan; ‡Department of Hematology, Kita-Fukushima Medical Center, Date 960-0502, Japan; xDepartment of to be studies on whether insufficient activation of Rho proteins is Cardiology and Hematology, School of Medicine, Fukushima Medical University, involved in aberrant fMLF-induced migration of MDS neutrophils. Fukushima 960-1295, Japan; {Department of Medical Oncology, School of Medi- ‖ Among the Rho family members, Cdc42 and Rac1 have been cine, Fukushima Medical University, Fukushima 960-1295, Japan; and Department of Blood Transfusion and Transplantation Immunology, School of Medicine, Fukushima extensively studied as key regulators for cell migration. Cdc42 is Medical University, Fukushima 960-1295, Japan required for actin polymerization and filopodial protrusion to ORCIDs: 0000-0001-5121-5130 (Y.S.); 0000-0002-5269-269X (K.I.). maintain polarity, whereas Rac1 promotes actin assembly to reg- Received for publication April 8, 2016. Accepted for publication December 30, 2016. ulate lamellipodia extension (19–21). Both Rac1 and Cdc42 act as This work was supported by Japanese Society for Promotion of Science Grants-in- molecular switches by cycling between an inactive GDP-bound Aid for Scientific Research (C) MO23591400 (to Y.S.), MO26461409 (to Y.S.), and form and an active GTP-bound form. In response to stimuli, GDP- MO24590325 (to J.K.). bound forms in the cytoplasm are recruited to the membrane, Address correspondence and reprint requests to Dr. Yayoi Shikama, Center for Med- ical Education and Career Development, Fukushima Medical University, 1 Hikarigaoka, where guanine nucleotide exchange factors (GEFs) convert GDP Fukushima 960-1295, Japan. E-mail address: [email protected] to GTP (22, 23). GEFs are categorized into two distinct classes, The online version of this article contains supplemental material. dedicator of cytokinesis (DOCK) proteins and the diffuse B cell Abbreviations used in this article: dbcAMP, dibutyryl cAMP; Dbl, diffuse B cell lymphoma (Dbl) family (23, 24). Of the DOCK proteins, DOCK8 lymphoma; dHL60, differentiated HL60; DOCK, dedicator of cytokinesis; FGD, is a Cdc42-specific GEF that critically regulates migration of FYVE, RhoGEF, and PH domain-containing; FPR, fMLF receptor; GEF, guanine nucleotide exchange factor; MDS, myelodysplastic syndromes; miRNA, microRNA; dendritic cells (25), whereas DOCK2 and DOCK5 are identified as MPO, myeloperoxidase; PKB, protein kinase B; RCMD, refractory cytopenia with potent Rac regulators in neutrophils (26). Like FYVE, RhoGEF, multilineage dysplasia; siRNA, small interfering RNA; TET2, Tet oncogene family and PH domain-containing 2 (FGD2) and FGD3, FGD4, also member 2. known as Frabin (FGD1-related F-actin binding protein), is a Copyright Ó 2017 by The American Association of Immunologists, Inc. 0022-1767/17/$30.00 Cdc42-specific GEF belonging to the Dbl family (27). www.jimmunol.org/cgi/doi/10.4049/jimmunol.1600622 1888 miR-34a AND miR-155 IMPAIRED NEUTROPHIL MIGRATION We recently reported that miR-34a and miR-155 were signifi- Materials and Methods cantly increased in neutrophils isolated from MDS patients com- Blood donors, ethics, and neutrophil isolation pared with those from healthy cells (28). Aberrant expression of Peripheral blood was obtained from 12 healthy volunteers and 11 MDS microRNAs (miRNAs) affects various cell functions. It has been patients consisting of 9 subjects with refractory cytopenia with multilineage shown that miR-34a, a target of p53 (29), not only inhibits pro- dysplasia (RCMD), 1 with refractory cytopenia with unilineage dysplasia, liferation by inducing apoptosis (30), but also suppresses migra- and 1 with refractory anemia with excess blasts-2, according to the World tion and/or invasion of malignant cell lines via reduction of Health Organization 2008 classification (38). Table I summarizes the metalloproteinases and Fra-1 (31–33). Regarding miR-155, it has clinical data of the patients and the genomic information obtained by target sequencing. Although none of the patients had experienced symptomatic been reported that its overexpression accelerates
Recommended publications
  • Snf2h-Mediated Chromatin Organization and Histone H1 Dynamics Govern Cerebellar Morphogenesis and Neural Maturation
    ARTICLE Received 12 Feb 2014 | Accepted 15 May 2014 | Published 20 Jun 2014 DOI: 10.1038/ncomms5181 OPEN Snf2h-mediated chromatin organization and histone H1 dynamics govern cerebellar morphogenesis and neural maturation Matı´as Alvarez-Saavedra1,2, Yves De Repentigny1, Pamela S. Lagali1, Edupuganti V.S. Raghu Ram3, Keqin Yan1, Emile Hashem1,2, Danton Ivanochko1,4, Michael S. Huh1, Doo Yang4,5, Alan J. Mears6, Matthew A.M. Todd1,4, Chelsea P. Corcoran1, Erin A. Bassett4, Nicholas J.A. Tokarew4, Juraj Kokavec7, Romit Majumder8, Ilya Ioshikhes4,5, Valerie A. Wallace4,6, Rashmi Kothary1,2, Eran Meshorer3, Tomas Stopka7, Arthur I. Skoultchi8 & David J. Picketts1,2,4 Chromatin compaction mediates progenitor to post-mitotic cell transitions and modulates gene expression programs, yet the mechanisms are poorly defined. Snf2h and Snf2l are ATP-dependent chromatin remodelling proteins that assemble, reposition and space nucleosomes, and are robustly expressed in the brain. Here we show that mice conditionally inactivated for Snf2h in neural progenitors have reduced levels of histone H1 and H2A variants that compromise chromatin fluidity and transcriptional programs within the developing cerebellum. Disorganized chromatin limits Purkinje and granule neuron progenitor expansion, resulting in abnormal post-natal foliation, while deregulated transcriptional programs contribute to altered neural maturation, motor dysfunction and death. However, mice survive to young adulthood, in part from Snf2l compensation that restores Engrailed-1 expression. Similarly, Purkinje-specific Snf2h ablation affects chromatin ultrastructure and dendritic arborization, but alters cognitive skills rather than motor control. Our studies reveal that Snf2h controls chromatin organization and histone H1 dynamics for the establishment of gene expression programs underlying cerebellar morphogenesis and neural maturation.
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • 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.
    [Show full text]
  • Whole Exome Sequencing in Families at High Risk for Hodgkin Lymphoma: Identification of a Predisposing Mutation in the KDR Gene
    Hodgkin Lymphoma SUPPLEMENTARY APPENDIX Whole exome sequencing in families at high risk for Hodgkin lymphoma: identification of a predisposing mutation in the KDR gene Melissa Rotunno, 1 Mary L. McMaster, 1 Joseph Boland, 2 Sara Bass, 2 Xijun Zhang, 2 Laurie Burdett, 2 Belynda Hicks, 2 Sarangan Ravichandran, 3 Brian T. Luke, 3 Meredith Yeager, 2 Laura Fontaine, 4 Paula L. Hyland, 1 Alisa M. Goldstein, 1 NCI DCEG Cancer Sequencing Working Group, NCI DCEG Cancer Genomics Research Laboratory, Stephen J. Chanock, 5 Neil E. Caporaso, 1 Margaret A. Tucker, 6 and Lynn R. Goldin 1 1Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 2Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 3Ad - vanced Biomedical Computing Center, Leidos Biomedical Research Inc.; Frederick National Laboratory for Cancer Research, Frederick, MD; 4Westat, Inc., Rockville MD; 5Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; and 6Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA ©2016 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol.2015.135475 Received: August 19, 2015. Accepted: January 7, 2016. Pre-published: June 13, 2016. Correspondence: [email protected] Supplemental Author Information: NCI DCEG Cancer Sequencing Working Group: Mark H. Greene, Allan Hildesheim, Nan Hu, Maria Theresa Landi, Jennifer Loud, Phuong Mai, Lisa Mirabello, Lindsay Morton, Dilys Parry, Anand Pathak, Douglas R. Stewart, Philip R. Taylor, Geoffrey S. Tobias, Xiaohong R. Yang, Guoqin Yu NCI DCEG Cancer Genomics Research Laboratory: Salma Chowdhury, Michael Cullen, Casey Dagnall, Herbert Higson, Amy A.
    [Show full text]
  • Human Tumors Instigate Granulin-Expressing Hematopoietic Cells That Promote Malignancy by Activating Stromal Fibroblasts in Mice
    Human tumors instigate granulin-expressing hematopoietic cells that promote malignancy by activating stromal fibroblasts in mice Moshe Elkabets, … , Robert A. Weinberg, Sandra S. McAllister J Clin Invest. 2011;121(2):784-799. https://doi.org/10.1172/JCI43757. Research Article Systemic instigation is a process by which endocrine signals sent from certain tumors (instigators) stimulate BM cells (BMCs), which are mobilized into the circulation and subsequently foster the growth of otherwise indolent carcinoma cells (responders) residing at distant anatomical sites. The identity of the BMCs and their specific contribution or contributions to responder tumor growth have been elusive. Here, we have demonstrated that Sca1+cKit– hematopoietic BMCs of mouse hosts bearing instigating tumors promote the growth of responding tumors that form with a myofibroblast-rich, desmoplastic stroma. Such stroma is almost always observed in malignant human adenocarcinomas and is an indicator of poor prognosis. We then identified granulin (GRN) as the most upregulated gene in instigating Sca1+cKit– BMCs relative to counterpart control cells. The GRN+ BMCs that were recruited to the responding tumors induced resident tissue fibroblasts to express genes that promoted malignant tumor progression; indeed, treatment with recombinant GRN alone was sufficient to promote desmoplastic responding tumor growth. Further, analysis of tumor tissues from a cohort of breast cancer patients revealed that high GRN expression correlated with the most aggressive triple-negative, basal-like tumor subtype and reduced patient survival. Our data suggest that GRN and the unique hematopoietic BMCs that produce it might serve as novel therapeutic targets. Find the latest version: https://jci.me/43757/pdf Research article Related Commentary, page 516 Human tumors instigate granulin-expressing hematopoietic cells that promote malignancy by activating stromal fibroblasts in mice Moshe Elkabets,1 Ann M.
    [Show full text]
  • Supplementary Table 1
    Supplementary Table 1. 492 genes are unique to 0 h post-heat timepoint. The name, p-value, fold change, location and family of each gene are indicated. Genes were filtered for an absolute value log2 ration 1.5 and a significance value of p ≤ 0.05. Symbol p-value Log Gene Name Location Family Ratio ABCA13 1.87E-02 3.292 ATP-binding cassette, sub-family unknown transporter A (ABC1), member 13 ABCB1 1.93E-02 −1.819 ATP-binding cassette, sub-family Plasma transporter B (MDR/TAP), member 1 Membrane ABCC3 2.83E-02 2.016 ATP-binding cassette, sub-family Plasma transporter C (CFTR/MRP), member 3 Membrane ABHD6 7.79E-03 −2.717 abhydrolase domain containing 6 Cytoplasm enzyme ACAT1 4.10E-02 3.009 acetyl-CoA acetyltransferase 1 Cytoplasm enzyme ACBD4 2.66E-03 1.722 acyl-CoA binding domain unknown other containing 4 ACSL5 1.86E-02 −2.876 acyl-CoA synthetase long-chain Cytoplasm enzyme family member 5 ADAM23 3.33E-02 −3.008 ADAM metallopeptidase domain Plasma peptidase 23 Membrane ADAM29 5.58E-03 3.463 ADAM metallopeptidase domain Plasma peptidase 29 Membrane ADAMTS17 2.67E-04 3.051 ADAM metallopeptidase with Extracellular other thrombospondin type 1 motif, 17 Space ADCYAP1R1 1.20E-02 1.848 adenylate cyclase activating Plasma G-protein polypeptide 1 (pituitary) receptor Membrane coupled type I receptor ADH6 (includes 4.02E-02 −1.845 alcohol dehydrogenase 6 (class Cytoplasm enzyme EG:130) V) AHSA2 1.54E-04 −1.6 AHA1, activator of heat shock unknown other 90kDa protein ATPase homolog 2 (yeast) AK5 3.32E-02 1.658 adenylate kinase 5 Cytoplasm kinase AK7
    [Show full text]
  • Atypical Guanine Nucleotide Exchange Factors for Rho Family Gtpases: Dock9 Activation of Cdc42 and Smggds Activation of Rhoa
    ATYPICAL GUANINE NUCLEOTIDE EXCHANGE FACTORS FOR RHO FAMILY GTPASES: DOCK9 ACTIVATION OF CDC42 AND SMGGDS ACTIVATION OF RHOA Brant L. Hamel A dissertation submitted to the faculty of the University of North Carolina at Chapel Hill in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biochemistry and Biophysics. Chapel Hill 2010 Approved by: Henrik Dohlman, Ph.D. Brian Kuhlman, Ph.D. Matthew Redinbo, Ph.D. David Siderovski, Ph.D. John Sondek, Ph.D. ABSTRACT BRANT L. HAMEL: Atypical Guanine Nucleotide Exchange Factors for Rho Family GTPases: DOCK9 Activation of Cdc42 and SmgGDS activation of RhoA (Under the direction of John Sondek) Rho GTPases regulate diverse cellular processes ranging from cell morphology and motility to mitosis. The activation of Rho GTPases is tightly controlled by the actions of guanine nucleotide exchange factors (GEFs). While the mechanism of canonical Dbl family exchange factors is established, both DOCK proteins and SmgGDS catalyze nucleotide exchange by distinct mechanisms. The structure of the DOCK9 GEF domain bound to Cdc42 was recently described, while no structural information on SmgGDS is available. Here, we describe a C- terminal DOCK9 fragment, soluble in bacteria, that is sufficient to catalyze nucleotide exchange on Cdc42. We also provide evidence that full-length DOCK9 is significantly more active than the minimal GEF domain, implicating the ability of other domains to contribute to the DOCK9 exchange mechanism. In contrast to the reported ability of SmgGDS to activate both Rho and Ras family GTPases, we find exclusive activation of RhoA and RhoC both in vitro and in vivo.
    [Show full text]
  • Loss of the Neural-Specific BAF Subunit ACTL6B Relieves PNAS PLUS Repression of Early Response Genes and Causes Recessive Autism
    Loss of the neural-specific BAF subunit ACTL6B relieves PNAS PLUS repression of early response genes and causes recessive autism Wendy Wenderskia,b,c,d, Lu Wange,f,g,1, Andrey Krokhotina,b,c,d,1, Jessica J. Walshh, Hongjie Lid,i, Hirotaka Shojij, Shereen Ghoshe,f,g, Renee D. Georgee,f,g, Erik L. Millera,b,c,d, Laura Eliasa,b,c,d, Mark A. Gillespiek, Esther Y. Sona,b,c,d, Brett T. Staahla,b,c,d, Seung Tae Baeke,f,g, Valentina Stanleye,f,g, Cynthia Moncadaa,b,c,d, Zohar Shiponya,b,c,d, Sara B. Linkerl, Maria C. N. Marchettol, Fred H. Gagel, Dillon Chene,f,g, Tipu Sultanm, Maha S. Zakin, Jeffrey A. Ranishk, Tsuyoshi Miyakawaj, Liqun Luod,i, Robert C. Malenkah, Gerald R. Crabtreea,b,c,d,2, and Joseph G. Gleesone,f,g,2 aDepartment of Pathology, Stanford Medical School, Palo Alto, CA 94305; bDepartment of Genetics, Stanford Medical School, Palo Alto, CA 94305; cDepartment of Developmental Biology, Stanford Medical School, Palo Alto, CA 94305; dHoward Hughes Medical Institute, Stanford University, Palo Alto, CA 94305; eDepartment of Neuroscience, University of California San Diego, La Jolla, CA 92037; fHoward Hughes Medical Institute, University of California San Diego, La Jolla, CA 92037; gRady Children’s Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92037; hNancy Pritztker Laboratory, Department of Psychiatry and Behavioral Sciences, Stanford Medical School, Palo Alto, CA 94305; iDepartment of Biology, Stanford University, Palo Alto, CA 94305; jDivision of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, 470-1192 Toyoake, Aichi, Japan; kInstitute for Systems Biology, Seattle, WA 98109; lLaboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037; mDepartment of Pediatric Neurology, Institute of Child Health, Children Hospital Lahore, 54000 Lahore, Pakistan; and nClinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, 12311 Cairo, Egypt Edited by Arthur L.
    [Show full text]
  • 1 Complexity and Graded Regulation of Neuronal Cell Type-Specific
    bioRxiv preprint doi: https://doi.org/10.1101/2021.01.27.428525; this version posted January 28, 2021. 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. Complexity and graded regulation of neuronal cell type-specific alternative splicing revealed by single-cell RNA sequencing Huijuan Feng1, Daniel F. Moakley1, Shuonan Chen1, Melissa G. McKenzie1, Vilas Menon2, Chaolin Zhang1 1Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York NY 10032, USA 2 Department of Neurology, Taub Institute for Research on Alzheimer Disease and the Aging Brain, Columbia University, New York NY 10032, USA *To whom correspondence should be addressed: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.27.428525; this version posted January 28, 2021. 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. Abstract The enormous neuronal cellular diversity in the mammalian brain, which is highly prototypical and organized in a hierarchical manner, is dictated by cell type-specific gene regulatory programs at the molecular level. Although prevalent in the brain, contribution of alternative splicing (AS) to the molecular diversity across neuronal cell types is just starting to emerge.
    [Show full text]
  • Expression Profile of Rhogtpases and Rhogefs During RANKL-Stimulated Osteoclastogenesis: Identification of Essential Genes in Osteoclasts
    Expression profile of RhoGTPases and RhoGEFs during RANKL-stimulated osteoclastogenesis: identification of essential genes in osteoclasts. Hélène Brazier, Sébastien Stephens, Stéphane Ory, Philippe Fort, Nigel Morrison, Anne Blangy To cite this version: Hélène Brazier, Sébastien Stephens, Stéphane Ory, Philippe Fort, Nigel Morrison, et al.. Expression profile of RhoGTPases and RhoGEFs during RANKL-stimulated osteoclastogenesis: identification of essential genes in osteoclasts.. Journal of Bone and Mineral Research, American Society for Bone and Mineral Research, 2006, 21 (9), pp.1387-98. 10.1359/jbmr.060613. hal-00189080 HAL Id: hal-00189080 https://hal.archives-ouvertes.fr/hal-00189080 Submitted on 20 Nov 2007 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. Revised Manuscript Expression profile of RhoGTPases and RhoGEFs during RANKL-stimulated osteoclastogenesis: identification of essential genes in osteoclasts. Hélène Brazier1,3, Sébastien Stephens1,2,3, Stéphane Ory1, Philippe Fort1, Nigel Morrison2 and Anne Blangy1,4. 1: Centre de Recherches en Biochimie Macromoléculaire, CNRS FRE 2593, Montpellier, FRANCE. 2: School of Medical Science, Griffith University, Queensland, Australia. 3: HB and SS contributed equally to this work. 4: Corresponding author. Anne Blangy. Centre de Recherches en Biochimie Macromoléculaire, CNRS FRE 2593.
    [Show full text]
  • Synthetic Lethal Interactions with Oncogenic KRAS
    Synthetic Lethal Interactions With Oncogenic KRAS The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Wang, Belinda. 2018. Synthetic Lethal Interactions With Oncogenic KRAS. Doctoral dissertation, Harvard Medical School. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:37006458 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Abstract KRAS is one of the most frequently mutated genes across human cancers, including 96% of pancreatic cancers, 40% of colorectal cancers, and 35% of lung cancers. The majority of human cancer cell lines and tumors from genetically engineered mouse models harboring an oncogenic mutant KRAS allele demonstrate a strong dependence on KRAS for proliferation and survival. This KRAS dependency is a type of ‘oncogene addiction,’ a state in which cancer cells depend on signaling from a single oncogene for survival. Unfortunately, the development of clinically effective KRAS-directed cancer therapies has been unsuccessful, and KRAS-mutant cancers are refractory to standard and targeted therapies. Alternative approaches to combatting KRAS-mutant cancers are clearly needed. We postulate that oncogenic KRAS signaling induces changes in cell signaling networks that cause cells to become dependent on certain genes, termed a ‘synthetic lethal’ interaction. Identifying these selective vulnerabilities would lend insight to the pathways altered in KRAS-mutant cancers and may inform novel strategies to target KRAS-addicted cancers.
    [Show full text]
  • 1 Supplementary Table 1
    Supplementary Table 1: Reference Reference Sample MSI Test / Study ID 829 gene 192 gene Type status Training classifier classifier Giacomin et al CRC cell line NCI-H508 MSS Training Y Y Giacomini et al CRC cell line LS-180 MSI Training Y Y Giacomini et al CRC cell line LS-174T MSI Training Y Y Giacomini et al CRC cell line SW-403 MSS Training Y Y Giacomini et al CRC cell line HCT116 MSI Training Y Y Giacomini et al CRC cell line LS411 MSI Test Giacomini et al CRC cell line T84 MSS Test Giacomini et al CRC cell line SW-480 MSS Training Y Y Giacomini et al CRC cell line COLO741 MSS Test Giacomini et al CRC cell line COLO320 MSS Test Giacomini et al CRC cell line DLD-1 MSI Training Y Y Giacomini et al CRC cell line COLO205 MSS Test Giacomini et al CRC cell line HT-29 MSS Training Y Y Giacomini et al CRC cell line SW620 MSS Training Y Y Giacomini et al CRC cell line LIM2412 MSI Test Giacomini et al CRC cell line SW-1116 MSS Training Y Y Giacomini et al CRC cell line LIM1215 MSI Test Giacomini et al CRC cell line RKO MSI Training Y Y Giacomini et al CRC cell line HCT15 MSI Training Y Y Giacomini et al CRC cell line GP5D MSI Training Y Y Giacomini et al CRC cell line SW48 MSI Training Y Y Giacomini et al CRC cell line SK-CO-1 MSS Training Y Y Giacomini et al CRC cell line HCA7 MSI Test Giacomini et al CRC cell line SNUC2B MSI Test Giacomini et al CRC cell line SW1417 MSS Test Giacomini et al CRC cell line SW948 MSS Test Giacomini et al CRC cell line GP2D MSI Training Y Y Giacomini et al CRC cell line LOVO MSI Training Y Y Giacomini et al CRC
    [Show full text]