RNA-Sequencing from Single Nuclei
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Systems Analysis Implicates WAVE2&Nbsp
JACC: BASIC TO TRANSLATIONAL SCIENCE VOL.5,NO.4,2020 ª 2020 THE AUTHORS. PUBLISHED BY ELSEVIER ON BEHALF OF THE AMERICAN COLLEGE OF CARDIOLOGY FOUNDATION. THIS IS AN OPEN ACCESS ARTICLE UNDER THE CC BY-NC-ND LICENSE (http://creativecommons.org/licenses/by-nc-nd/4.0/). PRECLINICAL RESEARCH Systems Analysis Implicates WAVE2 Complex in the Pathogenesis of Developmental Left-Sided Obstructive Heart Defects a b b b Jonathan J. Edwards, MD, Andrew D. Rouillard, PHD, Nicolas F. Fernandez, PHD, Zichen Wang, PHD, b c d d Alexander Lachmann, PHD, Sunita S. Shankaran, PHD, Brent W. Bisgrove, PHD, Bradley Demarest, MS, e f g h Nahid Turan, PHD, Deepak Srivastava, MD, Daniel Bernstein, MD, John Deanfield, MD, h i j k Alessandro Giardini, MD, PHD, George Porter, MD, PHD, Richard Kim, MD, Amy E. Roberts, MD, k l m m,n Jane W. Newburger, MD, MPH, Elizabeth Goldmuntz, MD, Martina Brueckner, MD, Richard P. Lifton, MD, PHD, o,p,q r,s t d Christine E. Seidman, MD, Wendy K. Chung, MD, PHD, Martin Tristani-Firouzi, MD, H. Joseph Yost, PHD, b u,v Avi Ma’ayan, PHD, Bruce D. Gelb, MD VISUAL ABSTRACT Edwards, J.J. et al. J Am Coll Cardiol Basic Trans Science. 2020;5(4):376–86. ISSN 2452-302X https://doi.org/10.1016/j.jacbts.2020.01.012 JACC: BASIC TO TRANSLATIONALSCIENCEVOL.5,NO.4,2020 Edwards et al. 377 APRIL 2020:376– 86 WAVE2 Complex in LVOTO HIGHLIGHTS ABBREVIATIONS AND ACRONYMS Combining CHD phenotype–driven gene set enrichment and CRISPR knockdown screening in zebrafish is an effective approach to identifying novel CHD genes. -
IL21R Expressing CD14+CD16+ Monocytes Expand in Multiple
Plasma Cell Disorders SUPPLEMENTARY APPENDIX IL21R expressing CD14 +CD16 + monocytes expand in multiple myeloma patients leading to increased osteoclasts Marina Bolzoni, 1 Domenica Ronchetti, 2,3 Paola Storti, 1,4 Gaetano Donofrio, 5 Valentina Marchica, 1,4 Federica Costa, 1 Luca Agnelli, 2,3 Denise Toscani, 1 Rosanna Vescovini, 1 Katia Todoerti, 6 Sabrina Bonomini, 7 Gabriella Sammarelli, 1,7 Andrea Vecchi, 8 Daniela Guasco, 1 Fabrizio Accardi, 1,7 Benedetta Dalla Palma, 1,7 Barbara Gamberi, 9 Carlo Ferrari, 8 Antonino Neri, 2,3 Franco Aversa 1,4,7 and Nicola Giuliani 1,4,7 1Myeloma Unit, Dept. of Medicine and Surgery, University of Parma; 2Dept. of Oncology and Hemato-Oncology, University of Milan; 3Hematology Unit, “Fondazione IRCCS Ca’ Granda”, Ospedale Maggiore Policlinico, Milan; 4CoreLab, University Hospital of Parma; 5Dept. of Medical-Veterinary Science, University of Parma; 6Laboratory of Pre-clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture; 7Hematology and BMT Center, University Hospital of Parma; 8Infectious Disease Unit, University Hospital of Parma and 9“Dip. Oncologico e Tecnologie Avanzate”, IRCCS Arcispedale Santa Maria Nuova, Reggio Emilia, Italy ©2017 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol. 2016.153841 Received: August 5, 2016. Accepted: December 23, 2016. Pre-published: January 5, 2017. Correspondence: [email protected] SUPPLEMENTAL METHODS Immunophenotype of BM CD14+ in patients with monoclonal gammopathies. Briefly, 100 μl of total BM aspirate was incubated in the dark with anti-human HLA-DR-PE (clone L243; BD), anti-human CD14-PerCP-Cy 5.5, anti-human CD16-PE-Cy7 (clone B73.1; BD) and anti-human CD45-APC-H 7 (clone 2D1; BD) for 20 min. -
PUF60 Variants Cause a Syndrome of ID, Short Stature, Microcephaly, Coloboma, Craniofacial, Cardiac, Renal and Spinal Features
European Journal of Human Genetics (2017) 25, 552–559 Official journal of The European Society of Human Genetics www.nature.com/ejhg ARTICLE PUF60 variants cause a syndrome of ID, short stature, microcephaly, coloboma, craniofacial, cardiac, renal and spinal features Karen J Low1,2, Morad Ansari3, Rami Abou Jamra4, Angus Clarke5, Salima El Chehadeh6, David R FitzPatrick3, Mark Greenslade7, Alex Henderson8, Jane Hurst9, Kory Keller10, Paul Kuentz11, Trine Prescott12, Franziska Roessler4, Kaja K Selmer12, Michael C Schneider13, Fiona Stewart14, Katrina Tatton-Brown15, Julien Thevenon11, Magnus D Vigeland12, Julie Vogt16, Marjolaine Willems17, Jonathan Zonana10, DDD Study18 and Sarah F Smithson*,1,2 PUF60 encodes a nucleic acid-binding protein, a component of multimeric complexes regulating RNA splicing and transcription. In 2013, patients with microdeletions of chromosome 8q24.3 including PUF60 were found to have developmental delay, microcephaly, craniofacial, renal and cardiac defects. Very similar phenotypes have been described in six patients with variants in PUF60, suggesting that it underlies the syndrome. We report 12 additional patients with PUF60 variants who were ascertained using exome sequencing: six through the Deciphering Developmental Disorders Study and six through similar projects. Detailed phenotypic analysis of all patients was undertaken. All 12 patients had de novo heterozygous PUF60 variants on exome analysis, each confirmed by Sanger sequencing: four frameshift variants resulting in premature stop codons, three missense variants that clustered within the RNA recognition motif of PUF60 and five essential splice-site (ESS) variant. Analysis of cDNA from a fibroblast cell line derived from one of the patients with an ESS variants revealed aberrant splicing. The consistent feature was developmental delay and most patients had short stature. -
Nuclear PTEN Safeguards Pre-Mrna Splicing to Link Golgi Apparatus for Its Tumor Suppressive Role
ARTICLE DOI: 10.1038/s41467-018-04760-1 OPEN Nuclear PTEN safeguards pre-mRNA splicing to link Golgi apparatus for its tumor suppressive role Shao-Ming Shen1, Yan Ji2, Cheng Zhang1, Shuang-Shu Dong2, Shuo Yang1, Zhong Xiong1, Meng-Kai Ge1, Yun Yu1, Li Xia1, Meng Guo1, Jin-Ke Cheng3, Jun-Ling Liu1,3, Jian-Xiu Yu1,3 & Guo-Qiang Chen1 Dysregulation of pre-mRNA alternative splicing (AS) is closely associated with cancers. However, the relationships between the AS and classic oncogenes/tumor suppressors are 1234567890():,; largely unknown. Here we show that the deletion of tumor suppressor PTEN alters pre-mRNA splicing in a phosphatase-independent manner, and identify 262 PTEN-regulated AS events in 293T cells by RNA sequencing, which are associated with significant worse outcome of cancer patients. Based on these findings, we report that nuclear PTEN interacts with the splicing machinery, spliceosome, to regulate its assembly and pre-mRNA splicing. We also identify a new exon 2b in GOLGA2 transcript and the exon exclusion contributes to PTEN knockdown-induced tumorigenesis by promoting dramatic Golgi extension and secretion, and PTEN depletion significantly sensitizes cancer cells to secretion inhibitors brefeldin A and golgicide A. Our results suggest that Golgi secretion inhibitors alone or in combination with PI3K/Akt kinase inhibitors may be therapeutically useful for PTEN-deficient cancers. 1 Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China. 2 Institute of Health Sciences, Shanghai Institutes for Biological Sciences of Chinese Academy of Sciences and SJTU-SM, Shanghai 200025, China. -
Exploring Autophagy with Gene Ontology
Autophagy ISSN: 1554-8627 (Print) 1554-8635 (Online) Journal homepage: https://www.tandfonline.com/loi/kaup20 Exploring autophagy with Gene Ontology Paul Denny, Marc Feuermann, David P. Hill, Ruth C. Lovering, Helene Plun- Favreau & Paola Roncaglia To cite this article: Paul Denny, Marc Feuermann, David P. Hill, Ruth C. Lovering, Helene Plun- Favreau & Paola Roncaglia (2018) Exploring autophagy with Gene Ontology, Autophagy, 14:3, 419-436, DOI: 10.1080/15548627.2017.1415189 To link to this article: https://doi.org/10.1080/15548627.2017.1415189 © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. View supplementary material Published online: 17 Feb 2018. Submit your article to this journal Article views: 1097 View Crossmark data Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=kaup20 AUTOPHAGY, 2018 VOL. 14, NO. 3, 419–436 https://doi.org/10.1080/15548627.2017.1415189 RESEARCH PAPER - BASIC SCIENCE Exploring autophagy with Gene Ontology Paul Denny a,†,§, Marc Feuermann b,§, David P. Hill c,f,§, Ruth C. Lovering a,§, Helene Plun-Favreau d and Paola Roncaglia e,f,§ aFunctional Gene Annotation, Institute of Cardiovascular Science, University College London, London, UK; bSIB Swiss Institute of Bioinformatics, Geneva, Switzerland; cThe Jackson Laboratory, Bar Harbor, ME, USA; dDepartment of Molecular Neuroscience, UCL Institute of Neurology, London, UK; eEuropean Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, UK; fThe Gene Ontology Consortium ABSTRACT ARTICLE HISTORY Autophagy is a fundamental cellular process that is well conserved among eukaryotes. It is one of the Received 18 May 2017 strategies that cells use to catabolize substances in a controlled way. -
Detailed Characterization of Human Induced Pluripotent Stem Cells Manufactured for Therapeutic Applications
Stem Cell Rev and Rep DOI 10.1007/s12015-016-9662-8 Detailed Characterization of Human Induced Pluripotent Stem Cells Manufactured for Therapeutic Applications Behnam Ahmadian Baghbaderani 1 & Adhikarla Syama2 & Renuka Sivapatham3 & Ying Pei4 & Odity Mukherjee2 & Thomas Fellner1 & Xianmin Zeng3,4 & Mahendra S. Rao5,6 # The Author(s) 2016. This article is published with open access at Springerlink.com Abstract We have recently described manufacturing of hu- help determine which set of tests will be most useful in mon- man induced pluripotent stem cells (iPSC) master cell banks itoring the cells and establishing criteria for discarding a line. (MCB) generated by a clinically compliant process using cord blood as a starting material (Baghbaderani et al. in Stem Cell Keywords Induced pluripotent stem cells . Embryonic stem Reports, 5(4), 647–659, 2015). In this manuscript, we de- cells . Manufacturing . cGMP . Consent . Markers scribe the detailed characterization of the two iPSC clones generated using this process, including whole genome se- quencing (WGS), microarray, and comparative genomic hy- Introduction bridization (aCGH) single nucleotide polymorphism (SNP) analysis. We compare their profiles with a proposed calibra- Induced pluripotent stem cells (iPSCs) are akin to embryonic tion material and with a reporter subclone and lines made by a stem cells (ESC) [2] in their developmental potential, but dif- similar process from different donors. We believe that iPSCs fer from ESC in the starting cell used and the requirement of a are likely to be used to make multiple clinical products. We set of proteins to induce pluripotency [3]. Although function- further believe that the lines used as input material will be used ally identical, iPSCs may differ from ESC in subtle ways, at different sites and, given their immortal status, will be used including in their epigenetic profile, exposure to the environ- for many years or even decades. -
Exploring Extracellular Vesicles Biogenesis in Hypothalamic Cells Through a Heavy Isotope Pulse/Trace Proteomic Approach
cells Article Exploring Extracellular Vesicles Biogenesis in Hypothalamic Cells through a Heavy Isotope Pulse/Trace Proteomic Approach Chee Fan Tan 1,2 , Hui San Teo 2, Jung Eun Park 2, Bamaprasad Dutta 2, Shun Wilford Tse 2, Melvin Khee-Shing Leow 3,4,5 , Walter Wahli 3,6 and Siu Kwan Sze 2,* 1 NTU Institute for Health Technologies, Interdisciplinary Graduate School, Nanyang Technological University, Singapore 637335, Singapore; [email protected] 2 School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; [email protected] (H.S.T.); [email protected] (J.E.P.); [email protected] (B.D.); [email protected] (S.W.T.) 3 Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore; [email protected] (M.K.-S.L.); [email protected] (W.W.) 4 Department of Endocrinology, Tan Tock Seng Hospital, Singapore 308433, Singapore 5 Cardiovascular and Metabolic Disorder Program, Duke-NUS Medical School, Singapore 169857, Singapore 6 Center for Integrative Genomics, University of Lausanne, Le Génopode, CH-1015 Lausanne, Switzerland * Correspondence: [email protected]; Tel.: +65-6514-1006; Fax: +65-6791-3856 Received: 24 March 2020; Accepted: 21 May 2020; Published: 25 May 2020 Abstract: Studies have shown that the process of extracellular vesicles (EVs) secretion and lysosome status are linked. When the lysosome is under stress, the cells would secrete more EVs to maintain cellular homeostasis. However, the process that governs lysosomal activity and EVs secretion remains poorly defined and we postulated that certain proteins essential for EVs biogenesis are constantly synthesized and preferentially sorted to the EVs rather than the lysosome. -
Peripherally Generated Foxp3+ Regulatory T Cells Mediate the Immunomodulatory Effects of Ivig in Allergic Airways Disease
Published February 20, 2017, doi:10.4049/jimmunol.1502361 The Journal of Immunology Peripherally Generated Foxp3+ Regulatory T Cells Mediate the Immunomodulatory Effects of IVIg in Allergic Airways Disease Amir H. Massoud,*,†,1 Gabriel N. Kaufman,* Di Xue,* Marianne Be´land,* Marieme Dembele,* Ciriaco A. Piccirillo,‡ Walid Mourad,† and Bruce D. Mazer* IVIg is widely used as an immunomodulatory therapy. We have recently demonstrated that IVIg protects against airway hyper- responsiveness (AHR) and inflammation in mouse models of allergic airways disease (AAD), associated with induction of Foxp3+ regulatory T cells (Treg). Using mice carrying a DTR/EGFP transgene under the control of the Foxp3 promoter (DEREG mice), we demonstrate in this study that IVIg generates a de novo population of peripheral Treg (pTreg) in the absence of endogenous Treg. IVIg-generated pTreg were sufficient for inhibition of OVA-induced AHR in an Ag-driven murine model of AAD. In the absence of endogenous Treg, IVIg failed to confer protection against AHR and airway inflammation. Adoptive transfer of purified IVIg-generated pTreg prior to Ag challenge effectively prevented airway inflammation and AHR in an Ag-specific manner. Microarray gene expression profiling of IVIg-generated pTreg revealed upregulation of genes associated with cell cycle, chroma- tin, cytoskeleton/motility, immunity, and apoptosis. These data demonstrate the importance of Treg in regulating AAD and show that IVIg-generated pTreg are necessary and sufficient for inhibition of allergen-induced AAD. The ability of IVIg to generate pure populations of highly Ag-specific pTreg represents a new avenue to study pTreg, the cross-talk between humoral and cellular immunity, and regulation of the inflammatory response to Ags. -
Dysregulation of Mitotic Machinery Genes Precedes Genome Instability
The Author(s) BMC Genomics 2016, 17(Suppl 8):728 DOI 10.1186/s12864-016-3068-5 RESEARCH Open Access Dysregulation of mitotic machinery genes precedes genome instability during spontaneous pre-malignant transformation of mouse ovarian surface epithelial cells Ulises Urzúa1*, Sandra Ampuero2, Katherine F. Roby3, Garrison A. Owens4,6 and David J. Munroe4,5 From 6th SolBio International Conference 2016 (SoIBio-IC&W-2016) Riviera Maya, Mexico. 22-26 April 2016 Abstract Background: Based in epidemiological evidence, repetitive ovulation has been proposed to play a role in the origin of ovarian cancer by inducing an aberrant wound rupture-repair process of the ovarian surface epithelium (OSE). Accordingly, long term cultures of isolated OSE cells undergo in vitro spontaneous transformation thus developing tumorigenic capacity upon extensive subcultivation. In this work, C57BL/6 mouse OSE (MOSE) cells were cultured up to passage 28 and their RNA and DNA copy number profiles obtained at passages 2, 5, 7, 10, 14, 18, 23, 25 and 28 by means of DNA microarrays. Gene ontology, pathway and network analyses were focused in passages earlier than 20, which is a hallmark of malignancy in this model. Results: At passage 14, 101 genes were up-regulated in absence of significant DNA copy number changes. Among these, the top-3 enriched functions (>30 fold, adj p < 0.05) comprised 7 genes coding for centralspindlin, chromosome passenger and minichromosome maintenance protein complexes. The genes Ccnb1 (Cyclin B1), Birc5 (Survivin), Nusap1 and Kif23 were the most recurrent in over a dozen GO terms related to the mitotic process. On the other hand, Pten plus the large non-coding RNAs Malat1 and Neat1 were among the 80 down-regulated genes with mRNA processing, nuclear bodies, ER-stress response and tumor suppression as relevant terms. -
Control of Pre-Mrna Splicing by the General Splicing Factors PUF60 and U2AF 65 M Hastings, Eric Allemand, D Duelli, M
Control of Pre-mRNA Splicing by the General Splicing Factors PUF60 and U2AF 65 M Hastings, Eric Allemand, D Duelli, M. Myers, A. R. Krainer To cite this version: M Hastings, Eric Allemand, D Duelli, M. Myers, A. R. Krainer. Control of Pre-mRNA Splicing by the General Splicing Factors PUF60 and U2AF 65. PLoS ONE, Public Library of Science, 2007, 2 (6), pp.e538. 10.1371/journal.pone.0000538. hal-02462773 HAL Id: hal-02462773 https://hal.archives-ouvertes.fr/hal-02462773 Submitted on 31 Jan 2020 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. Control of Pre-mRNA Splicing by the General Splicing Factors PUF60 and U2AF65 Michelle L. Hastings, Eric Allemand¤, Dominik M. Duelli, Michael P. Myers, Adrian R. Krainer* Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America Pre-mRNA splicing is a crucial step in gene expression, and accurate recognition of splice sites is an essential part of this process. Splice sites with weak matches to the consensus sequences are common, though it is not clear how such sites are efficiently utilized. Using an in vitro splicing-complementation approach, we identified PUF60 as a factor that promotes splicing of an intron with a weak 39 splice-site. -
Far Upstream Element Binding Protein 1: a Commander of Transcription, Translation and Beyond
Oncogene (2013) 32, 2907–2916 & 2013 Macmillan Publishers Limited All rights reserved 0950-9232/13 www.nature.com/onc REVIEW Far upstream element binding protein 1: a commander of transcription, translation and beyond J Zhang and QM Chen The far upstream binding protein 1 (FBP1) was first identified as a DNA-binding protein that regulates c-Myc gene transcription through binding to the far upstream element (FUSE) in the promoter region 1.5 kb upstream of the transcription start site. FBP1 collaborates with TFIIH and additional transcription factors for optimal transcription of the c-Myc gene. In recent years, mounting evidence suggests that FBP1 acts as an RNA-binding protein and regulates mRNA translation or stability of genes, such as GAP43, p27 Kip and nucleophosmin. During retroviral infection, FBP1 binds to and mediates replication of RNA from Hepatitis C and Enterovirus 71. As a nuclear protein, FBP1 may translocate to the cytoplasm in apoptotic cells. The interaction of FBP1 with p38/ JTV-1 results in FBP1 ubiquitination and degradation by the proteasomes. Transcriptional and post-transcriptional regulations by FBP1 contribute to cell proliferation, migration or cell death. FBP1 association with carcinogenesis has been reported in c-Myc dependent or independent manner. This review summarizes biochemical features of FBP1, its mechanism of action, FBP family members and the involvement of FBP1 in carcinogenesis. Oncogene (2013) 32, 2907–2916; doi:10.1038/onc.2012.350; published online 27 August 2012 Keywords: FBP1; FUSE; cancer INTRODUCTION IDENTIFICATION OF FBP1 The far upstream element binding protein 1 (FBP1) was first FBP1 was first cloned from a cDNA library generated from the discovered as a transcriptional regulator of the proto-oncogene undifferentiated human monoblastic line U937.6 Such an c-Myc. -
Identification of Novel Biomarkers in Hepatocellular Carcinoma By
Identication of Novel Biomarkers in Hepatocellular Carcinoma by Integrated Bioinformatical Analysis and Experimental Validation Chen Liao Yunnan University of Traditional Chinese Medicine Lanlan Wang Shaanxi University of Chinese Medicine Xiaoqiang Li Fourth Military Medical University Department of Social Sciences: Air Force Medical University Jinyu Bai Yunnan University of Traditional Chinese Medicine Jieqiong Wu Shaanxi University of Chinese Medicine Wei Zhang Shaanxi University of Chinese Medicine Hailong Shi Shaanxi University of Chinese Medicine Xuesong Feng Shaanxi University of Chinese Medicine Xu Chao ( [email protected] ) Shaanxi University of Chinese Medicine https://orcid.org/0000-0001-5520-4834 Research Keywords: Hepatocellular carcinoma, novel biomarkers, candidate small molecules, prognosis, bioinformatics analysis Posted Date: June 16th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-533830/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/14 Abstract Background: Hepatocellular carcinoma (HCC) is one of the most common poorly prognosed virulent neoplasms of the digestive system. In this study, we identied novel biomarkers associated with the pathogenesis of HCC aiming to provide new diagnostic and therapeutic approaches for HCC. Methods: Gene expression proles of GSE62232, GSE84402,GSE121248 and GSE45267 were obtained in GEO database. Differential expressed genes (DEGs) between HCC and normal samples were identied using the GEO2R tool and Venn diagram software.Database for Annotation, Visualization and Integrated Discovery (DAVID) were used to carry out enrichment analysis on gene ontology (GO) and the Kyoto Encyclopaedia of Genes and Genomes pathway (KEGG). The protein-protein interaction (PPI) network of DEGs was constructed by the Search Tool for the Retrieval of Interacting Genes (STRING) and visualized by Cytoscape.