GRASP55 Is Dispensable for Normal Hematopoiesis but Necessary for Myc-Dependent Leukemic Growth
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Supplemental Note Hominoid Fission of Chromosome 14/15 and Role Of
Supplemental Note Supplemental Note Hominoid fission of chromosome 14/15 and role of segmental duplications Giuliana Giannuzzi, Michele Pazienza, John Huddleston, Francesca Antonacci, Maika Malig, Laura Vives, Evan E. Eichler and Mario Ventura 1. Analysis of the macaque contig spanning the hominoid 14/15 fission site We grouped contig clones based on their FISH pattern on human and macaque chromosomes (Groups F1, F2, F3, G1, G2, G3, and G4). Group F2 clones (Hsa15b- and Hsa15c-positive) showed a single signal on macaque 7q and three signal clusters on human chromosome 15: at the orthologous 15q26, as expected, as well as at 15q11–14 and 15q24–25, which correspond to the actual and ancestral pericentromeric regions, respectively (Ventura et al. 2003). Indeed, this locus contains an LCR15 copy (Pujana et al. 2001) in both the macaque and human genomes. Most BAC clones were one-end anchored in the human genome (chr15:100,028–100,071 kb). In macaque this region experienced a 64 kb duplicative insertion from chromosome 17 (orthologous to human chromosome 13) (Figure 2), with the human configuration (absence of insertion) likely being the ancestral state because it is identical in orangutan and marmoset. Four Hsa15b- positive clones mapped on macaque and human chromosome 19, but neither human nor macaque assemblies report the STS Hsa15b duplicated at this locus. The presence of assembly gaps in macaque may explain why the STS is not annotated in this region. We aligned the sequence of macaque CH250-70H12 (AC187495.2) versus its human orthologous sequence (hg18 chr15:100,039k-100,170k) and found a 12 kb human expansion through tandem duplication of a ~100 bp unit corresponding to a portion of exon 20 of DNM1 (Figure S3). -
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Barlow et al. BMC Biology (2018) 16:27 https://doi.org/10.1186/s12915-018-0492-9 RESEARCHARTICLE Open Access A sophisticated, differentiated Golgi in the ancestor of eukaryotes Lael D. Barlow1, Eva Nývltová2,3, Maria Aguilar1, Jan Tachezy2 and Joel B. Dacks1,4* Abstract Background: The Golgi apparatus is a central meeting point for the endocytic and exocytic systems in eukaryotic cells, and the organelle’s dysfunction results in human disease. Its characteristic morphology of multiple differentiated compartments organized into stacked flattened cisternae is one of the most recognizable features of modern eukaryotic cells, and yet how this is maintained is not well understood. The Golgi is also an ancient aspect of eukaryotes, but the extent and nature of its complexity in the ancestor of eukaryotes is unclear. Various proteins have roles in organizing the Golgi, chief among them being the golgins. Results: We address Golgi evolution by analyzing genome sequences from organisms which have lost stacked cisternae as a feature of their Golgi and those that have not. Using genomics and immunomicroscopy, we first identify Golgi in the anaerobic amoeba Mastigamoeba balamuthi. We then searched 87 genomes spanning eukaryotic diversity for presence of the most prominent proteins implicated in Golgi structure, focusing on golgins. We show some candidates as animal specific and others as ancestral to eukaryotes. Conclusions: None of the proteins examined show a phyletic distribution that correlates with the morphology of stacked cisternae, suggesting the possibility of stacking as an emergent property. Strikingly, however, the combination of golgins conserved among diverse eukaryotes allows for the most detailed reconstruction of the organelle to date, showing a sophisticated Golgi with differentiated compartments and trafficking pathways in the common eukaryotic ancestor. -
Protein Interaction Network of Alternatively Spliced Isoforms from Brain Links Genetic Risk Factors for Autism
ARTICLE Received 24 Aug 2013 | Accepted 14 Mar 2014 | Published 11 Apr 2014 DOI: 10.1038/ncomms4650 OPEN Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism Roser Corominas1,*, Xinping Yang2,3,*, Guan Ning Lin1,*, Shuli Kang1,*, Yun Shen2,3, Lila Ghamsari2,3,w, Martin Broly2,3, Maria Rodriguez2,3, Stanley Tam2,3, Shelly A. Trigg2,3,w, Changyu Fan2,3, Song Yi2,3, Murat Tasan4, Irma Lemmens5, Xingyan Kuang6, Nan Zhao6, Dheeraj Malhotra7, Jacob J. Michaelson7,w, Vladimir Vacic8, Michael A. Calderwood2,3, Frederick P. Roth2,3,4, Jan Tavernier5, Steve Horvath9, Kourosh Salehi-Ashtiani2,3,w, Dmitry Korkin6, Jonathan Sebat7, David E. Hill2,3, Tong Hao2,3, Marc Vidal2,3 & Lilia M. Iakoucheva1 Increased risk for autism spectrum disorders (ASD) is attributed to hundreds of genetic loci. The convergence of ASD variants have been investigated using various approaches, including protein interactions extracted from the published literature. However, these datasets are frequently incomplete, carry biases and are limited to interactions of a single splicing isoform, which may not be expressed in the disease-relevant tissue. Here we introduce a new interactome mapping approach by experimentally identifying interactions between brain-expressed alternatively spliced variants of ASD risk factors. The Autism Spliceform Interaction Network reveals that almost half of the detected interactions and about 30% of the newly identified interacting partners represent contribution from splicing variants, emphasizing the importance of isoform networks. Isoform interactions greatly contribute to establishing direct physical connections between proteins from the de novo autism CNVs. Our findings demonstrate the critical role of spliceform networks for translating genetic knowledge into a better understanding of human diseases. -
GOLGA2/GM130 Is a Novel Target for Neuroprotection Therapy in Intracerebral Hemorrhage
GOLGA2/GM130 is a Novel Target for Neuroprotection Therapy in Intracerebral Hemorrhage Shuwen Deng Second Xiangya Hospital Qing Hu Second Xiangya Hospital Qiang He Second Xiangya Hospital Xiqian Chen Second Xiangya Hospital Wei Lu ( [email protected] ) Second Xiangya Hospital, central south university https://orcid.org/0000-0002-3760-1550 Research Article Keywords: Golgi apparatus, therapy, intracerebral hemorrhage, autophagy, blood–brain barrier Posted Date: June 1st, 2021 DOI: https://doi.org/10.21203/rs.3.rs-547422/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/25 Abstract Blood–brain barrier (BBB) impairment after intracerebral hemorrhage (ICH) can lead to secondary brain injury and aggravate neurological decits. Currently, there are no effective methods for its prevention or treatment partly because of to our lack of understanding of the mechanism of ICH injury to the BBB. Here, we explored the role of Golgi apparatus protein GM130 in the BBB and neurological function after ICH. The levels of the tight junction-associated proteins ZO-1 and occludin decreased, whereas those of LC3-II, an autophagosome marker, increased in hemin-treated Bend.3 cells (p < 0.05). Additionally, GM130 overexpression increased ZO-1 and occludin levels, while decreasing LC3-II levels (p < 0.05). GM130 silencing reversed these effects and mimicked the effect of hemin treatment (p < 0.05). Moreover, tight junctions were disrupted after hemin treatment or GM130 silencing and repaired by GM130 overexpression. GM130 silencing in Bend.3 cells increased autophagic ux, whereas GM130 overexpression downregulated this activity. Furthermore, GM130 silencing-induced tight junction disruption was partially restored by 3-methyladenine (an autophagy inhibitor) administration. -
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. -
A Pro-Tumorigenic Secretory Pathway Activated by P53 Deficiency in Lung Adenocarcinoma
A pro-tumorigenic secretory pathway activated by p53 deficiency in lung adenocarcinoma Xiaochao Tan, … , Chad J. Creighton, Jonathan M. Kurie J Clin Invest. 2020. https://doi.org/10.1172/JCI137186. Research In-Press Preview Cell biology Oncology Graphical abstract Find the latest version: https://jci.me/137186/pdf Title: A pro-tumorigenic secretory pathway activated by p53 deficiency in lung adenocarcinoma Authors: Xiaochao Tan1,*, Lei Shi1, Priyam Banerjee1, Xin Liu1, Hou-Fu Guo1, Jiang Yu1, Neus Bota-Rabassedas1, B. Leticia Rodriguez1, Don L. Gibbons1, William K. Russell2, Chad J. Creighton3,4, Jonathan M. Kurie1,* 1 Affiliations: Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. 2Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA. 3Department of Medicine, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas. 4Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas. *To whom Correspondence should be addressed: Jonathan M. Kurie, Department of Thoracic/Head and Neck Medical Oncology, Box 432, MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030; email: [email protected]; Xiaochao Tan, Department of Thoracic/Head and Neck Medical Oncology, Box 432, MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030; email: [email protected]. Conflict of interest D.L.G. serves on scientific advisory committees for Astrazeneca, GlaxoSmithKline, Sanofi and Janssen, provides consults for Ribon Therapeutics, and has research support from Janssen, Takeda, and Astrazeneca. J.M.K. has received consulting fees from Halozyme. All other authors declare that they have no competing interests. -
E-Mutpath: Computational Modelling Reveals the Functional Landscape of Genetic Mutations Rewiring Interactome Networks
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.22.262386; this version posted August 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. e-MutPath: Computational modelling reveals the functional landscape of genetic mutations rewiring interactome networks Yongsheng Li1, Daniel J. McGrail1, Brandon Burgman2,3, S. Stephen Yi2,3,4,5 and Nidhi Sahni1,6,7,8,* 1Department oF Systems Biology, The University oF Texas MD Anderson Cancer Center, Houston, TX 77030, USA 2Department oF Oncology, Livestrong Cancer Institutes, Dell Medical School, The University oF Texas at Austin, Austin, TX 78712, USA 3Institute For Cellular and Molecular Biology (ICMB), The University oF Texas at Austin, Austin, TX 78712, USA 4Institute For Computational Engineering and Sciences (ICES), The University oF Texas at Austin, Austin, TX 78712, USA 5Department oF Biomedical Engineering, Cockrell School of Engineering, The University oF Texas at Austin, Austin, TX 78712, USA 6Department oF Epigenetics and Molecular Carcinogenesis, The University oF Texas MD Anderson Science Park, Smithville, TX 78957, USA 7Department oF BioinFormatics and Computational Biology, The University oF Texas MD Anderson Cancer Center, Houston, TX 77030, USA 8Program in Quantitative and Computational Biosciences (QCB), Baylor College oF Medicine, Houston, TX 77030, USA *To whom correspondence should be addressed. Nidhi Sahni. Tel: +1 512 2379506; Email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.22.262386; this version posted August 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
Unconventional Secretion Factor GRASP55 Is Increased by Pharmacological Unfolded Protein Response Inducers in Neurons
www.nature.com/scientificreports OPEN Unconventional secretion factor GRASP55 is increased by pharmacological unfolded protein Received: 6 July 2018 Accepted: 19 December 2018 response inducers in neurons Published: xx xx xxxx Anna Maria van Ziel1,2, Pablo Largo-Barrientos1, Kimberly Wolzak1, Matthijs Verhage1,2 & Wiep Scheper1,2,3 Accumulation of misfolded proteins in the endoplasmic reticulum (ER), defned as ER stress, results in activation of the unfolded protein response (UPR). UPR activation is commonly observed in neurodegenerative diseases. ER stress can trigger unconventional secretion mediated by Golgi reassembly and stacking proteins (GRASP) relocalization in cell lines. Here we study the regulation of GRASP55 by the UPR upon pharmacological induction of ER stress in primary mouse neurons. We demonstrate that UPR activation induces mRNA and protein expression of GRASP55, but not GRASP65, in cortical neurons. UPR activation does not result in relocalization of GRASP55. UPR- induced GRASP55 expression is reduced by inhibition of the PERK pathway of the UPR and abolished by inhibition of the endonuclease activity of the UPR transducer IRE1. Expression of the IRE1 target XBP1s in the absence of ER stress is not sufcient to increase GRASP55 expression. Knockdown of GRASP55 afects neither induction nor recovery of the UPR. We conclude that the UPR regulates the unconventional secretion factor GRASP55 via a mechanism that requires the IRE1 and the PERK pathway of the UPR in neurons. Since neurons are non-proliferative and secretory cells, protein homeostasis or proteostasis is of great importance and hence tightly regulated. Te endoplasmic reticulum (ER) is a vital organelle for protein synthesis, folding and posttranslational modifcations of proteins destined for the secretory pathway. -
UBXN2B (His-Tag) Human Protein – AR50979PU-S | Origene
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for AR50979PU-S UBXN2B (His-tag) Human Protein Product data: Product Type: Recombinant Proteins Description: UBXN2B (His-tag) human protein, 50 µg Species: Human Expression Host: E. coli Tag: His-tag Predicted MW: 39.5 kDa Concentration: lot specific Purity: >90% by SDS - PAGE Buffer: Presentation State: Purified State: Liquid purified protein Buffer System: 20 mM Tris-HCl buffer (pH 8.0) containing 10% glycerol Preparation: Liquid purified protein Storage: Store undiluted at 2-8°C for one week or (in aliquots) at -20°C to -80°C for longer. Avoid repeated freezing and thawing. Stability: Shelf life: one year from despatch. RefSeq: NP_001071087 Locus ID: 137886 UniProt ID: Q14CS0 Cytogenetics: 8q12.1 Synonyms: p37 This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 UBXN2B (His-tag) Human Protein – AR50979PU-S Summary: Adapter protein required for Golgi and endoplasmic reticulum biogenesis (PubMed:17141156). Involved in Golgi and endoplasmic reticulum maintenance during interphase and in their reassembly at the end of mitosis (PubMed:17141156). The complex formed with VCP has membrane fusion activity; membrane fusion activity requires USO1- GOLGA2 tethering and BET1L (PubMed:17141156). VCPIP1 is also required, but not its deubiquitinating activity (PubMed:17141156). Together with NSFL1C/p47, regulates the centrosomal levels of kinase AURKA/Aurora A during mitotic progression by promoting AURKA removal from centrosomes in prophase (PubMed:23649807). -
GRASP55, a Second Mammalian GRASP Protein Involved in the Stacking of Golgi Cisternae in a Cell-Free System
The EMBO Journal Vol.18 No.18 pp.4949–4960, 1999 GRASP55, a second mammalian GRASP protein involved in the stacking of Golgi cisternae in a cell-free system James Shorter, Rose Watson, give rise to cisternae, and in the subsequent stacking of Maria-Eleni Giannakou1, Mairi Clarke1, these cisternae to form stacks. These studies have used Graham Warren2 and Francis A.Barr1,3 in vitro assays in which the Golgi apparatus can be disassembled and reassembled under defined conditions, Cell Biology Laboratory, Imperial Cancer Research Fund, 44 Lincoln’s thus allowing the identification of components important 1 Inn Fields, London WC2A 3PX and IBLS, Division of Biochemistry for different aspects of Golgi structure (Acharya et al., and Molecular Biology, Davidson Building, University of Glasgow, Glasgow G12 8QQ, Scotland, UK 1995; Rabouille et al., 1995a). One cell-free system 2 (Rabouille et al., 1995a) has exploited the disassembly of Present address: Department of Cell Biology, SHM, C441, the Golgi apparatus into many small vesicles and mem- Yale University School of Medicine, 33 Cedar Street, PO Box 208002, New Haven, CT 06520-8002, USA brane fragments during cell division (Lucocq et al., 1987, 1989). In this system, isolated Golgi membranes are 3Corresponding author e-mail: [email protected] treated with mitotic cell cytosol to generate a population of mitotic Golgi fragments (MGFs) that can reassemble We have identified a 55 kDa protein, named GRASP55 into stacked Golgi membranes when incubated under (Golgi reassembly stacking protein of 55 kDa), as a the correct conditions. The N-ethylmaleimide (NEM)- component of the Golgi stacking machinery. -
FUNCTIONAL CHARACTERIZATION of P24δ SUBFAMILY PROTEINS in A. Thaliana”
UNIVERSITAT DE VALÈNCIA Departamento de Bioquímica y Biología Molecular Programa de doctorado en Biotecnología “FUNCTIONAL CHARACTERIZATION OF p24δ SUBFAMILY PROTEINS IN A. thaliana” Tesis doctoral con Mención Internacional presentada por Noelia Pastor Cantizano Tesis dirigida por: Dr. Fernando Aniento Company Dra. María Jesús Marcote Zaragoza Valencia, Octubre 2016 FERNANDO ANIENTO COMPANY, Catedrático del departamento de Bioquímica y Biología Molecular de la Universidad de Valencia y MARIA JESÚS MARCOTE ZARAGOZA, Profesora titular del departamento de Bioquímica y Biología Molecular de la Universidad de Valencia, CERTIFICAN: Que la presente memoria titulada: “FUNCTIONAL CHARACTERIZATION OF p24δ SUBFAMILY PROTEINS IN A. thaliana” ha sido realizada por la Licenciada en Farmacia Noelia Pastor Cantizano bajo nuestra dirección, y que, habiendo revisado el trabajo, autorizamos su presentación para que sea calificada como tesis doctoral y obtener así el TITULO DE DOCTOR CON MENCIÓN INTERNACIONAL. Y para que conste a los efectos oportunos, se expide la presente certificación en Burjassot, a 19 de octubre de 2016. Fdo: Fernando Aniento Company Fdo: María Jesús Marcote Zaragoza Esta Tesis Doctoral se ha realizado con la financiación de los siguientes proyectos: 1. “Tráfico intracelular de proteínas en células vegetales”. Plan Nacional de I + D. Programa de Biología Fundamental (BFU2009-07039). I.P.: Dr. Fernando Aniento Company. 2. “Tráfico intracelular de proteínas en células vegetales”. Plan Nacional de I + D. Programa de Biología Fundamental -
Transforming Growth Factor ß1-Mediated Functional Inhibition Of
Myelodysplastic Syndromes SUPPLEMENTARY APPENDIX Transforming growth factor 1- mediated functional inhibition of mesenchymal stromal celβls in myelodysplastic syndromes and acute myeloid leukemia Stefanie Geyh, 1* Manuel Rodríguez-Paredes, 1,2 * Paul Jäger, 1 Annemarie Koch, 1 Felix Bormann, 2 Julian Gutekunst, 2 Christoph Zilkens, 3 Ulrich Germing, 1 Guido Kobbe, 1 Frank Lyko, 2 Rainer Haas 1 and Thomas Schroeder 1 1Department of Hematology, Oncology and Clinical Immunology, University of Duesseldorf, Medical Faculty; 2Division of Epigenetics, DKFZ- ZMBH Alliance, German Cancer Research Center, Heidelberg and 3Department of Orthopedic Surgery, University of Duesseldorf, Medical Faculty, Germany *SG and MR-P contributed equally to this work. ©2018 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol. 2017.186734 Received: December 19, 2017. Accepted: May 14, 2018. Pre-published: May 17, 2018. Correspondence: [email protected] Figure S1 Downregulated genes Downregulated genes Upregulated Figure S1. Heatmaps showing the 50 most upregulated and downregulated genes between the 3 healthy MSC controls and the 9 RCMD-, RAEB- and AML-derived MSC samples. Color scale depicts the rlog-transformed FPKM values for each gene and every sample. Figure S2 Downregulated genes Downregulated genes Upregulated Figure S2. Heatmaps showing the 50 most upregulated and downregulated genes between the 3 healthy MSC controls and the 3 RCMD, RAEB and AML MSC samples, respectively. Color scales depict the rlog-transformed FPKM values for each gene and every sample. Figure S3 A. B. 0.0015 *** ** <-3 -2 0.0010 RCMD RAEB AML -1 0 1 0.0005 Log2FC LTF 2 CCL26/GAPDH INHBB >3 0.0000 TGFB2 y S h D ML M A ealt ll LTF H a EGF 0.003 *** ** INHBB TGFB2 0.002 INHBB IGFBP7 0.001 GDF11 LIF/GAPDH BMP1 0.000 y L th M TNFSF12 l A FGF13 ea ll MDS H a FGF13 0.0015 * TNFSF10 TNFSF10 0.0010 0.0005 SPP1/GAPDH 0.0000 y th l AML ea H all MDS Figure S3.