Oncogenic Kinases and Perturbations in Protein Synthesis Machinery and Energetics in Neoplasia
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(12) Patent Application Publication (10) Pub. No.: US 2002/0152483 A1 Reue Et Al
US 2002O1524.83A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2002/0152483 A1 Reue et al. (43) Pub. Date: Oct. 17, 2002 (54) NOVEL GENE ASSOCATED WITH Publication Classification REGULATION OF ADPOSITY AND INSULIN RESPONSE (51) Int. Cl." ............................ A01K 67/00; C12O 1/68; C12P 19/34 (75) Inventors: Karen Reue, Torrance, CA (US); (52) U.S. Cl. .................................. 800/9; 435/6; 435/91.2 Miklos Peterfy, Los Angeles, CA (US) (57) ABSTRACT Correspondence Address: This invention pertains to the identification and isolation of LAW OFFICES OF JONATHAN ALAN QUINE a gene implicated in the fatty liver dystrophy (fld) pheno PO BOX 458 type. Mouse and human forms of the novel gene, designated ALAMEDA, CA 94501 herein as Lpin1/LPIN1 (mouse and human genes, respec tively), are identified. This invention additionally provides (73) Assignee: The Regents of the University of Cali methods of Screening for agents that alter adipose tissue fornia development. The methods involve contacting a cell con taining a Lpin1 gene With a test agent, and detecting a (21) Appl. No.: 10/028,056 change in the expression or activity of a Lpin1 gene product, (22) Filed: Dec. 19, 2001 where a difference in the expression or activity of Lpin1 in the contacted cell indicates that the agent alters or is likely Related U.S. Application Data to alter adipose tissue development. Also provided are methods of identifying Lpin1 mutations, and methods of (60) Provisional application No. 60/257,772, filed on Dec. mitigating Symptoms of lipodystrophy, obesity, diabetes, 22, 2000. atherOSclerosis and related pathologies. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Genome-Wide Analysis of Transcriptional Bursting-Induced Noise in Mammalian Cells
bioRxiv preprint doi: https://doi.org/10.1101/736207; this version posted August 15, 2019. 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. Title: Genome-wide analysis of transcriptional bursting-induced noise in mammalian cells Authors: Hiroshi Ochiai1*, Tetsutaro Hayashi2, Mana Umeda2, Mika Yoshimura2, Akihito Harada3, Yukiko Shimizu4, Kenta Nakano4, Noriko Saitoh5, Hiroshi Kimura6, Zhe Liu7, Takashi Yamamoto1, Tadashi Okamura4,8, Yasuyuki Ohkawa3, Itoshi Nikaido2,9* Affiliations: 1Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-0046, Japan 2Laboratory for Bioinformatics Research, RIKEN BDR, Wako, Saitama, 351-0198, Japan 3Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-0054, Japan 4Department of Animal Medicine, National Center for Global Health and Medicine (NCGM), Tokyo, 812-0054, Japan 5Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo, 135-8550, Japan 6Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503, Japan 7Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA 8Section of Animal Models, Department of Infectious Diseases, National Center for Global Health and Medicine (NCGM), Tokyo, 812-0054, Japan 9Bioinformatics Course, Master’s/Doctoral Program in Life Science Innovation (T-LSI), School of Integrative and Global Majors (SIGMA), University of Tsukuba, Wako, 351-0198, Japan *Corresponding authors Corresponding authors e-mail addresses Hiroshi Ochiai, [email protected] Itoshi Nikaido, [email protected] bioRxiv preprint doi: https://doi.org/10.1101/736207; this version posted August 15, 2019. -
4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4). -
Manuscript for Proximity Interactome Analysis of Lassa
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.16.452739; this version posted July 17, 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 4.0 International license. 1 Main Manuscript for 2 Proximity interactome analysis of Lassa polymerase reveals 3 eRF3a/GSPT1 as a druggable target for host directed antivirals. 4 Jingru Fang1,2, Colette Pietzsch3,4, George Tsaprailis5, Gogce Crynen5, Kelvin Frank Cho6, Alice 5 Y. Ting7,8, Alexander Bukreyev3,4,9, Erica Ollmann Saphire2* and Juan Carlos de la Torre1* 6 1 Department of Immunology and Microbiology, Scripps Research, La Jolla CA 92037 7 2La Jolla Institute for Immunology, La Jolla CA 92037 8 3Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550 9 4Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550 10 5Proteomics Core, Scripps Research, Jupiter, FL 33458 11 6Cancer Biology Program, Stanford University, Stanford, CA 94305 12 7Department of Genetics, Department of Biology and Department of Chemistry, Stanford 13 University, Stanford, CA 94305 14 8Chan Zuckerberg Biohub, San Francisco, CA 94158 15 9Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, 16 TX 77550 17 *Erica Ollmann Saphire; Juan Carlos de la Torre. 18 Email: [email protected] and [email protected] 19 Author Contributions: J.F., E.O.S., and J.C.T designed research; J.F. performed all non-BSL4 20 experiments and analyzed data; C.P. -
Genes with 5' Terminal Oligopyrimidine Tracts Preferentially Escape Global Suppression of Translation by the SARS-Cov-2 NSP1 Protein
Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Genes with 5′ terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein Shilpa Raoa, Ian Hoskinsa, Tori Tonna, P. Daniela Garciaa, Hakan Ozadama, Elif Sarinay Cenika, Can Cenika,1 a Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA 1Corresponding author: [email protected] Key words: SARS-CoV-2, Nsp1, MeTAFlow, translation, ribosome profiling, RNA-Seq, 5′ TOP, Ribo-Seq, gene expression 1 Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms to co-opt host translation for their survival. SARS-CoV-2 relies on a non-structural protein, Nsp1, for shutting down host translation. However, it is currently unknown how viral proteins and host factors critical for viral replication can escape a global shutdown of host translation. Here, using a novel FACS-based assay called MeTAFlow, we report a dose-dependent reduction in both nascent protein synthesis and mRNA abundance in cells expressing Nsp1. We perform RNA-Seq and matched ribosome profiling experiments to identify gene-specific changes both at the mRNA expression and translation level. We discover that a functionally-coherent subset of human genes are preferentially translated in the context of Nsp1 expression. These genes include the translation machinery components, RNA binding proteins, and others important for viral pathogenicity. Importantly, we uncovered a remarkable enrichment of 5′ terminal oligo-pyrimidine (TOP) tracts among preferentially translated genes. -
Anti-Inflammatory Role of Curcumin in LPS Treated A549 Cells at Global Proteome Level and on Mycobacterial Infection
Anti-inflammatory Role of Curcumin in LPS Treated A549 cells at Global Proteome level and on Mycobacterial infection. Suchita Singh1,+, Rakesh Arya2,3,+, Rhishikesh R Bargaje1, Mrinal Kumar Das2,4, Subia Akram2, Hossain Md. Faruquee2,5, Rajendra Kumar Behera3, Ranjan Kumar Nanda2,*, Anurag Agrawal1 1Center of Excellence for Translational Research in Asthma and Lung Disease, CSIR- Institute of Genomics and Integrative Biology, New Delhi, 110025, India. 2Translational Health Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India. 3School of Life Sciences, Sambalpur University, Jyoti Vihar, Sambalpur, Orissa, 768019, India. 4Department of Respiratory Sciences, #211, Maurice Shock Building, University of Leicester, LE1 9HN 5Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia- 7003, Bangladesh. +Contributed equally for this work. S-1 70 G1 S 60 G2/M 50 40 30 % of cells 20 10 0 CURI LPSI LPSCUR Figure S1: Effect of curcumin and/or LPS treatment on A549 cell viability A549 cells were treated with curcumin (10 µM) and/or LPS or 1 µg/ml for the indicated times and after fixation were stained with propidium iodide and Annexin V-FITC. The DNA contents were determined by flow cytometry to calculate percentage of cells present in each phase of the cell cycle (G1, S and G2/M) using Flowing analysis software. S-2 Figure S2: Total proteins identified in all the three experiments and their distribution betwee curcumin and/or LPS treated conditions. The proteins showing differential expressions (log2 fold change≥2) in these experiments were presented in the venn diagram and certain number of proteins are common in all three experiments. -
862F50a0ea63c82ca473bf845b5
Brain region Type Enriched GO annotation Gene symbol AQR, ARMC7, BTBD9, HACL1, KCTD10, KCTD13, LSM6, MT2A, MYBPC1, POLD2, SRPX, TNFAIP1, USP25, EC Common type DNA replication, Protein catabolic process, Transport USP28, ZMYND19 EC Common type Transport KIAA1549, MBD5, MYO5B, RAB11A, RAB11FIP1, RAB11FIP2, RAB11FIP3, RAB11FIP4, RAB11FIP5, REPS1 ACD, BMP2K, C1orf63, CDK13, CLK3, CYLC2, DDX3Y, FOXJ3, GNL3L, GRPEL1, KIAA2022, MACROD2, Cellular component organization, Kinase activity, Localization, EC Common type NANOG, PAK1IP1, PCBP1, PCMT1, PLOD1, PLOD2, POT1, PRPS1L1, RASGEF1C, RBM15B, RPS7, RSBN1L, Response to stimulus, Transcription SALL1, SEC16A, TDRD6, TERF1, TERF2IP, TINF2, YTHDF1, YTHDF3, ZC3HAV1L, ZNF281 AGFG1, AKR1C3, ARIH1, ARIH2, BCL10, BFAR, BIRC2, BIRC3, BIRC6, BIRC7, C9orf89, CADPS2, CNOT4, DDX58, DIABLO, DTX1, DTX3L, DZIP3, EIF4E2, EML4, EPS15, EXTL3, FBXL19, FCHO2, GPR108, HLTF, HPCA, HTRA2, INF2, ISG15, KIAA1107, KIAA1797, LNX2, LOC147791, LRSAM1, LTN1, MAGEL2, MAP3K1, MARCH5, MARCH7, MC1R, MFN1, MGRN1, MID1, MID2, MKRN1, MKRN2, MKRN3, MRAP, MUL1, NAIP, PARP9, PCNP, PDZRN3, PJA2, PLCD4, RBCK1, RLIM, RMND5B, RNF10, RNF103, RNF11, RNF111, RNF114, DNA repair, Apoptosis, Protein catabolic process, Protein EC Common type RNF115, RNF125, RNF126, RNF128, RNF13, RNF130, RNF138, RNF14, RNF144A, RNF150, RNF165, RNF166, metabolic process, Protein modification process RNF167, RNF181, RNF182, RNF25, RNF26, RNF38, RNF4, RNF41, RSPRY1, SGCE, SH3RF2, STRADB, TMBIM6, TMEM189, TOPORS, TRAF7, TRIM2, TRIM25, TRIM26, TRIM27, TRIM32, TRIM35, TRIM39, -
1 First Presentation of LPIN1 Acute Rhabdomyolysis in Adolescence and Adulthood
Manuscript File Click here to view linked References 1 First presentation of LPIN1 acute rhabdomyolysis in adolescence and adulthood 2 3 Chiara Pizzamiglioa, Nayana Lahirib, Niranjanan Nirmalananthanc, Bhrigu Soodd, Subash 4 Somalankad, Philip Ostrowskie, Rahul Phadkef, Dominic Gerard O’Donovang, Francesco 5 Muntonih, Rosaline Quinlivana 6 7 a. MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for 8 Neurology and Neurosurgery, Queen Square, London, United Kingdom 9 10 b. Clinical Genetics Department, St George's University Hospitals NHS Foundation Trust, London, 11 United Kingdom 12 13 c. Departments of Neurology and Neuroradiology, Atkinson Morley Regional Neurosciences 14 Centre, St George's Hospital, London, United Kingdom 15 16 d. South West Thames Renal & Transplantation Unit and South West Thames Institute for Renal 17 Research, Saint Helier Hospital, Carshalton, Surrey, United Kingdom 18 19 e. South West Thames Regional Genetics Service, St George's University NHS Foundation Trust, 20 London, United Kingdom 21 22 f. Division of Neuropathology, Dubowitz Neuromuscular Centre, UCL Great Ormond Street 23 Hospital for Children, United Kingdom; Division of Neuropathology, National Hospital for 24 Neurology and Neurosurgery, Queen Square, London, United Kingdom 25 1 26 g. Neuropathology, Department of Histopathology, Addenbrooke’s Hospital, Cambridge University 27 Hospitals NHS Foundation Trust, Cambridge, United Kingdom 28 29 h. Paediatric Neurology, Dubowitz Neuromuscular Centre, UCL Institute of Child Health and Great 30 Ormond Street Hospital for Children, London, United Kingdom 31 32 Corresponding author: Chiara Pizzamiglio ([email protected]) 33 34 Abstract: LPIN1 mutations are a known common cause of autosomal recessive, recurrent and life- 35 threatening acute rhabdomyolysis of childhood-onset. -
Functional Interactomes of the Ebola Virus Polymerase Identified by Proximity Proteomics 2 in the Context of Viral Replication
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.20.453153; this version posted July 21, 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 4.0 International license. 1 Functional interactomes of the Ebola virus polymerase identified by proximity proteomics 2 in the context of viral replication 3 Jingru Fang1,2, Colette Pietzsch3,4, George Tsaprailis5, Gogce Crynen6, Kelvin Frank Cho7, Alice 4 Y. Ting8,9, Alexander Bukreyev3,4,10*, Juan Carlos de la Torre2*, Erica Ollmann Saphire1* 5 1La Jolla Institute for Immunology, La Jolla CA 92037 6 2Department of Immunology and Microbiology, Scripps Research, La Jolla CA 92037 7 3Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550 8 4Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550 9 5Proteomics Core, Scripps Research, Jupiter, FL 33458 10 6Bioinformatics and Statistics Core, Scripps Research, Jupiter, FL 33458 11 7Cancer Biology Program, Stanford University, Stanford, CA 94305 12 8Department of Genetics, Department of Biology and Department of Chemistry, Stanford 13 University, Stanford, CA 94305 14 9Chan Zuckerberg Biohub, San Francisco, CA 94158 15 10 Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, 16 TX 77550 17 Correspondence: [email protected], [email protected], [email protected] 18 Lead contact: [email protected] 19 SUMMARY 20 Ebola virus (EBOV) critically depends on the viral polymerase to replicate and transcribe the viral 21 RNA genome. -
A Transcriptional Signature of Postmitotic Maintenance in Neural Tissues
Neurobiology of Aging 74 (2019) 147e160 Contents lists available at ScienceDirect Neurobiology of Aging journal homepage: www.elsevier.com/locate/neuaging Postmitotic cell longevityeassociated genes: a transcriptional signature of postmitotic maintenance in neural tissues Atahualpa Castillo-Morales a,b, Jimena Monzón-Sandoval a,b, Araxi O. Urrutia b,c,*, Humberto Gutiérrez a,** a School of Life Sciences, University of Lincoln, Lincoln, UK b Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK c Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico article info abstract Article history: Different cell types have different postmitotic maintenance requirements. Nerve cells, however, are Received 11 April 2018 unique in this respect as they need to survive and preserve their functional complexity for the entire Received in revised form 3 October 2018 lifetime of the organism, and failure at any level of their supporting mechanisms leads to a wide range of Accepted 11 October 2018 neurodegenerative conditions. Whether these differences across tissues arise from the activation of Available online 19 October 2018 distinct cell typeespecific maintenance mechanisms or the differential activation of a common molecular repertoire is not known. To identify the transcriptional signature of postmitotic cellular longevity (PMCL), Keywords: we compared whole-genome transcriptome data from human tissues ranging in longevity from 120 days Neural maintenance Cell longevity to over 70 years and found a set of 81 genes whose expression levels are closely associated with Transcriptional signature increased cell longevity. Using expression data from 10 independent sources, we found that these genes Functional genomics are more highly coexpressed in longer-living tissues and are enriched in specific biological processes and transcription factor targets compared with randomly selected gene samples. -
Evolutionary Fate of Retroposed Gene Copies in the Human Genome
Evolutionary fate of retroposed gene copies in the human genome Nicolas Vinckenbosch*, Isabelle Dupanloup*†, and Henrik Kaessmann*‡ *Center for Integrative Genomics, University of Lausanne, Ge´nopode, 1015 Lausanne, Switzerland; and †Computational and Molecular Population Genetics Laboratory, Zoological Institute, University of Bern, 3012 Bern, Switzerland Communicated by Wen-Hsiung Li, University of Chicago, Chicago, IL, December 30, 2005 (received for review December 14, 2005) Given that retroposed copies of genes are presumed to lack the and rodent genomes (7–12). In addition, three recent studies regulatory elements required for their expression, retroposition using EST data (13, 14) and tiling-microarray data from chro- has long been considered a mechanism without functional rele- mosome 22 (15) indicated that retrocopy transcription may be vance. However, through an in silico assay for transcriptional widespread, although these surveys were limited, and potential activity, we identify here >1,000 transcribed retrocopies in the functional implications were not addressed. human genome, of which at least Ϸ120 have evolved into bona To further explore the functional significance of retroposition fide genes. Among these, Ϸ50 retrogenes have evolved functions in the human genome, we systematically screened for signatures in testes, more than half of which were recruited as functional of selection related to retrocopy transcription. Our results autosomal counterparts of X-linked genes during spermatogene- suggest that retrocopy transcription is not rare and that the sis. Generally, retrogenes emerge ‘‘out of the testis,’’ because they pattern of transcription of human retrocopies has been pro- are often initially transcribed in testis and later evolve stronger and foundly shaped by natural selection, acting both for and against sometimes more diverse spatial expression patterns.