Distinct Actions of Rab3 and Rab27 Gtpases on Late Stages of Exocytosis of Insulin
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Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Investigation of the underlying hub genes and molexular pathogensis in gastric cancer by integrated bioinformatic analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Abstract The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a proteinprotein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes. -
Supplementary Materials
Supplementary Materials COMPARATIVE ANALYSIS OF THE TRANSCRIPTOME, PROTEOME AND miRNA PROFILE OF KUPFFER CELLS AND MONOCYTES Andrey Elchaninov1,3*, Anastasiya Lokhonina1,3, Maria Nikitina2, Polina Vishnyakova1,3, Andrey Makarov1, Irina Arutyunyan1, Anastasiya Poltavets1, Evgeniya Kananykhina2, Sergey Kovalchuk4, Evgeny Karpulevich5,6, Galina Bolshakova2, Gennady Sukhikh1, Timur Fatkhudinov2,3 1 Laboratory of Regenerative Medicine, National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, Moscow, Russia 2 Laboratory of Growth and Development, Scientific Research Institute of Human Morphology, Moscow, Russia 3 Histology Department, Medical Institute, Peoples' Friendship University of Russia, Moscow, Russia 4 Laboratory of Bioinformatic methods for Combinatorial Chemistry and Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia 5 Information Systems Department, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia 6 Genome Engineering Laboratory, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia Figure S1. Flow cytometry analysis of unsorted blood sample. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S2. Flow cytometry analysis of unsorted liver stromal cells. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S3. MiRNAs expression analysis in monocytes and Kupffer cells. Full-length of heatmaps are presented. -
A Chemical Proteomic Approach to Investigate Rab Prenylation in Living Systems
A chemical proteomic approach to investigate Rab prenylation in living systems By Alexandra Fay Helen Berry A thesis submitted to Imperial College London in candidature for the degree of Doctor of Philosophy of Imperial College. Department of Chemistry Imperial College London Exhibition Road London SW7 2AZ August 2012 Declaration of Originality I, Alexandra Fay Helen Berry, hereby declare that this thesis, and all the work presented in it, is my own and that it has been generated by me as the result of my own original research, unless otherwise stated. 2 Abstract Protein prenylation is an important post-translational modification that occurs in all eukaryotes; defects in the prenylation machinery can lead to toxicity or pathogenesis. Prenylation is the modification of a protein with a farnesyl or geranylgeranyl isoprenoid, and it facilitates protein- membrane and protein-protein interactions. Proteins of the Ras superfamily of small GTPases are almost all prenylated and of these the Rab family of proteins forms the largest group. Rab proteins are geranylgeranylated with up to two geranylgeranyl groups by the enzyme Rab geranylgeranyltransferase (RGGT). Prenylation of Rabs allows them to locate to the correct intracellular membranes and carry out their roles in vesicle trafficking. Traditional methods for probing prenylation involve the use of tritiated geranylgeranyl pyrophosphate which is hazardous, has lengthy detection times, and is insufficiently sensitive. The work described in this thesis developed systems for labelling Rabs and other geranylgeranylated proteins using a technique known as tagging-by-substrate, enabling rapid analysis of defective Rab prenylation in cells and tissues. An azide analogue of the geranylgeranyl pyrophosphate substrate of RGGT (AzGGpp) was applied for in vitro prenylation of Rabs by recombinant enzyme. -
Rap1 Acts Via Multiple Mechanisms to Position Canoe/Afadin and Adherens Junctions and Mediate Apical-Basal Polarity Establishment
bioRxiv preprint doi: https://doi.org/10.1101/170977; this version posted July 31, 2017. 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. Rap1 acts via multiple mechanisms to position Canoe/Afadin and adherens junctions and mediate apical-basal polarity establishment Teresa T. Bonello1, Kia Z. Perez-Vale2, Kaelyn D. Sumigray3, and Mark Peifer1,2,3* 1 Department of Biology, University of North Carolina at Chapel Hill, CB#3280, Chapel Hill, NC 27599-3280, USA 2 Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA 3 Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Running Title Active Rap1 positions Canoe and AJs 6950 words * To whom correspondence should be addressed Email: [email protected] Phone: (919) 962-2272 Abbreviations used: α-cat, alpha-catenin; β-cat, beta-catenin; AJ, adherens junction; Arm, Armadillo; Baz, BazooKa; CA, constitutively active; Cno, Canoe; DE-cad, Drosophila E-cadherin; Dzy, Dizzy; GAP, GTPase activating protein; GDP, guanosine diphosphate; GEF, guanine nucleotide exchange factor; GFP, green fluorescent protein; GTP, guanosine triphosphate; IF, immunofluorescence; MIP, maximum intensity projection; RA, Ras-associated; RFP, red fluorescent protein; SAJ, spot adherens junction; shRNA, short hairpin RNA; TCJ, tricellular junction; WT, wildtype 1 bioRxiv preprint doi: https://doi.org/10.1101/170977; this version posted July 31, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. -
The Role of Stress-Derived Vesicles in the Bystander Effect and Cancer Related Cachexia
THE ROLE OF STRESS-DERIVED VESICLES IN THE BYSTANDER EFFECT AND CANCER RELATED CACHEXIA Thesis is submitted in partial fulfilment of the requirements of the award of Doctor of Philosophy FINDLAY REDVERS BEWICKE-COPLEY Department of Biological and Medical Sciences Degree awarded by Oxford Brookes University First submitted for examination: January 2018 ACKNOWLEDGEMENTS Thank you to Oxford Brookes for providing funding for my research, and especially to Professor Nigel Groome whose research and generosity has allowed so many to complete their PhDs. I would also like to say thank you to the Cancer and Polio trust for providing some of the funding for my PhD I would like to thank my Supervisors Dave and Ryan for their support throughout my PhD and for only occasionally saddling me with unrelated projects. Without your guidance and support I would have curled up into a ball in the corner of the office and gently sobbed to myself for the last 5 years. Thanks to Priya for her tireless work ensuring the lab functions correctly and supporting all other members of the lab. I’d also like to thank past members of the lab, Laura Jacobs and Laura Mulcahy for their support throughout both my MSc and my PhD. Sunny Vijen for chatting with me whilst he smoked and making me leave lunch early, so he could have another smoke before going back to work. Thank you to Robbie Crickley for all the lunch time chats. To Lia I would like to say χασμουριέμαι! Thanks to Bianca for all her help getting to know the world of immunocytochemistry. -
And Pancreatic Cancer: from the Role of Evs to the Interference with EV-Mediated Reciprocal Communication
biomedicines Review Extracellular Vesicles (EVs) and Pancreatic Cancer: From the Role of EVs to the Interference with EV-Mediated Reciprocal Communication 1, 1, 1 1 1 Sokviseth Moeng y, Seung Wan Son y, Jong Sun Lee , Han Yeoung Lee , Tae Hee Kim , Soo Young Choi 1, Hyo Jeong Kuh 2 and Jong Kook Park 1,* 1 Department of Biomedical Science and Research Institute for Bioscience & Biotechnology, Hallym University, Chunchon 24252, Korea; [email protected] (S.M.); [email protected] (S.W.S.); [email protected] (J.S.L.); [email protected] (H.Y.L.); [email protected] (T.H.K.); [email protected] (S.Y.C.) 2 Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; [email protected] * Correspondence: [email protected]; Tel.: +82-33-248-2114 These authors contributed equally. y Received: 29 June 2020; Accepted: 1 August 2020; Published: 3 August 2020 Abstract: Pancreatic cancer is malignant and the seventh leading cause of cancer-related deaths worldwide. However, chemotherapy and radiotherapy are—at most—moderately effective, indicating the need for new and different kinds of therapies to manage this disease. It has been proposed that the biologic properties of pancreatic cancer cells are finely tuned by the dynamic microenvironment, which includes extracellular matrix, cancer-associated cells, and diverse immune cells. Accumulating evidence has demonstrated that extracellular vesicles (EVs) play an essential role in communication between heterogeneous subpopulations of cells by transmitting multiplex biomolecules. EV-mediated cell–cell communication ultimately contributes to several aspects of pancreatic cancer, such as growth, angiogenesis, metastasis and therapeutic resistance. -
Rap1 Regulates Hepatic Stellate Cell Migration Through the Modulation of Rhoa Activity in Response to TGF‑Β1
INTERNATIONAL JOURNAL OF MOleCular meDICine 44: 491-502, 2019 Rap1 regulates hepatic stellate cell migration through the modulation of RhoA activity in response to TGF‑β1 MI-YOUNG MOON1, HEE-JUN KIM2, MO-JONG KIM2, SUNHO UHM1, JI‑WON PARK1, KI-TAE SUK3, JAE‑BONG PARK4, DONG-JUN KIM3 and SUNG-EUN KIM1 1Department of Internal Medicine, Hallym University Sacred Heart Hospital, College of Medicine, Hallym University, Anyang, Gyeonggi 14068; 2Ilsong Institute of Life Science, Hallym University, Anyang, Gyeonggi 14066; 3Department of Internal Medicine, Hallym University Chuncheon Sacred Heart Hospital, College of Medicine, Hallym University, Chuncheon, Gangwon 24253; 4Department of Biochemistry, College of Medicine, Hallym University, Chuncheon, Gangwon 24252, Republic of Korea Received November 1, 2018; Accepted May 28, 2019 DOI: 10.3892/ijmm.2019.4215 Abstract. Although the migration of hepatic stellate cells activation of RhoA in TGF‑β1-stimulated HSC‑T6 cells. These (HSCs) is important for hepatic fibrosis, the regulation of this findings suggest that TGF‑β1 regulates Rap1, resulting in the migration is poorly understood. Notably, transforming growth suppression of RhoA, activation of and formation of F‑actin factor (TGF)-β1 induces monocyte migration to sites of injury during the migration of HSCs. or inflammation during the early phase, but inhibits cell migra- tion during the late phase. In the present study, the role of Introduction transforming protein RhoA signaling in TGF-β1-induced HSC migration was investigated. TGF‑β1 was found to increase Hepatic fibrosis is characterized by the excessive deposition the protein and mRNA levels of smooth muscle actin and of extracellular matrix (ECM) mediated by activated hepatic collagen type I in HSC‑T6 cells. -
Diagnosis of Metastatic Melanoma and Monitoring Indicators of Immunosuppression Through Blood Leukocyte Microarray Analysis
(19) TZZ __T (11) EP 2 579 174 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 10.04.2013 Bulletin 2013/15 G06F 19/00 (2011.01) (21) Application number: 12196231.0 (22) Date of filing: 03.11.2007 (84) Designated Contracting States: • Banchereau, Jacques F. AT BE BG CH CY CZ DE DK EE ES FI FR GB GR Montclair, NJ 07042 (US) HU IE IS IT LI LT LU LV MC MT NL PL PT RO SE • Chaussabel, Damien SI SK TR Bainbridge Island, WA 98110 (US) (30) Priority: 03.11.2006 US 856406 P (74) Representative: Sonn & Partner Patentanwälte Riemergasse 14 (62) Document number(s) of the earlier application(s) in 1010 Wien (AT) accordance with Art. 76 EPC: 07871360.9 / 2 080 140 Remarks: This application was filed on 10-12-2012 as a (71) Applicant: Baylor Research Institute divisional application to the application mentioned Dallas, TX 75204 (US) under INID code 62. (72) Inventors: • Palucka, Anna Karolina Dallas, TX 75204 (US) (54) Diagnosis of metastatic melanoma and monitoring indicators of immunosuppression through blood leukocyte microarray analysis (57) The present invention includes compositions, or more expression vectors from the expression of one systems and methods for the early detection and con- or more genes. sistent determination of metastatic melanoma and/or im- munosuppression using microarrays by calculating one EP 2 579 174 A1 Printed by Jouve, 75001 PARIS (FR) EP 2 579 174 A1 Description TECHNICAL FIELD OF THE INVENTION 5 [0001] The presentinvention relates in generalto the field of diagnostic for monitoring indicatorsof metastatic melanoma and/or immunosuppression, and more particularly, to a system, method and apparatus for the diagnosis, prognosis and tracking of metastatic melanoma and monitoring indicators of immunosuppression associated with transplant recipients (e.g., liver). -
Graduate Program in Biochemistry
RHAMM PROMOTES NEOPLASTIC CONVERSION AND PROGRESSION THROUGH THE REGULATION OF ERK1,2 ACTIVITY AND AP-1 MEDIATED TRANSCRIPTION (Spine title: Rhamm Regulates ERK1,2 and AP-1 Mediated Transcription) (Thesis format: Integrated-Article) by Sara Rae Hamilton Graduate Program in Biochemistry A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Faculty of Graduate Studies The University of Western Ontario London, Ontario, Canada September, 2007 © Sara R. Hamilton 2007 Library and Bibliotheque et 1*1 Archives Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'edition 395 Wellington Street 395, rue Wellington Ottawa ON K1A0N4 Ottawa ON K1A0N4 Canada Canada Your file Votre reference ISBN: 978-0-494-39274-4 Our file Notre reference ISBN: 978-0-494-39274-4 NOTICE: AVIS: The author has granted a non L'auteur a accorde une licence non exclusive exclusive license allowing Library permettant a la Bibliotheque et Archives and Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par telecommunication ou par Plntemet, prefer, telecommunication or on the Internet, distribuer et vendre des theses partout dans loan, distribute and sell theses le monde, a des fins commerciales ou autres, worldwide, for commercial or non sur support microforme, papier, electronique commercial purposes, in microform, et/ou autres formats. paper, electronic and/or any other formats. The author retains copyright L'auteur conserve la propriete du droit d'auteur ownership and moral rights in et des droits moraux qui protege cette these. -
Rap1a and Rap1b Ras-Family Proteins Are Prominently Expressed in the Nucleus of Squamous Carcinomas: Nuclear Translocation of GTP-Bound Active Form
Oncogene (2003) 22, 6243–6256 & 2003 Nature Publishing Group All rights reserved 0950-9232/03 $25.00 www.nature.com/onc Rap1A and rap1B ras-family proteins are prominently expressed in the nucleus of squamous carcinomas: nuclear translocation of GTP-bound active form Raj S Mitra1,4, Zhaocheng Zhang1,4, Bradley S Henson1, David M Kurnit2, Thomas ECarey 1,3, Nisha J D’Silva*,1 1Department of Oral Medicine, Pathology and Oncology, University of Michigan School of Dentistry, Ann Arbor, MI 48109-1078, USA; 2Departments of Pediatrics and Human Genetics, University of Michigan Medical School, Ann Arbor, MI 481091, USA; 3Department of Otolaryngology, Laboratory of Head and Neck Cancer Biology, The University of Michigan Medical School and the Comprehensive Cancer Center, Ann Arbor, MI 48109-0506, USA We recently showed that rap1 regulates growth and exclusively in eukaryotes (Takai et al., 2001). Those proliferation in normal keratinocytes, which provoked us SMGs that have been identified (currently 4100) have to investigate its expression and regulation in malignant homology to ras, and belong to one of the five cells. Rap1 is variably expressed in whole cell lysates of subfamilies namely ras, rho, rab, sar1/arf and ran squamous cell carcinoma (SCC) cell lines. Immunoblot (Takai et al., 2001). These ras-like proteins shuttle analysis of nuclear and cytosolic fractions and immuno- between inactive GDP- and active GTP-bound states. histochemistry revealed that in addition to cytoplasmic Ras subfamily proteins, including ras and rap1, are key expression, SCC cells also exhibit prominent punctate players in receptor-linked signaling pathways that rap1 expression in the nucleus. -
A Novel Rab11-Rab3a Cascade Required for Lysosome Exocytosis
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.06.434066; this version posted March 6, 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. A novel Rab11-Rab3a cascade required for lysosome exocytosis Cristina Escrevente1,*, Liliana Bento-Lopes1*, José S Ramalho1, Duarte C Barral1,† 1 iNOVA4Health, CDOC, NOVA Medical School, NMS, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal. * These authors contributed equally to this work. † Correspondence should be sent to: Duarte C Barral, CEDOC, NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria 130, 1169-056, Lisboa, Portugal, Tel: +351 218 803 102, Fax: +351 218 803 006, [email protected]. (ORCID 0000-0001-8867-2407). Abbreviations used in this paper: FIP, Rab11-family of interacting protein; GEF, guanine nucleotide exchange factor; LE, late endosomes; LRO, lysosome-related organelle; NMIIA, non-muscle myosin heavy chain IIA; Slp-4a, synaptotagmin-like protein 4a. 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.06.434066; this version posted March 6, 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 Lysosomes are dynamic organelles, capable of undergoing exocytosis. This process is crucial for several cellular functions, namely plasma membrane repair. -
Site-Specific Processing of Ras and Rap1 Switch I by a MARTX Toxin
ARTICLE Received 8 Jan 2015 | Accepted 1 May 2015 | Published 8 Jun 2015 DOI: 10.1038/ncomms8396 OPEN Site-specific processing of Ras and Rap1 Switch I by a MARTX toxin effector domain Irena Antic1,*, Marco Biancucci1,*, Yueming Zhu2, David R. Gius2 & Karla J.F. Satchell1 Ras (Rat sarcoma) protein is a central regulator of cell growth and proliferation. Mutations in the RAS gene are known to occur in human cancers and have been shown to contribute to carcinogenesis. In this study, we show that the multifunctional-autoprocessing repeats-in- toxin (MARTX) toxin-effector domain DUF5Vv from Vibrio vulnificus to be a site-specific endopeptidase that cleaves within the Switch 1 region of Ras and Rap1. DUF5Vv processing of Ras, which occurs both biochemically and in mammalian cell culture, inactivates ERK1/2, thereby inhibiting cell proliferation. The ability to cleave Ras and Rap1 is shared by DUF5Vv homologues found in other bacteria. In addition, DUF5Vv can cleave all Ras isoforms and KRas with mutations commonly implicated in malignancies. Therefore, we speculate that this new family of Ras/Rap1-specific endopeptidases (RRSPs) has potential to inactivate both wild-type and mutant Ras proteins expressed in malignancies. 1 Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, 303 East Chicago Avenue, Ward 6-225, Chicago, Illinois 60611, USA. 2 Department of Radiation Oncology and Pharmacology, Feinberg School of Medicine, Northwestern University, 303 East Superior Avenue, Lurie 3-119, Chicago, Illinois 60611, USA. * These authors contributed equally to this work. Correspondence and requests for materials should be addressedto K.J.F.S.