Soluble Α-Synuclein Facilitates Priming and Fusion by Releasing Ca2+ From
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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. -
The Role of Molecular Scaffolds at the Active Zone in Synaptic Vesicle Distribution and Release Probability
The Role of Molecular Scaffolds at the Active Zone in Synaptic Vesicle Distribution and Release Probability DISSERTATION To obtain the academic degree Doctor rerum naturalium (Dr. rer. nat.) submitted to the Department of Biology, Chemistry and Pharmacy Freie Universität Berlin Berlin, 2016 by Christina Beis (née Hollmann) This thesis was completed under the supervision of Prof. Dr. Stephan Sigrist from February 2011 to June 2016 at the Institute for Biology/ Genetics of Freie Universität Berlin, Germany. 1st reviewer: Prof. Dr. Stephan Sigrist 2nd reviewer: Prof. Dr. Hans-Joachim Pflüger Date of Defense: 21.11.2016 Statement of Authorship I hereby declare that the work presented in this thesis has been written independently and without inappropriate support. All sources of information are referenced. I hereby declare that this thesis has not been submitted, either in the same or in a different form, to this or any other university for a degree. ____________________________ Christina Beis Contents 1. Summary / Zusammenfassung .................................................................................................. 1 Summary....................................................................................................................................... 1 Zusammenfassung ........................................................................................................................ 3 2. Introduction .................................................................................................................................... -
Circular RNA Hsa Circ 0005114‑Mir‑142‑3P/Mir‑590‑5P‑ Adenomatous
ONCOLOGY LETTERS 21: 58, 2021 Circular RNA hsa_circ_0005114‑miR‑142‑3p/miR‑590‑5p‑ adenomatous polyposis coli protein axis as a potential target for treatment of glioma BO WEI1*, LE WANG2* and JINGWEI ZHAO1 1Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033; 2Department of Ophthalmology, The First Hospital of Jilin University, Jilin University, Changchun, Jilin 130021, P.R. China Received September 12, 2019; Accepted October 22, 2020 DOI: 10.3892/ol.2020.12320 Abstract. Glioma is the most common type of brain tumor APC expression with a good overall survival rate. UALCAN and is associated with a high mortality rate. Despite recent analysis using TCGA data of glioblastoma multiforme and the advances in treatment options, the overall prognosis in patients GSE25632 and GSE103229 microarray datasets showed that with glioma remains poor. Studies have suggested that circular hsa‑miR‑142‑3p/hsa‑miR‑590‑5p was upregulated and APC (circ)RNAs serve important roles in the development and was downregulated. Thus, hsa‑miR‑142‑3p/hsa‑miR‑590‑5p‑ progression of glioma and may have potential as therapeutic APC‑related circ/ceRNA axes may be important in glioma, targets. However, the expression profiles of circRNAs and their and hsa_circ_0005114 interacted with both of these miRNAs. functions in glioma have rarely been studied. The present study Functional analysis showed that hsa_circ_0005114 was aimed to screen differentially expressed circRNAs (DECs) involved in insulin secretion, while APC was associated with between glioma and normal brain tissues using sequencing the Wnt signaling pathway. In conclusion, hsa_circ_0005114‑ data collected from the Gene Expression Omnibus database miR‑142‑3p/miR‑590‑5p‑APC ceRNA axes may be potential (GSE86202 and GSE92322 datasets) and explain their mecha‑ targets for the treatment of glioma. -
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. -
Inaugural Dissertation
Molecular Mechanisms that Regulate Neurotransmission and Establish Presynaptic Homeostasis at the Drosophila melanogaster Neuromuscular Junction Inaugural Dissertation to obtain the academic degree Doctor rerum naturalium (Dr. rer. nat.) submitted to the Department of Biology, Chemistry and Pharmacy of Freie Universität Berlin by Anthony William McCarthy from Dublin, Ireland February 2020 The experimental part of this thesis was conducted from September 2015 to November 2019 under the supervision of Dr. Alexander Walter at the Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) and at the CharitéCrossOver, Charité Campus Berlin Mitte. 1st Reviewer: Dr. Alexander Walter 2nd Reviewer: Prof. Dr. Stephan Sigrist Date of Defence: Statement of Authorship I hereby declare that I am the sole author of this thesis and that I have not used any sources or tools other than those quoted. Use of work by any other author is identified as such and appropriately referenced. Berlin, February 2020 Anthony William McCarthy Acknowledgments I would like to take the opportunity to thank all the people who have been important and made an impact on me during my time in Berlin. I would first like to thank my supervisor, Dr. Alexander Walter, for his guidance and supervision over the years. His passion for science and expert knowledge as well as approachable nature made for insightful conversation, projecting me forward with my projects. I would also like to thank Prof. Dr. Stephan Sigrist for his valuable input during thesis committee meetings and for acting as a reviewer. I am grateful to Prof. Dr. Volker Haucke, the members of his lab and all those at the FMP in Buch for the plentiful feedback I received following thesis committee meetings and progress presentations. -
Circular RNA Expression Profiles in Pediatric Ependymomas Ulvi Ahmadov1, Meile M
medRxiv preprint doi: https://doi.org/10.1101/2020.08.04.20167312; this version posted August 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Circular RNA expression profiles in pediatric ependymomas Ulvi Ahmadov1, Meile M. Bendikas2, Karoline K. Ebbesen2,3, Astrid M. Sehested4, Jørgen Kjems2,3, Helle Broholm5 and Lasse S. Kristensen1# 1. Department of Biomedicine, Aarhus University, Aarhus, Denmark 2. Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark 3. Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark 4. Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital, Copenhagen, Denmark 5. Department of Pathology, Center of Diagnostic Investigation, Rigshospitalet, Copenhagen, Denmark # corresponding author Running title: CircRNAs expression profiles in pediatric ependymomas Correspondence should be addressed to: Lasse Sommer Kristensen, PhD, Department of Biomedicine, Høegh- Guldbergs Gade 10, building 1116, room 268, Aarhus University, 8000 Aarhus, Denmark. Phone: +45 28880562, E-mail: [email protected] Key words: Pediatric ependymoma, pilocytic astrocytoma, medulloblastoma, circular RNA, RNA-sequencing, NanoString nCounter 1 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.08.04.20167312; this version posted August 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. -
Transcriptome Alterations of Vascular Smooth Muscle Cells in Aortic Wall of Myocardial Infarction Patients
This document is downloaded from DR‑NTU (https://dr.ntu.edu.sg) Nanyang Technological University, Singapore. Transcriptome alterations of vascular smooth muscle cells in aortic wall of myocardial infarction patients Wongsurawat, Thidathip; Woo, Chin Cheng; Giannakakis, Antonis; Lin, Xiao Yun; Cheow, Esther Sok Hwee; Lee, Chuen Neng; Richards, Mark; Sze, Siu Kwan; Nookaew, Intawat; Sorokin, Vitaly; Kuznetsov, Vladimir Andreevich 2018 Wongsurawat, T., Woo, C. C., Giannakakis, A., Lin, X. Y., Cheow, E. S. H., Lee, C. N., et al. (2018). Transcriptome alterations of vascular smooth muscle cells in aortic wall of myocardial infarction patients. Data in Brief, 17, 1112‑1135. https://hdl.handle.net/10356/85590 https://doi.org/10.1016/j.dib.2018.01.108 © 2018 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Downloaded on 09 Oct 2021 06:21:01 SGT Data in Brief 17 (2018) 1112–1135 Contents lists available at ScienceDirect Data in Brief journal homepage: www.elsevier.com/locate/dib Data Article Transcriptome alterations of vascular smooth muscle cells in aortic wall of myocardial infarction patients Thidathip Wongsurawat a,b, Chin Cheng Woo c, Antonis Giannakakis a, Xiao Yun Lin d, Esther Sok Hwee Cheow e, Chuen Neng Lee c,d, Mark Richards f,g, Siu Kwan Sze e, Intawat Nookaew b, Vladimir A. Kuznetsov a,h, Vitaly Sorokin c,d,⁎ a Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), -
Meta-Analysis of Pharmacogenetic Interactions in Amyotrophic Lateral Sclerosis Clinical Trials
Published Ahead of Print on October 4, 2017 as 10.1212/WNL.0000000000004606 Meta-analysis of pharmacogenetic interactions in amyotrophic lateral sclerosis clinical trials Ruben P.A. van Eijk, MD ABSTRACT Ashley R. Jones, PhD Objective: To assess whether genetic subgroups in recent amyotrophic lateral sclerosis (ALS) tri- William Sproviero, PhD als responded to treatment with lithium carbonate, but that the treatment effect was lost in a large Aleksey Shatunov, PhD cohort of nonresponders. Pamela J. Shaw, MD, PhD Methods: Individual participant data were obtained from 3 randomized trials investigating the P. Nigel Leigh, MD, PhD efficacy of lithium carbonate. We matched clinical data with data regarding the UNC13A and Carolyn A. Young, MD, C9orf72 genotype. Our primary outcome was survival at 12 months. On an exploratory basis, we PhD assessed whether the effect of lithium depended on the genotype. Christopher E. Shaw, MD, PhD Results: Clinical data were available for 518 of the 606 participants. Overall, treatment with lith- Gabriele Mora, MD ium carbonate did not improve 12-month survival (hazard ratio [HR] 1.0, 95% confidence interval – p 5 UNC13A C9orf72 Jessica Mandrioli, MD [CI] 0.7 1.4; 0.96). Both the and genotype were independent predictors – p 5 – p 5 Giuseppe Borghero, MD of survival (HR 2.4, 95% CI 1.3 4.3; 0.006 and HR 2.5, 95% CI 1.1 5.2; 0.032, UNC13A p 5 Paolo Volanti, MD respectively). The effect of lithium was different for carriers ( 0.027), but not for C9orf72 p 5 UNC13A Frank P. Diekstra, MD, carriers ( 0.22). -
Cognitive Characterization of Schizophrenia Risk Variants Involved in Synaptic Transmission: Evidence of CACNA1C 'S Role in Working Memory
Neuropsychopharmacology (2017) 42, 2612–2622 © 2017 American College of Neuropsychopharmacology. All rights reserved 0893-133X/17 www.neuropsychopharmacology.org Cognitive Characterization of Schizophrenia Risk Variants Involved in Synaptic Transmission: Evidence of CACNA1C 's Role in Working Memory 1 1 2 3 4,5 3 Donna Cosgrove , Omar Mothersill , Kimberley Kendall , Bettina Konte , Denise Harold , Ina Giegling , 3 6 6 7 Annette Hartmann , Alex Richards , Kiran Mantripragada , The Wellcome Trust Case Control Consortium , Michael J Owen6, Michael C O’Donovan6, Michael Gill4, Dan Rujescu3, James Walters2, Aiden Corvin4, Derek W Morris1 and Gary Donohoe*,1 1 The Cognitive Genetics & Cognitive Therapy Group, The School of Psychology and Discipline of Biochemistry, The Centre for Neuroimaging & Cognitive Genomics, National University of Ireland Galway, Galway, Ireland; 2Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK; 3Department of Psychiatry, Psychotherapy and Psychosomatics, Martin-Luther-University Halle-Wittenberg, Halle, Germany; 4 Neuropsychiatric Genetics Research Group, Department of Psychiatry, Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland; 5 6 School of Biotechnology, Dublin City University, Dublin, Ireland; MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK With 4100 common variants associated with schizophrenia risk, establishing their biological significance is a priority. We sought to establish cognitive effects of -
High Expression of PPFIA1 Is Associated with Tumor Progression and a Poor Prognosis in Esophageal Squamous Cell Carcinoma
High Expression of PPFIA1 Is Associated With Tumor Progression and a Poor Prognosis in Esophageal Squamous Cell Carcinoma Hongdian Zhang Tianjin Cancer Institute: Tianjin Tumor Hospital Ran Jia Tianjin Cancer Institute: Tianjin Tumor Hospital Yueyang Yang Tianjin Cancer Institute: Tianjin Tumor Hospital Zhilin Sui Tianjin Cancer Institute: Tianjin Tumor Hospital Wanyi Xiao Tianjin Cancer Institute: Tianjin Tumor Hospital Xianxian Wu Tianjin Cancer Institute: Tianjin Tumor Hospital Lei Gong Tianjin Cancer Institute: Tianjin Tumor Hospital Zhentao Yu National Cancer Center Peng Tang ( [email protected] ) Tianjin Cancer Institute: Tianjin Tumor Hospital https://orcid.org/0000-0002-5403-0817 Research article Keywords: Esophageal squamous cell carcinoma, PPFIA1, Bioinformatics analysis, Immunohistochemistry, Prognosis Posted Date: May 25th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-554718/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/24 Abstract Background: PTPRF interacting protein alpha 1 (PPFIA1) is reportedly related to the occurrence and progression of several types of malignancies. However, its role in esophageal squamous cell carcinoma (ESCC) remains unknown. We aimed to investigate the expression and clinical value of PPFIA1 in ESCC. Methods: The Oncomine, Gene Expression Proling Enrichment Analysis (GEPIA), and Gene Expression Omnibus (GEO) databases were utilized to explore PPFIA1 mRNA expression in esophageal cancer. The associations of PPFIA1 expression with clinicopathological variables and prognosis were evaluated in the GSE53625 dataset and veried in quantitative real-time polymerase chain reaction (qRT-PCR)-based cDNA array and immunohistochemistry (IHC)-based tissue microarray (TMA) datasets. The interactions between PPFIA1 and other genes based on the protein-protein interaction (PPI) network was analyzed via the STRING website. -
High-Throughput Drug Screens for Amyotrophic Lateral Sclerosis Drug Discovery
This is a repository copy of High-throughput drug screens for amyotrophic lateral sclerosis drug discovery. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/137336/ Version: Accepted Version Article: McGown, A. orcid.org/0000-0002-3213-1895 and Stopford, M.J. orcid.org/0000-0002-1298-4102 (2018) High-throughput drug screens for amyotrophic lateral sclerosis drug discovery. Expert Opinion on Drug Discovery. ISSN 1746-0441 https://doi.org/10.1080/17460441.2018.1533953 This is an Accepted Manuscript of an article published by Taylor & Francis in Expert Opinion on Drug Discovery on 13/10/18, available online: http://www.tandfonline.com/10.1080/17460441.2018.1533953 Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Title: High-throughput drug screens for amyotrophic lateral sclerosis drug discovery Abstract: Amyotrophic lateral sclerosis (ALS) is a rapid adult onset neurodegenerative disorder characterised by the progressive loss of upper and lower motor neurons. -
LGI1–ADAM22–MAGUK Configures Transsynaptic Nanoalignment for Synaptic Transmission and Epilepsy Prevention
LGI1–ADAM22–MAGUK configures transsynaptic nanoalignment for synaptic transmission and epilepsy prevention Yuko Fukataa,b,1, Xiumin Chenc,d,1, Satomi Chikenb,e, Yoko Hiranoa,f, Atsushi Yamagatag, Hiroki Inahashia, Makoto Sanboh, Hiromi Sanob,e, Teppei Gotoh, Masumi Hirabayashib,h, Hans-Christian Kornaui,j, Harald Prüssi,k, Atsushi Nambub,e, Shuya Fukail, Roger A. Nicollc,d,2, and Masaki Fukataa,b,2 aDivision of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Aichi 444-8787, Japan; bDepartment of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Aichi 444-8585, Japan; cDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158; dDepartment of Physiology, University of California, San Francisco, CA 94158; eDivision of System Neurophysiology, Department of System Neuroscience, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Aichi 444-8585, Japan; fDepartment of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; gLaboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan; hCenter for Genetic Analysis of Behavior, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki 444-8787, Japan; iGerman Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany; jNeuroscience Research Center, Cluster NeuroCure, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; kDepartment of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; and lDepartment of Chemistry, Graduate School of Science, Kyoto University, 606-8502 Kyoto, Japan Contributed by Roger A. Nicoll, December 1, 2020 (sent for review October 29, 2020; reviewed by David S.