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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. -
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. -
Autophagy Suppresses Ras-Driven Epithelial Tumourigenesis by Limiting the Accumulation of Reactive Oxygen Species
OPEN Oncogene (2017) 36, 5576–5592 www.nature.com/onc ORIGINAL ARTICLE Autophagy suppresses Ras-driven epithelial tumourigenesis by limiting the accumulation of reactive oxygen species This article has been corrected since Advance Online Publication and a corrigendum is also printed in this issue. J Manent1,2,3,4,5,12, S Banerjee2,3,4,5, R de Matos Simoes6, T Zoranovic7,13, C Mitsiades6, JM Penninger7, KJ Simpson4,5, PO Humbert3,5,8,9,10 and HE Richardson1,2,5,8,11 Activation of Ras signalling occurs in ~ 30% of human cancers; however, activated Ras alone is not sufficient for tumourigenesis. In a screen for tumour suppressors that cooperate with oncogenic Ras (RasV12)inDrosophila, we identified genes involved in the autophagy pathway. Bioinformatic analysis of human tumours revealed that several core autophagy genes, including GABARAP, correlate with oncogenic KRAS mutations and poor prognosis in human pancreatic cancer, supporting a potential tumour- suppressive effect of the pathway in Ras-driven human cancers. In Drosophila, we demonstrate that blocking autophagy at any step of the pathway enhances RasV12-driven epithelial tissue overgrowth via the accumulation of reactive oxygen species and activation of the Jun kinase stress response pathway. Blocking autophagy in RasV12 clones also results in non-cell-autonomous effects with autophagy, cell proliferation and caspase activation induced in adjacent wild-type cells. Our study has implications for understanding the interplay between perturbations in Ras signalling and autophagy in tumourigenesis, -
Selective Expression of a SNARE-Cleaving Protease in Peripheral Sensory Neurons Attenuates Pain-Related Gene Transcription and Neuropeptide Release
International Journal of Molecular Sciences Article Selective Expression of a SNARE-Cleaving Protease in Peripheral Sensory Neurons Attenuates Pain-Related Gene Transcription and Neuropeptide Release Wanzhi Wang 1, Miaomiao Kong 1, Yu Dou 1, Shanghai Xue 1, Yang Liu 1, Yinghao Zhang 1, Weiwei Chen 1, Yanqing Li 1, Xiaolong Dai 1, Jianghui Meng 1,2,* and Jiafu Wang 1,2,* 1 School of Life Sciences, Henan University, Kaifeng 475001, China; [email protected] (W.W.); [email protected] (M.K.); [email protected] (Y.D.); [email protected] (S.X.); [email protected] (Y.L.); [email protected] (Y.Z.); [email protected] (W.C.); [email protected] (Y.L.); [email protected] (X.D.) 2 School of Biotechnology, Faculty of Science and Health, Dublin City University, Glasnevin, Dublin 9, Ireland * Correspondence: [email protected] (J.M.); [email protected] (J.W.) Abstract: Chronic pain is a leading health and socioeconomic problem and an unmet need exists for long-lasting analgesics. SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) are required for neuropeptide release and noxious signal transducer surface trafficking, thus, selective expression of the SNARE-cleaving light-chain protease of botulinum neurotoxin A (LCA) in peripheral sensory neurons could alleviate chronic pain. However, a safety concern to Citation: Wang, W.; Kong, M.; this approach is the lack of a sensory neuronal promoter to prevent the expression of LCA in the Dou, Y.; Xue, S.; Liu, Y.; Zhang, Y.; central nervous system. Towards this, we exploit the unique characteristics of Pirt (phosphoinositide- Chen, W.; Li, Y.; Dai, X.; Meng, J.; et al. -
Widespread Sequence Variations in VAMP1 Across Vertebrates Suggest a Potential Selective Pressure from Botulinum Neurotoxins
Widespread Sequence Variations in VAMP1 across Vertebrates Suggest a Potential Selective Pressure from Botulinum Neurotoxins The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Peng, L., M. Adler, A. Demogines, A. Borrell, H. Liu, L. Tao, W. H. Tepp, et al. 2014. “Widespread Sequence Variations in VAMP1 across Vertebrates Suggest a Potential Selective Pressure from Botulinum Neurotoxins.” PLoS Pathogens 10 (7): e1004177. doi:10.1371/journal.ppat.1004177. http://dx.doi.org/10.1371/ journal.ppat.1004177. Published Version doi:10.1371/journal.ppat.1004177 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:12717507 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Widespread Sequence Variations in VAMP1 across Vertebrates Suggest a Potential Selective Pressure from Botulinum Neurotoxins Lisheng Peng1, Michael Adler2*, Ann Demogines3, Andrew Borrell2, Huisheng Liu4, Liang Tao1, William H. Tepp5, Su-Chun Zhang4, Eric A. Johnson5, Sara L. Sawyer3*, Min Dong1* 1 Department of Microbiology and Immunobiology, Harvard Medical School and Division of Neuroscience, New England Primate Research Center, Southborough, Massachusetts, United States of America, 2 Neurobehavioral Toxicology Branch, U.S. Army Medical Research Institute of Chemical Defense, Aberdeen -
Transcriptional Recapitulation and Subversion Of
Open Access Research2007KaiseretVolume al. 8, Issue 7, Article R131 Transcriptional recapitulation and subversion of embryonic colon comment development by mouse colon tumor models and human colon cancer Sergio Kaiser¤*, Young-Kyu Park¤†, Jeffrey L Franklin†, Richard B Halberg‡, Ming Yu§, Walter J Jessen*, Johannes Freudenberg*, Xiaodi Chen‡, Kevin Haigis¶, Anil G Jegga*, Sue Kong*, Bhuvaneswari Sakthivel*, Huan Xu*, Timothy Reichling¥, Mohammad Azhar#, Gregory P Boivin**, reviews Reade B Roberts§, Anika C Bissahoyo§, Fausto Gonzales††, Greg C Bloom††, Steven Eschrich††, Scott L Carter‡‡, Jeremy E Aronow*, John Kleimeyer*, Michael Kleimeyer*, Vivek Ramaswamy*, Stephen H Settle†, Braden Boone†, Shawn Levy†, Jonathan M Graff§§, Thomas Doetschman#, Joanna Groden¥, William F Dove‡, David W Threadgill§, Timothy J Yeatman††, reports Robert J Coffey Jr† and Bruce J Aronow* Addresses: *Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA. †Departments of Medicine, and Cell and Developmental Biology, Vanderbilt University and Department of Veterans Affairs Medical Center, Nashville, TN 37232, USA. ‡McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53706, USA. §Department of Genetics and Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA. ¶Molecular Pathology Unit and Center for Cancer Research, Massachusetts deposited research General Hospital, Charlestown, MA 02129, USA. ¥Division of Human Cancer Genetics, The Ohio State University College of Medicine, Columbus, Ohio 43210-2207, USA. #Institute for Collaborative BioResearch, University of Arizona, Tucson, AZ 85721-0036, USA. **University of Cincinnati, Department of Pathology and Laboratory Medicine, Cincinnati, OH 45267, USA. ††H Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA. ‡‡Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology (CHIP@HST), Harvard Medical School, Boston, Massachusetts 02115, USA. -
VAMP1 Polyclonal Antibody Catalog Number:13115-1-AP 2 Publications
For Research Use Only VAMP1 Polyclonal antibody Catalog Number:13115-1-AP 2 Publications www.ptglab.com Catalog Number: GenBank Accession Number: Purification Method: Basic Information 13115-1-AP BC023286 Antigen affinity purification Size: GeneID (NCBI): Recommended Dilutions: 150ul , Concentration: 500 μg/ml by 6843 WB 1:500-1:2000 Nanodrop and 213 μg/ml by Bradford Full Name: IF 1:20-1:200 method using BSA as the standard; vesicle-associated membrane protein Source: 1 (synaptobrevin 1) Rabbit Calculated MW: Isotype: 117 aa, 13 kDa IgG Observed MW: Immunogen Catalog Number: 13 kDa AG3787 Applications Tested Applications: Positive Controls: IF, WB,ELISA WB : human brain tissue, Cited Applications: IF : SH-SY5Y cells, WB Species Specificity: human, mouse, rat Cited Species: mouse, rat VAMP1, also named as synaptobrevin 1, is a member of the vesicle-associated membrane protein Background Information (VAMP)/synaptobrevin family. VAMP1 is a part of the SNARE (soluble NSF-attachment protein receptor) complex. Characterized by a common sequence called the SNARE motif, SNARE proteins are involved in membrane fusion and vesicular transport (PMID: 11252968). VAMP1 is involved in synaptic vesicle exocytosis, a fundamental step in neurotransmitter release. Notable Publications Author Pubmed ID Journal Application Hailei Yu 34116208 Pharmacol Res WB Xing-Lian Duan 31962145 Neuroscience WB Storage: Storage Store at -20°C. Stable for one year after shipment. Storage Buffer: PBS with 0.02% sodium azide and 50% glycerol pH 7.3. Aliquoting is unnecessary for -20ºC storage For technical support and original validation data for this product please contact: This product is exclusively available under Proteintech T: 1 (888) 4PTGLAB (1-888-478-4522) (toll free E: [email protected] Group brand and is not available to purchase from any in USA), or 1(312) 455-8498 (outside USA) W: ptglab.com other manufacturer. -
Novel Targets of Apparently Idiopathic Male Infertility
International Journal of Molecular Sciences Review Molecular Biology of Spermatogenesis: Novel Targets of Apparently Idiopathic Male Infertility Rossella Cannarella * , Rosita A. Condorelli , Laura M. Mongioì, Sandro La Vignera * and Aldo E. Calogero Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; [email protected] (R.A.C.); [email protected] (L.M.M.); [email protected] (A.E.C.) * Correspondence: [email protected] (R.C.); [email protected] (S.L.V.) Received: 8 February 2020; Accepted: 2 March 2020; Published: 3 March 2020 Abstract: Male infertility affects half of infertile couples and, currently, a relevant percentage of cases of male infertility is considered as idiopathic. Although the male contribution to human fertilization has traditionally been restricted to sperm DNA, current evidence suggest that a relevant number of sperm transcripts and proteins are involved in acrosome reactions, sperm-oocyte fusion and, once released into the oocyte, embryo growth and development. The aim of this review is to provide updated and comprehensive insight into the molecular biology of spermatogenesis, including evidence on spermatogenetic failure and underlining the role of the sperm-carried molecular factors involved in oocyte fertilization and embryo growth. This represents the first step in the identification of new possible diagnostic and, possibly, therapeutic markers in the field of apparently idiopathic male infertility. Keywords: spermatogenetic failure; embryo growth; male infertility; spermatogenesis; recurrent pregnancy loss; sperm proteome; DNA fragmentation; sperm transcriptome 1. Introduction Infertility is a widespread condition in industrialized countries, affecting up to 15% of couples of childbearing age [1]. It is defined as the inability to achieve conception after 1–2 years of unprotected sexual intercourse [2]. -
CENTOGENE's Severe and Early Onset Disorder Gene List
CENTOGENE’s severe and early onset disorder gene list USED IN PRENATAL WES ANALYSIS AND IDENTIFICATION OF “PATHOGENIC” AND “LIKELY PATHOGENIC” CENTOMD® VARIANTS IN NGS PRODUCTS The following gene list shows all genes assessed in prenatal WES tests or analysed for P/LP CentoMD® variants in NGS products after April 1st, 2020. For searching a single gene coverage, just use the search on www.centoportal.com AAAS, AARS1, AARS2, ABAT, ABCA12, ABCA3, ABCB11, ABCB4, ABCB7, ABCC6, ABCC8, ABCC9, ABCD1, ABCD4, ABHD12, ABHD5, ACACA, ACAD9, ACADM, ACADS, ACADVL, ACAN, ACAT1, ACE, ACO2, ACOX1, ACP5, ACSL4, ACTA1, ACTA2, ACTB, ACTG1, ACTL6B, ACTN2, ACVR2B, ACVRL1, ACY1, ADA, ADAM17, ADAMTS2, ADAMTSL2, ADAR, ADARB1, ADAT3, ADCY5, ADGRG1, ADGRG6, ADGRV1, ADK, ADNP, ADPRHL2, ADSL, AFF2, AFG3L2, AGA, AGK, AGL, AGPAT2, AGPS, AGRN, AGT, AGTPBP1, AGTR1, AGXT, AHCY, AHDC1, AHI1, AIFM1, AIMP1, AIPL1, AIRE, AK2, AKR1D1, AKT1, AKT2, AKT3, ALAD, ALDH18A1, ALDH1A3, ALDH3A2, ALDH4A1, ALDH5A1, ALDH6A1, ALDH7A1, ALDOA, ALDOB, ALG1, ALG11, ALG12, ALG13, ALG14, ALG2, ALG3, ALG6, ALG8, ALG9, ALMS1, ALOX12B, ALPL, ALS2, ALX3, ALX4, AMACR, AMER1, AMN, AMPD1, AMPD2, AMT, ANK2, ANK3, ANKH, ANKRD11, ANKS6, ANO10, ANO5, ANOS1, ANTXR1, ANTXR2, AP1B1, AP1S1, AP1S2, AP3B1, AP3B2, AP4B1, AP4E1, AP4M1, AP4S1, APC2, APTX, AR, ARCN1, ARFGEF2, ARG1, ARHGAP31, ARHGDIA, ARHGEF9, ARID1A, ARID1B, ARID2, ARL13B, ARL3, ARL6, ARL6IP1, ARMC4, ARMC9, ARSA, ARSB, ARSL, ARV1, ARX, ASAH1, ASCC1, ASH1L, ASL, ASNS, ASPA, ASPH, ASPM, ASS1, ASXL1, ASXL2, ASXL3, ATAD3A, ATCAY, ATIC, ATL1, ATM, ATOH7, -
11056.Full.Pdf
11056 • The Journal of Neuroscience, October 10, 2007 • 27(41):11056–11064 Neurobiology of Disease Huntingtin-Interacting Protein 1 Influences Worm and Mouse Presynaptic Function and Protects Caenorhabditis elegans Neurons against Mutant Polyglutamine Toxicity J. Alex Parker,1,2 Martina Metzler,3 John Georgiou,4 Marilyne Mage,1,2 John C. Roder,4,5 Ann M. Rose,6 Michael R. Hayden,3 and Christian Ne´ri1,2 1Inserm, Unit 857 “Neuronal Cell Biology and Pathology,” and 2University of Paris Rene´ Descartes, Equipe d’Accueil 4059, Centre Paul Broca, 75014 Paris, France, 3Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada V5Z 4H4, 4Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5, 5Department of Physiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and 6Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3 Huntingtin-interacting protein 1 (HIP1) was identified through its interaction with htt (huntingtin), the Huntington’s disease (HD) protein. HIP1 is an endocytic protein that influences transport and function of AMPA and NMDA receptors in the brain. However, little is known about its contribution to neuronal dysfunction in HD. We report that the Caenorhabditis elegans HIP1 homolog hipr-1 modulates presynaptic activity and the abundance of synaptobrevin, a protein involved in synaptic vesicle fusion. Presynaptic function was also altered in hippocampal brain slices of HIP1 Ϫ/Ϫ mice dem- onstrating delayed recovery from synaptic depression and a reduction in paired-pulse facilitation, a form of presynaptic plasticity. -
Starting a Molecular Systems View of Endocytosis
ANRV356-CB24-20 ARI 3 September 2008 19:11 ANNUAL Protein Kinases: Starting REVIEWS Further Click here for quick links to Annual Reviews content online, a Molecular Systems View including: • Other articles in this volume of Endocytosis • Top cited articles • Top downloaded articles • Our comprehensive search Prisca Liberali, Pauli Ram¨ o,¨ and Lucas Pelkmans Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland; email: [email protected] Annu. Rev. Cell Dev. Biol. 2008. 24:501–23 Key Words First published online as a Review in Advance on membrane trafficking, phosphorylation, signal transduction, July 3, 2008 complexity, nonlinear systems, genetical physics The Annual Review of Cell and Developmental Biology is online at cellbio.annualreviews.org Abstract This article’s doi: The field of endocytosis is in strong need of formal biophysical model- 10.1146/annurev.cellbio.041008.145637 ing and mathematical analysis. At the same time, endocytosis must be Copyright c 2008 by Annual Reviews. much better integrated into cellular physiology to understand the for- by Universitat Zurich- Hauptbibliothek Irchel on 04/05/13. For personal use only. All rights reserved mer’s complex behavior in such a wide range of phenotypic variations. Annu. Rev. Cell Dev. Biol. 2008.24:501-523. Downloaded from www.annualreviews.org 1081-0706/08/1110-0501$20.00 Furthermore, the concept that endocytosis provides the space-time for signal transduction can now be experimentally addressed. In this review, we discuss these principles and argue for a systematic and top-down ap- proach to study the endocytic membrane system. We provide a summary of published observations on protein kinases regulating endocytic ma- chinery components and discuss global unbiased approaches to further map out kinase regulatory networks. -
The Molecular Basis of Transcriptional Activation by the CDP/Cux Transcription Factor
The Molecular Basis of Transcriptional Activation by the CDP/Cux Transcription Factor Mary Truscott A thesis submitted to the Faculty of Graduate and Post-doctoral Studies in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of B iochemistry McGill University Montreal, Quebec, Canada August 2006 © Mary Truscott, 2006 Library and Bibliothèque et 1+1 Archives Canada Archives Canada Published Heritage Direction du Branch Patrimoine de l'édition 395 Wellington Street 395, rue Wellington Ottawa ON K1A ON4 Ottawa ON K1A ON4 Canada Canada Your file Votre référence ISBN: 978-0-494-32391-5 Our file Notre référence ISBN: 978-0-494-32391-5 NOTICE: AVIS: The author has granted a non L'auteur a accordé une licence non exclusive exclusive license allowing Library permettant à la Bibliothèque 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 télécommunication ou par l'Internet, prêter, telecommunication or on the Internet, distribuer et vendre des thèses partout dans loan, distribute and sell th es es le monde, à des fins commerciales ou autres, worldwide, for commercial or non sur support microforme, papier, électronique commercial purposes, in microform, et/ou autres formats. paper, electronic and/or any other formats. The author retains copyright L'auteur conserve la propriété du droit d'auteur ownership and moral rights in et des droits moraux qui protège cette thèse. this thesis. Neither the thesis Ni la thèse ni des extraits substantiels de nor substantial extracts from it celle-ci ne doivent être imprimés ou autrement may be printed or otherwise reproduits sans son autorisation.