Irsp53/BAIAP2 in Dendritic Spine Development, NMDA Receptor Regulation, and Psychiatric Disorders
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Regulation of Cdc42 and Its Effectors in Epithelial Morphogenesis Franck Pichaud1,2,*, Rhian F
© 2019. Published by The Company of Biologists Ltd | Journal of Cell Science (2019) 132, jcs217869. doi:10.1242/jcs.217869 REVIEW SUBJECT COLLECTION: ADHESION Regulation of Cdc42 and its effectors in epithelial morphogenesis Franck Pichaud1,2,*, Rhian F. Walther1 and Francisca Nunes de Almeida1 ABSTRACT An overview of Cdc42 Cdc42 – a member of the small Rho GTPase family – regulates cell Cdc42 was discovered in yeast and belongs to a large family of small – polarity across organisms from yeast to humans. It is an essential (20 30 kDa) GTP-binding proteins (Adams et al., 1990; Johnson regulator of polarized morphogenesis in epithelial cells, through and Pringle, 1990). It is part of the Ras-homologous Rho subfamily coordination of apical membrane morphogenesis, lumen formation and of GTPases, of which there are 20 members in humans, including junction maturation. In parallel, work in yeast and Caenorhabditis elegans the RhoA and Rac GTPases, (Hall, 2012). Rho, Rac and Cdc42 has provided important clues as to how this molecular switch can homologues are found in all eukaryotes, except for plants, which do generate and regulate polarity through localized activation or inhibition, not have a clear homologue for Cdc42. Together, the function of and cytoskeleton regulation. Recent studies have revealed how Rho GTPases influences most, if not all, cellular processes. important and complex these regulations can be during epithelial In the early 1990s, seminal work from Alan Hall and his morphogenesis. This complexity is mirrored by the fact that Cdc42 can collaborators identified Rho, Rac and Cdc42 as main regulators of exert its function through many effector proteins. -
1 Running Head
medRxiv preprint doi: https://doi.org/10.1101/2020.09.16.20194639; this version posted August 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . RUNNING HEAD: Alcohol use disorder dual methylation study Dual methylation and hydroxymethylation study of alcohol use disorder Shaunna L. Clark1, Robin F. Chan2, Min Zhao2, Lin Y. Xie2, William E. Copeland3, Brenda W.J.H. Penninx3, Karolina A. Aberg2, Edwin J.C.G. van den Oord2 1Department of Psychiatry, Texas A&M University 2Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University 3 Department of Psychiatry, University of Vermont 4 Department of Psychiatry, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands Corresponding Author: Shaunna L. Clark, Email: [email protected]; Address: 8441 Riverside Parkway, Bryan, TX, 77807; Phone: (979) 436-0179 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. 1 medRxiv preprint doi: https://doi.org/10.1101/2020.09.16.20194639; this version posted August 3, 2021. 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. It is made available under a CC-BY-NC-ND 4.0 International license . ABSTRACT Using an integrative, multi-tissue design we sought to characterize methylation and hydroxymethylation changes in blood and brain associated with alcohol use disorder (AUD). -
Effects and Mechanisms of Eps8 on the Biological Behaviour of Malignant Tumours (Review)
824 ONCOLOGY REPORTS 45: 824-834, 2021 Effects and mechanisms of Eps8 on the biological behaviour of malignant tumours (Review) KAILI LUO1, LEI ZHANG2, YUAN LIAO1, HONGYU ZHOU1, HONGYING YANG2, MIN LUO1 and CHEN QING1 1School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, Yunnan 650500; 2Department of Gynecology, Yunnan Tumor Hospital and The Third Affiliated Hospital of Kunming Medical University; Kunming, Yunnan 650118, P.R. China Received August 29, 2020; Accepted December 9, 2020 DOI: 10.3892/or.2021.7927 Abstract. Epidermal growth factor receptor pathway substrate 8 1. Introduction (Eps8) was initially identified as the substrate for the kinase activity of EGFR, improving the responsiveness of EGF, which Malignant tumours are uncontrolled cell proliferation diseases is involved in cell mitosis, differentiation and other physiological caused by oncogenes and ultimately lead to organ and body functions. Numerous studies over the last decade have demon- dysfunction (1). In recent decades, great progress has been strated that Eps8 is overexpressed in most ubiquitous malignant made in the study of genes and signalling pathways in tumours and subsequently binds with its receptor to activate tumorigenesis. Eps8 was identified by Fazioli et al in NIH-3T3 multiple signalling pathways. Eps8 not only participates in the murine fibroblasts via an approach that allows direct cloning regulation of malignant phenotypes, such as tumour proliferation, of intracellular substrates for receptor tyrosine kinases (RTKs) invasion, metastasis and drug resistance, but is also related to that was designed to study the EGFR signalling pathway. Eps8 the clinicopathological characteristics and prognosis of patients. -
Eps8l2 (F-8): Sc-514673
SAN TA C RUZ BI OTEC HNOL OG Y, INC . Eps8L2 (F-8): sc-514673 BACKGROUND APPLICATIONS Eps8L2 (epidermal growth factor receptor kinase substrate 8-like protein 2), Eps8L2 (F-8) is recommended for detection of Eps8L2 of human origin by also known as EPS8R2 or PP13181, is a 715 amino acid protein that localizes Western Blotting (starting dilution 1:100, dilution range 1:100-1:1000), to the cytoplasm and belongs to the Eps8 (epidermal growth factor receptor immunoprecipitation [1-2 µg per 100-500 µg of total protein (1 ml of cell pathway substrate 8) family. Expressed in placenta and fibroblasts, Eps8L2 lysate)], immunofluorescence (starting dilution 1:50, dilution range 1:50- functions to stimulate the guanine exchange activity of Sos 1 (son of seven - 1:500) and solid phase ELISA (starting dilution 1:30, dilution range 1:30- less homolog 1), a protein that promotes the exchange of Ras-bound GDP 1:3000). for GTP. Additionally, Eps8L2 is thought to associate with Actin and, via this Suitable for use as control antibody for Eps8L2 siRNA (h): sc-96954, Eps8L2 association, may play a role in membrane ruffling and remodeling of the shRNA Plasmid (h): sc-96954-SH and Eps8L2 shRNA (h) Lentiviral Particles: Actin cytoskeleton. Through its ability to regulate protein activation and cyto- sc-96954-V. skeleton dynamics, Eps8L2 may participate in cell growth and differentiation events within the cell. Eps8L2, a protein that is expressed as two isoforms Molecular Weight of Eps8L2: 81 kDa. due to alternative splicing, contains one PID (phosphotyrosine interaction) Positive Controls: A-431 whole cell lysate: sc-2201, HeLa whole cell lysate: domain and one SH3 domain. -
Deciphering the Molecular Profile of Plaques, Memory Decline And
ORIGINAL RESEARCH ARTICLE published: 16 April 2014 AGING NEUROSCIENCE doi: 10.3389/fnagi.2014.00075 Deciphering the molecular profile of plaques, memory decline and neuron loss in two mouse models for Alzheimer’s disease by deep sequencing Yvonne Bouter 1†,Tim Kacprowski 2,3†, Robert Weissmann4, Katharina Dietrich1, Henning Borgers 1, Andreas Brauß1, Christian Sperling 4, Oliver Wirths 1, Mario Albrecht 2,5, Lars R. Jensen4, Andreas W. Kuss 4* andThomas A. Bayer 1* 1 Division of Molecular Psychiatry, Georg-August-University Goettingen, University Medicine Goettingen, Goettingen, Germany 2 Department of Bioinformatics, Institute of Biometrics and Medical Informatics, University Medicine Greifswald, Greifswald, Germany 3 Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany 4 Human Molecular Genetics, Department for Human Genetics of the Institute for Genetics and Functional Genomics, Institute for Human Genetics, University Medicine Greifswald, Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany 5 Institute for Knowledge Discovery, Graz University of Technology, Graz, Austria Edited by: One of the central research questions on the etiology of Alzheimer’s disease (AD) is the Isidro Ferrer, University of Barcelona, elucidation of the molecular signatures triggered by the amyloid cascade of pathological Spain events. Next-generation sequencing allows the identification of genes involved in disease Reviewed by: Isidro Ferrer, University of Barcelona, processes in an unbiased manner. We have combined this technique with the analysis of Spain two AD mouse models: (1) The 5XFAD model develops early plaque formation, intraneu- Dietmar R. Thal, University of Ulm, ronal Ab aggregation, neuron loss, and behavioral deficits. (2)TheTg4–42 model expresses Germany N-truncated Ab4–42 and develops neuron loss and behavioral deficits albeit without plaque *Correspondence: formation. -
Supplementary Table 1. Mutated Genes That Contain Protein Domains Identified Through Mutation Enrichment Analysis
Supplementary Table 1. Mutated genes that contain protein domains identified through mutation enrichment analysis A. Breast cancers InterPro ID Mutated genes (number of mutations) IPR000219 ARHGEF4(2), ECT2(1), FARP1(1), FLJ20184(1), MCF2L2(1), NET1(1), OBSCN(5), RASGRF2(2), TRAD(1), VAV3(1) IPR000225 APC2(2), JUP(1), KPNA5(2), SPAG6(1) IPR000357 ARFGEF2(2), CMYA4(1), DRIM(2), JUP(1), KPNA5(2), PIK3R4(1), SPAG6(1) IPR000533 AKAP9(2), C10orf39(1), C20orf23(1), CUTL1(1), HOOK1(1), HOOK3(1), KTN1(2), LRRFIP1(3), MYH1(3), MYH9(2), NEF3(1), NF2(1), RSN(1), TAX1BP1(1), TPM4(1) IPR000694 ADAM12(3), ADAMTS19(1), APC2(2), APXL(1), ARID1B(1), BAT2(2), BAT3(1), BCAR1(1), BCL11A(2), BCORL1(1), C14orf155(3), C1orf2(1), C1QB(1), C6orf31(1), C7orf11(1), CD2(1), CENTD3(3), CHD5(3), CIC(3), CMYA1(2), COL11A1(3), COL19A1(2), COL7A1(3), DAZAP1(1), DBN1(3), DVL3(1), EIF5(1), FAM44A(1), FAM47B(1), FHOD1(1), FLJ20584(1), G3BP2(2), GAB1(2), GGA3(1), GLI1(3), GPNMB(2), GRIN2D(3), HCN3(1), HOXA3(2), HOXA4(1), IRS4(1), KCNA5(1), KCNC2(1), LIP8(1), LOC374955(1), MAGEE1(2), MICAL1(2), MICAL‐L1(1), MLLT2(1), MMP15(1), N4BP2(1), NCOA6(2), NHS(1), NUP214(3), ODZ1(3), PER1(2), PER2(1), PHC1(1), PLXNB1(1), PPM1E(2), RAI17(2), RAPH1(2), RBAF600(2), SCARF2(1), SEMA4G(1), SLC16A2(1), SORBS1(1), SPEN(2), SPG4(1), TBX1(1), TCF1(2), TCF7L1(1), TESK1(1), THG‐1(1), TP53(18), TRIF(1), ZBTB3(2), ZNF318(2) IPR000909 CENTB1(2), PLCB1(1), PLCG1(1) IPR000998 AEGP(3), EGFL6(2), PRSS7(1) IPR001140 ABCB10(2), ABCB6(1), ABCB8(2) IPR001164 ARFGAP3(1), CENTB1(2), CENTD3(3), CENTG1(2) IPR001589 -
The Human Gene Connectome As a Map of Short Cuts for Morbid Allele Discovery
The human gene connectome as a map of short cuts for morbid allele discovery Yuval Itana,1, Shen-Ying Zhanga,b, Guillaume Vogta,b, Avinash Abhyankara, Melina Hermana, Patrick Nitschkec, Dror Friedd, Lluis Quintana-Murcie, Laurent Abela,b, and Jean-Laurent Casanovaa,b,f aSt. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065; bLaboratory of Human Genetics of Infectious Diseases, Necker Branch, Paris Descartes University, Institut National de la Santé et de la Recherche Médicale U980, Necker Medical School, 75015 Paris, France; cPlateforme Bioinformatique, Université Paris Descartes, 75116 Paris, France; dDepartment of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; eUnit of Human Evolutionary Genetics, Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Institut Pasteur, F-75015 Paris, France; and fPediatric Immunology-Hematology Unit, Necker Hospital for Sick Children, 75015 Paris, France Edited* by Bruce Beutler, University of Texas Southwestern Medical Center, Dallas, TX, and approved February 15, 2013 (received for review October 19, 2012) High-throughput genomic data reveal thousands of gene variants to detect a single mutated gene, with the other polymorphic genes per patient, and it is often difficult to determine which of these being of less interest. This goes some way to explaining why, variants underlies disease in a given individual. However, at the despite the abundance of NGS data, the discovery of disease- population level, there may be some degree of phenotypic homo- causing alleles from such data remains somewhat limited. geneity, with alterations of specific physiological pathways under- We developed the human gene connectome (HGC) to over- come this problem. -
Rare Gene Deletions in Genetic Generalized and Rolandic Epilepsies
RESEARCH ARTICLE Rare gene deletions in genetic generalized and Rolandic epilepsies Kamel Jabbari1,2☯, Dheeraj R. Bobbili3☯, Dennis Lal1,4,5,6, Eva M. Reinthaler7, Julian Schubert8, Stefan Wolking8, Vishal Sinha9, Susanne Motameny1, Holger Thiele1, Amit Kawalia1, Janine AltmuÈ ller1,10, Mohammad Reza Toliat1, Robert Kraaij11, Jeroen van Rooij11, Andre G. Uitterlinden11, M. Arfan Ikram12, EuroEPINOMICS CoGIE Consortium¶, Federico Zara13, Anna-Elina Lehesjoki14,15, Roland Krause3, Fritz Zimprich7, Thomas Sander1, Bernd A. Neubauer16, Patrick May3, Holger Lerche8, Peter NuÈrnberg1,17,18* a1111111111 1 Cologne Center for Genomics, University of Cologne, Cologne, Germany, 2 Cologne Biocenter, Institute a1111111111 for Genetics, University of Cologne, Cologne, Germany, 3 Luxembourg Centre for Systems Biomedicine, a1111111111 University of Luxembourg, Esch-sur-Alzette, Luxembourg, 4 Psychiatric and Neurodevelopmental Genetics a1111111111 Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of a1111111111 America, 5 Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, 6 Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, 7 Department of Neurology, Medical University of Vienna, Vienna, Austria, 8 Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of TuÈbingen, TuÈbingen, Germany, 9 Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland, 10 Institute of Human Genetics, University of Cologne, OPEN ACCESS Cologne, Germany, 11 Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands, 12 Departments of Epidemiology, Neurology, and Radiology, Erasmus Medical Center, Citation: Jabbari K, Bobbili DR, Lal D, Reinthaler Rotterdam, The Netherlands, 13 Laboratory of Neurogenetics and Neuroscience, Institute G. -
Mouse Baiap2 Knockout Project (CRISPR/Cas9)
https://www.alphaknockout.com Mouse Baiap2 Knockout Project (CRISPR/Cas9) Objective: To create a Baiap2 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Baiap2 gene (NCBI Reference Sequence: NM_130862 ; Ensembl: ENSMUSG00000025372 ) is located on Mouse chromosome 11. 14 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 14 (Transcript: ENSMUST00000075180). Exon 2~3 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Homozygotes for a knock-out allele show mid to late gestation lethality, developmental delay, oligodactyly, subcutaneous edema, and severely impaired cardiac and placental development. Adult homozygotes fail to regulate synaptic plasticity and exhibit hippocampus-associated learning deficits. Exon 2 starts from about 3.51% of the coding region. Exon 2~3 covers 10.41% of the coding region. The size of effective KO region: ~3142 bp. The KO region does not have any other known gene. Page 1 of 9 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 14 Legends Exon of mouse Baiap2 Knockout region Page 2 of 9 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section upstream of Exon 2 is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. -
Essential Role for Abi1 in Embryonic Survival and WAVE2 Complex Integrity
Essential role for Abi1 in embryonic survival and WAVE2 complex integrity Patrycja M. Dubieleckaa,1, Kathrin I. Ladweinb,1, Xiaoling Xionga, Isabelle Migeottec, Anna Chorzalskaa, Kathryn V. Andersonc, Janet A. Sawickid, Klemens Rottnerb,e, Theresia E. Stradalb,f, and Leszek Kotulaa,2 aLaboratory of Cell Signaling, New York Blood Center, New York, NY 10065; bHelmholtz Centre for Infection Research, D-38124 Braunschweig, Germany; cDevelopmental Biology Program, Sloan-Kettering Institute, New York, NY 10065; dLankenau Institute for Medical Research, Wynnewood, PA 19096; eInstitute of Genetics, University of Bonn, 53117 Bonn, Germany; and fInstitute for Molecular Cell Biology, University of Münster, D-48149 Münster, Germany Edited* by Hilary Koprowski, Thomas Jefferson University, Philadelphia, PA, and approved March 15, 2011 (received for review November 11, 2010) Abl interactor 1 (Abi1) plays a critical function in actin cytoskeleton activation to actin polymerization that drives lamellipodia pro- dynamics through participation in the WAVE2 complex. To gain trusion at the plasma membrane (13, 14). WAVE1 and WAVE3 a better understanding of the specific role of Abi1, we generated were proposed to have roles analogous to WAVE2 in the complex (8). Although the function of WAVE3 is less defined, the critical a conditional Abi1-KO mouse model and MEFs lacking Abi1 expres- fl sion. Abi1-KO cells displayed defective regulation of the actin cyto- role of the other two WAVEs in dorsal ruf e formation was demonstrated (15, 16). Mechanistically, it is proposed that native skeleton, and this dysregulation was ascribed to altered activity of WAVE2 complex is inactive (17–19) but is activated at the the WAVE2 complex. -
Characterization of in Vivo Resistance to Osimertinib and JNJ-61186372
Published OnlineFirst August 22, 2017; DOI: 10.1158/1535-7163.MCT-17-0413 Cancer Biology and Translational Studies Molecular Cancer Therapeutics Characterization of In Vivo Resistance to Osimertinib and JNJ-61186372, an EGFR/Met Bispecific Antibody, Reveals Unique and Consensus Mechanisms of Resistance Kristina B. Emdal1, Antje Dittmann1, Raven J. Reddy1, Rebecca S. Lescarbeau1, Sheri L. Moores2, Sylvie Laquerre2, and Forest M. White1 Abstract Approximately 10% of non–small cell lung cancer (NSCLC) targeting EGFR/Met antibody, JNJ-61186372. Tumor-specific patients in the United States and 40% of NSCLC patients in Asia increases in tyrosine-phosphorylated peptides from EGFR family have activating epidermal growth factor receptor (EGFR) muta- members, Shc1 and Gab1 or Src family kinase (SFK) substrates tions and are eligible to receive targeted anti-EGFR therapy. were observed, underscoring a differential ability of tumors to Despite an extension of life expectancy associated with this uniquely escape EGFR inhibition. Although most resistant tumors treatment, resistance to EGFR tyrosine kinase inhibitors and within each treatment group displayed a marked inhibition of anti-EGFR antibodies is almost inevitable. To identify additional EGFR as well as SFK signaling, the combination of EGFR inhibi- signaling routes that can be cotargeted to overcome resistance, we tion (osimertinib) and SFK inhibition (saracatinib or dasatinib) quantified tumor-specific molecular changes that govern resistant led to further decrease in cell growth in vitro. This result suggests cancer cell growth and survival. Mass spectrometry–based quan- that residual SFK signaling mediates therapeutic resistance and titative proteomics was used to profile in vivo signaling changes in that elimination of this signal through combination therapy may 41 therapy-resistant tumors from four xenograft NSCLC models. -
Whole Genome Sequencing Puts Forward Hypotheses on Metastasis Evolution and Therapy in Colorectal Cancer
ARTICLE DOI: 10.1038/s41467-018-07041-z OPEN Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer Naveed Ishaque1,2,3, Mohammed L. Abba4,5, Christine Hauser4,5, Nitin Patil4,5, Nagarajan Paramasivam3,6, Daniel Huebschmann 3, Jörg Hendrik Leupold4,5, Gnana Prakash Balasubramanian2, Kortine Kleinheinz 3, Umut H. Toprak3, Barbara Hutter 2, Axel Benner7, Anna Shavinskaya4, Chan Zhou4,5, Zuguang Gu1,3, Jules Kerssemakers 3, Alexander Marx8, Marcin Moniuszko9, Miroslaw Kozlowski9, Joanna Reszec9, Jacek Niklinski9, Jürgen Eils3, Matthias Schlesner 3,10, Roland Eils 1,3,11, Benedikt Brors 2,12 & 1234567890():,; Heike Allgayer 4,5 Incomplete understanding of the metastatic process hinders personalized therapy. Here we report the most comprehensive whole-genome study of colorectal metastases vs. matched primary tumors. 65% of somatic mutations originate from a common progenitor, with 15% being tumor- and 19% metastasis-specific, implicating a higher mutation rate in metastases. Tumor- and metastasis-specific mutations harbor elevated levels of BRCAness. We confirm multistage progression with new components ARHGEF7/ARHGEF33. Recurrently mutated non-coding elements include ncRNAs RP11-594N15.3, AC010091, SNHG14,3’ UTRs of FOXP2, DACH2, TRPM3, XKR4, ANO5, CBL, CBLB, the latter four potentially dual protagonists in metastasis and efferocytosis-/PD-L1 mediated immunosuppression. Actionable metastasis- specific lesions include FAT1, FGF1, BRCA2, KDR, and AKT2-, AKT3-, and PDGFRA-3’ UTRs. Metastasis specific mutations are enriched in PI3K-Akt signaling, cell adhesion, ECM and hepatic stellate activation genes, suggesting genetic programs for site-specific colonization. Our results put forward hypotheses on tumor and metastasis evolution, and evidence for metastasis-specific events relevant for personalized therapy.