Expression Profiling of Small Intestinal Neuroendocrine Tumors Identifies
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Supporting Information
Supporting Information Goh et al. 10.1073/pnas.1304046110 SI Materials and Methods signal amplification kit was used to amplify the GFP signal Immunofluorescence. For immunofluorescence studies, liver tissue (Perkin-Elmer). was fixed in 4% (vol/vol) paraformaldehyde for 2 h, transferred to a 30% sucrose solution (vol/vol) overnight at 4°C, and sub- ALT and Necrotic Area Quantification. Serum alanine aminotrans- sequently frozen in optimal cutting temperature (OCT) medium. ferase (ALT) levels were measured using an ALT-SL kit (Genzyme To stain for GFP, frozen tissue sections (5 μm) were fixed in Diagnostics). To quantify necrotic cell area, liver sections were 4% paraformaldehyde (vol/vol), permeabilized, and then stained stained with H&E, and 10 random fields from each animal with anti-GFP antibody (1:1,000, Novus Biologicals). A tyramide were analyzed, using ImageJ software. Fig. S1. Immune cell repertoire of regenerating livers. (A and B) Liver regeneration after partial hepatectomy (PH) or toxin-induced injury [carbon tetra- chloride (CCl4)] is associated with recruitment of innate immune cells. Infiltration by innate immune cells was analyzed 2 d after PH or CCl4-mediated injury (n = 4 mice per group). (C and D) The percentages of adaptive immune cells were analyzed 2 d after PH and CCl4-mediated injury in wild-type (WT) BALB/cJ mice (n = 4 mice per group). (E and F) Expression of eotaxin-1 (Ccl11) after PH and/or CCl4-mediated injury (n = 3–8 mice per group and time). *P < 0.05, as de- termined by Student t test. All data are presented as mean ± SEM. -
Ran-GTP Is Non-Essential to Activate Numa for Spindle Pole Focusing, but Dynamically Polarizes HURP to Control Mitotic Spindle
bioRxiv preprint doi: https://doi.org/10.1101/473538; this version posted April 23, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. 1 Ran-GTP is non-essential to activate NuMA for spindle pole focusing, 2 but dynamically polarizes HURP to control mitotic spindle length 3 4 5 Kenta Tsuchiya1#, Hisato Hayashi1#, Momoko Nishina1#, Masako Okumura1#, 6 Yoshikatsu Sato1, Masato T. Kanemaki2,3, Gohta Goshima1, Tomomi Kiyomitsu1,2,4* 7 8 1 Division of Biological Science, Graduate School of Science, Nagoya University, 9 Chikusa-ku, Nagoya 464-8602, Japan. 10 2 Precursory Research for Embryonic Science and Technology (PRESTO) Program, 11 Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, 12 Japan. 13 3 Department of Chromosome Science, National Institute of Genetics, Research 14 Organization of Information and Systems (ROIS), and Department of Genetics, 15 SOKENDAI (The Graduate University of Advanced Studies), Yata 1111, Mishima, 16 Shizuoka 411-8540, Japan. 17 4 Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, 18 Onna-son, Kunigami-gun, Okinawa 904-0495, Japan 19 20 # These authors contributed equally to this work. 21 * Corresponding author: 22 E-mail: [email protected] 23 Phone & Fax: +81-98-966-1609 24 Characters: 5,173 words 25 1 bioRxiv preprint doi: https://doi.org/10.1101/473538; this version posted April 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. -
Supplemental Material For
Supplemental material for Epithelial to mesenchymal transition rewires the molecular path to PI3-Kinase-dependent proliferation Megan B. Salt1,2, Sourav Bandyopadhyay1,3 and Frank McCormick1 Authors Affiliations: 1-Helen Diller Family Comprehensive Cancer Center; 2-Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, California; 3-California Institute for Quantitative Biosciences, San Francisco, California. Supplemental Figure Legends Table S1. EMT associated changes in gene expression. Significantly (A) up- and (B) down- regulated genes in comparing H358-TwistER cells to control H358-GFP expressing cells treated with 100nM 4OHT for 12 days. The four columns on the right are associated with significantly upregulated genes, while the four columns furthest left described significantly downregulated genes. The first column for the up- and downregulated genes shows the Probe ID associated with each gene from the Affymetric Human Gene 1.0 ST microarrays. The gene name are shown in the next column, followed by the log2(fold change) in expression for each gene after 4OHT treatment in the H358-TwistER cells. The final column shows the p-value for each gene adjusted for the false discovery rate. Figure S1. Akt inhibition reduces serum-independent proliferation. (A) Proliferation of H358- TwistER cells with increasing concentrations (uM) of GSK-690693 (top) or MK-2206 (bottom). (B) Lysates from H358-TwistER cells treated for 48hrs in serum free media with indicated concentrations of GSK-690693 (top), or MK-2206 (bottom). Figure S2. The effects of TGFβ1 are specific to epithelial cells and lead to reduced serum- independent proliferation. (A) Proliferation of untreated (top) or TGFβ1 pre-treated (bottom) H358 and H441 cells in the presence (10%) or absence (SS) of serum. -
Analysis of Protein Complexes Through Model-Based Biclustering of Label-Free Quantitative AP-MS Data
Molecular Systems Biology 6; Article number 385; doi:10.1038/msb.2010.41 Citation: Molecular Systems Biology 6:385 & 2010 EMBO and Macmillan Publishers Limited All rights reserved 1744-4292/10 www.molecularsystemsbiology.com REPORT Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data Hyungwon Choi1, Sinae Kim2, Anne-Claude Gingras3,4 and Alexey I Nesvizhskii1,5,* 1 Department of Pathology, University of Michigan, Ann Arbor, MI, USA, 2 Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA, 3 Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, Ontario, Canada, 4 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada and 5 Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA * Corresponding author. Department of Pathology, University of Michigan, 1301 Catherine, 4237 MS1, Ann Arbor, MI 48109, USA. Tel.: þ 1 734 764 3516; Fax: þ 1 734 936 7361; E-mail: [email protected] Received 28.8.09; accepted 7.5.10 Affinity purification followed by mass spectrometry (AP-MS) has become a common approach for identifying protein–protein interactions (PPIs) and complexes. However, data analysis and visualization often rely on generic approaches that do not take advantage of the quantitative nature of AP-MS. We present a novel computational method, nested clustering, for biclustering of label-free quantitative AP-MS data. Our approach forms bait clusters based on the similarity of quantitative interaction profiles and identifies submatrices of prey proteins showing consistent quantitative association within bait clusters. In doing so, nested clustering effectively addresses the problem of overrepresentation of interactions involving baits proteins as compared with proteins only identified as preys. -
The Expanded Endocannabinoid System/Endocannabinoidome As a Potential Target for Treating Diabetes Mellitus
Current Diabetes Reports (2019) 19:117 https://doi.org/10.1007/s11892-019-1248-9 OBESITY (KM GADDE, SECTION EDITOR) The Expanded Endocannabinoid System/Endocannabinoidome as a Potential Target for Treating Diabetes Mellitus Alain Veilleux1,2,3 & Vincenzo Di Marzo1,2,3,4,5 & Cristoforo Silvestri3,4,5 # Springer Science+Business Media, LLC, part of Springer Nature 2019 Abstract Purpose of Review The endocannabinoid (eCB) system, i.e. the receptors that respond to the psychoactive component of cannabis, their endogenous ligands and the ligand metabolic enzymes, is part of a larger family of lipid signals termed the endocannabinoidome (eCBome). We summarize recent discoveries of the roles that the eCBome plays within peripheral tissues in diabetes, and how it is being targeted, in an effort to develop novel therapeutics for the treatment of this increasingly prevalent disease. Recent Findings As with the eCB system, many eCBome members regulate several physiological processes, including energy intake and storage, glucose and lipid metabolism and pancreatic health, which contribute to the development of type 2 diabetes (T2D). Preclinical studies increasingly support the notion that targeting the eCBome may beneficially affect T2D. Summary The eCBome is implicated in T2D at several levels and in a variety of tissues, making this complex lipid signaling system a potential source of many potential therapeutics for the treatments for T2D. Keywords Endocannabinoidome . Bioactive lipids . Peripheral tissues . Glucose . Insulin Introduction: The Endocannabinoid System cannabis-derived natural product, Δ9-tetrahydrocannabinol and its Subsequent Expansion (THC), responsible for most of the psychotropic, euphoric to the “Endocannabinoidome” and appetite-stimulating actions (via CB1 receptors) and immune-modulatory effects (via CB2 receptors) of marijuana, The discovery of two G protein-coupled receptors, the canna- opened the way to the identification of the endocannabinoids binoid receptor type-1 (CB1) and − 2 (CB2) [1, 2], for the (eCBs). -
Globin Gene Expression in Correlation with G Protein-Related Genes During
Čokić et al. BMC Genomics 2013, 14:116 http://www.biomedcentral.com/1471-2164/14/116 RESEARCH ARTICLE Open Access Globin gene expression in correlation with G protein-related genes during erythroid differentiation Vladan P Čokić1*, Reginald D Smith2, Angélique Biancotto3, Constance T Noguchi4, Raj K Puri5 and Alan N Schechter4 Abstract Background: The guanine nucleotide binding protein (G protein)-coupled receptors (GPCRs) regulate cell growth, proliferation and differentiation. G proteins are also implicated in erythroid differentiation, and some of them are expressed principally in hematopoietic cells. GPCRs-linked NO/cGMP and p38 MAPK signaling pathways already demonstrated potency for globin gene stimulation. By analyzing erythroid progenitors, derived from hematopoietic cells through in vitro ontogeny, our study intends to determine early markers and signaling pathways of globin gene regulation and their relation to GPCR expression. Results: Human hematopoietic CD34+ progenitors are isolated from fetal liver (FL), cord blood (CB), adult bone marrow (BM), peripheral blood (PB) and G-CSF stimulated mobilized PB (mPB), and then differentiated in vitro into erythroid progenitors. We find that growth capacity is most abundant in FL- and CB-derived erythroid cells. The erythroid progenitor cells are sorted as 100% CD71+, but we did not find statistical significance in the variations of CD34, CD36 and GlyA antigens and that confirms similarity in maturation of studied ontogenic periods. During ontogeny, beta-globin gene expression reaches maximum levels in cells of adult blood origin (176 fmol/μg), while gamma-globin gene expression is consistently up-regulated in CB-derived cells (60 fmol/μg). During gamma-globin induction by hydroxycarbamide, we identify stimulated GPCRs (PTGDR, PTGER1) and GPCRs-coupled genes known to be activated via the cAMP/PKA (ADIPOQ), MAPK pathway (JUN) and NO/cGMP (PRPF18) signaling pathways. -
Synaptamide Activates the Adhesion GPCR GPR110 (ADGRF1) Through GAIN Domain Binding
ARTICLE https://doi.org/10.1038/s42003-020-0831-6 OPEN Synaptamide activates the adhesion GPCR GPR110 (ADGRF1) through GAIN domain binding Bill X. Huang1, Xin Hu2, Heung-Sun Kwon1, Cheng Fu1, Ji-Won Lee1, Noel Southall2, Juan Marugan2 & ✉ Hee-Yong Kim1 1234567890():,; Adhesion G protein-coupled receptors (aGPCR) are characterized by a large extracellular region containing a conserved GPCR-autoproteolysis-inducing (GAIN) domain. Despite their relevance to several disease conditions, we do not understand the molecular mechanism by which aGPCRs are physiologically activated. GPR110 (ADGRF1) was recently deorphanized as the functional receptor of N-docosahexaenoylethanolamine (synaptamide), a potent synap- togenic metabolite of docosahexaenoic acid. Thus far, synaptamide is the first and only small- molecule endogenous ligand of an aGPCR. Here, we demonstrate the molecular basis of synaptamide-induced activation of GPR110 in living cells. Using in-cell chemical cross-linking/ mass spectrometry, computational modeling and mutagenesis-assisted functional assays, we discover that synaptamide specifically binds to the interface of GPR110 GAIN subdomains through interactions with residues Q511, N512 and Y513, causing an intracellular conforma- tional change near TM6 that triggers downstream signaling. This ligand-induced GAIN-tar- geted activation mechanism provides a framework for understanding the physiological function of aGPCRs and therapeutic targeting in the GAIN domain. 1 Laboratory of Molecular Signaling, National Institute on Alcohol Abuse -
Functional Annotation of Genes Overlapping Copy Number Variants in Autistic Patients: Focus on Axon Pathfinding
136 Current Genomics, 2010, 11, 136-145 Functional Annotation of Genes Overlapping Copy Number Variants in Autistic Patients: Focus on Axon Pathfinding Silvia Sbacchi1, Francesco Acquadro2, Ignazio Calò1, Francesco Calì3 and Valentino Romano*,1,3 1Dipartimento di Oncologia Sperimentale e Applicazioni Cliniche, Università degli Studi di Palermo, Palermo; 2Molecular Cytogenetics Group, Centro Nacional de Investigaciones Oncologicas (C.N.I.O.), and Centro de Investiga- ciones de Enfermidades Raras (CIBERER), Madrid, Spain; 3Associazione Oasi Maria SS. (I.R.C.C.S.), Troina (EN), Italy Abstract: We have used Gene Ontology (GO) and pathway analyses to uncover the common functions associated to the genes overlapping Copy Number Variants (CNVs) in autistic patients. Our source of data were four published studies [1- 4]. We first applied a two-step enrichment strategy for autism-specific genes. We fished out from the four mentioned stud- ies a list of 2928 genes overall overlapping 328 CNVs in patients and we first selected a sub-group of 2044 genes after excluding those ones that are also involved in CNVs reported in the Database of Genomic Variants (enrichment step 1). We then selected from the step 1-enriched list a sub-group of 514 genes each of which was found to be deleted or dupli- cated in at least two patients (enrichment step 2). The number of statistically significant processes and pathways identified by the Database for Annotation, Visualization and Integrated Discovery and Ingenuity Pathways Analysis softwares with the step 2-enriched list was significantly higher compared to the step 1-enriched list. In addition, statistically significant GO terms, biofunctions and pathways related to nervous system development and function were exclusively identified by the step 2-enriched list of genes. -
Small Gtpase Ran and Ran-Binding Proteins
BioMol Concepts, Vol. 3 (2012), pp. 307–318 • Copyright © by Walter de Gruyter • Berlin • Boston. DOI 10.1515/bmc-2011-0068 Review Small GTPase Ran and Ran-binding proteins Masahiro Nagai 1 and Yoshihiro Yoneda 1 – 3, * highly abundant and strongly conserved GTPase encoding ∼ 1 Biomolecular Dynamics Laboratory , Department a 25 kDa protein primarily located in the nucleus (2) . On of Frontier Biosciences, Graduate School of Frontier the one hand, as revealed by a substantial body of work, Biosciences, Osaka University, 1-3 Yamada-oka, Suita, Ran has been found to have widespread functions since Osaka 565-0871 , Japan its initial discovery. Like other small GTPases, Ran func- 2 Department of Biochemistry , Graduate School of Medicine, tions as a molecular switch by binding to either GTP or Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871 , GDP. However, Ran possesses only weak GTPase activ- Japan ity, and several well-known ‘ Ran-binding proteins ’ aid in 3 Japan Science and Technology Agency , Core Research for the regulation of the GTPase cycle. Among such partner Evolutional Science and Technology, Osaka University, 1-3 molecules, RCC1 was originally identifi ed as a regulator of Yamada-oka, Suita, Osaka 565-0871 , Japan mitosis in tsBN2, a temperature-sensitive hamster cell line (3) ; RCC1 mediates the conversion of RanGDP to RanGTP * Corresponding author in the nucleus and is mainly associated with chromatin (4) e-mail: [email protected] through its interactions with histones H2A and H2B (5) . On the other hand, the GTP hydrolysis of Ran is stimulated by the Ran GTPase-activating protein (RanGAP) (6) , in con- Abstract junction with Ran-binding protein 1 (RanBP1) and/or the large nucleoporin Ran-binding protein 2 (RanBP2, also Like many other small GTPases, Ran functions in eukaryotic known as Nup358). -
The Role of P53 in Progression of Cutaneous Squamous Cell Carcinoma
cancers Review The Role of p53 in Progression of Cutaneous Squamous Cell Carcinoma Minna Piipponen 1,2,3,† , Pilvi Riihilä 1,2,† , Liisa Nissinen 1,2 and Veli-Matti Kähäri 1,2,* 1 Department of Dermatology, University of Turku and Turku University Hospital, Hämeentie 11 TE6, FI-20520 Turku, Finland; mmpiip@utu.fi (M.P.); pimati@utu.fi (P.R.); liinis@utu.fi (L.N.) 2 FICAN West Cancer Centre Research Laboratory, University of Turku and Turku University Hospital, Kiinamyllynkatu 10, FI-20520 Turku, Finland 3 Center for Molecular Medicine, Department of Medicine Solna, Dermatology and Venereology Division, Karolinska Institute, 17176 Stockholm, Sweden * Correspondence: veli-matti.kahari@utu.fi; Tel.: +358-2-3131600 † These authors contributed equally to this work. Simple Summary: Skin cancers are the most common types of cancer worldwide, and their incidence is increasing. Epidermal keratinocyte-derived cutaneous squamous cell carcinoma (cSCC) is the most common metastatic skin cancer, and it is associated with poor prognosis in the advanced stage. The most important risk factor for cSCC is long-term exposure to solar ultraviolet radiation, which induces oncogenic mutations in epidermal keratinocytes. The most common mutations are inactivating mutations in tumor suppressor p53, which result in accumulation of additional mutations. Recently, the role of p53 in the progression and invasion of cSCC has also been elucidated. In this review we will discuss the role of p53 in development of cSCC and as a potential new therapeutic target in advanced cSCC. Citation: Piipponen, M.; Riihilä, P.; Abstract: Skin cancers are the most common types of cancer worldwide, and their incidence is Nissinen, L.; Kähäri, V.-M. -
STRIPAK Complexes in Cell Signaling and Cancer
Oncogene (2016), 1–9 © 2016 Macmillan Publishers Limited All rights reserved 0950-9232/16 www.nature.com/onc REVIEW STRIPAK complexes in cell signaling and cancer Z Shi1,2, S Jiao1 and Z Zhou1,3 Striatin-interacting phosphatase and kinase (STRIPAK) complexes are striatin-centered multicomponent supramolecular structures containing both kinases and phosphatases. STRIPAK complexes are evolutionarily conserved and have critical roles in protein (de) phosphorylation. Recent studies indicate that STRIPAK complexes are emerging mediators and regulators of multiple vital signaling pathways including Hippo, MAPK (mitogen-activated protein kinase), nuclear receptor and cytoskeleton remodeling. Different types of STRIPAK complexes are extensively involved in a variety of fundamental biological processes ranging from cell growth, differentiation, proliferation and apoptosis to metabolism, immune regulation and tumorigenesis. Growing evidence correlates dysregulation of STRIPAK complexes with human diseases including cancer. In this review, we summarize the current understanding of the assembly and functions of STRIPAK complexes, with a special focus on cell signaling and cancer. Oncogene advance online publication, 15 February 2016; doi:10.1038/onc.2016.9 INTRODUCTION in the central nervous system and STRN4 is mostly abundant in Recent proteomic studies identified a group of novel multi- the brain and lung, whereas STRN3 is ubiquitously expressed in 5–9 component complexes named striatin (STRN)-interacting phos- almost all tissues. STRNs share a -
Exploring the Conformational Landscape and Stability of Aurora a Using Ion-Mobility Mass Spectrometry and Molecular Modelling
bioRxiv preprint doi: https://doi.org/10.1101/2021.08.30.458190; this version posted August 31, 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. Exploring the conformational landscape and stability of Aurora A using ion-mobility mass spectrometry and molecular modelling Lauren J. Tomlinson1, 2, Matthew Batchelor3, Joscelyn Sarsby1, Dominic P. Byrne2, Philip Brown- ridge1, Richard Bayliss3, Patrick A. Eyers2 and Claire E. Eyers1, 2*. 1 Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, U.K. 2 Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K. 3 Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, U.K. *Correspondence: Claire E. Eyers ([email protected]) ABSTRACT: Protein kinase inhibitors are proving highly effective in helping treat a number of non- communicable diseases driven by aberrant kinase signaling. They are also extremely valuable as chemical tools to help delineate cellular roles of kinase signaling complexes. The binding of small molecule inhibitors induces conformational effects on kinase dynamics; evaluating the effect of such interactions can assist in developing specific inhibitors and is deemed imperative to under- stand both inhibition and resistance mechanisms. Using gas-phase ion mobility-mass spectrome- try (IM-MS) we characterized changes in the conformational landscape and stability of the protein kinase Aurora A (Aur A) driven by binding of the physiological activator TPX2 or small molecule inhibition.