Molecular Mechanisms of Leukocyte Migration and Its Potential Targeting&Mdash;Lessons Learned from MKL1/SRF-Related Primary
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Lectin-Affinity Chromatography Brain Glycoproteomics and Alzheimer
50 DOI 10.1002/prca.201000070 Proteomics Clin. Appl. 2011, 5, 50–56 REVIEW Lectin-affinity chromatography brain glycoproteomics and Alzheimer disease: Insights into protein alterations consistent with the pathology and progression of this dementing disorder D. Allan Butterfield and Joshua B. Owen Department of Chemistry, Center of Membrane Sciences, and Sanders-Brown Center on Aging, University of Kentucky, Lexington KY, USA Alzheimer disease (AD) is a neurodegenerative disorder characterized pathologically by the Received: July 7, 2010 accumulation of senile plaques and neurofibrillary tangles, and both these pathological Revised: August 4, 2010 hallmarks of AD are extensively modified by glycosylation. Mounting evidence shows that Accepted: August 10, 2010 alterations in glycosylation patterns influence the pathogenesis and progression of AD, but the vast number of glycan motifs and potential glycosylation sites of glycoproteins has made the field of glycobiology difficult. However, the advent of glycoproteomics has produced major strides in glycoprotein identification and glycosylation site mapping. The use of lectins, proteins that have strong affinity for specific carbohydrate epitopes, to enrich glycoprotein fractions coupled with modern MS, have yielded techniques to elucidate the glycoproteome in AD. Proteomic studies have identified brain proteins in AD and arguably the earliest form of AD, mild cognitive impairment, with altered affinity for Concanavalin-A and wheat germ agglutinin lectins that are consistent with the pathology and progression of this disorder. This is a relatively nascent field of proteomics research in brain, so future studies of lectin-based brain protein separations may lead to additional insights into AD pathogenesis and progression. Keywords: Alzheimers disease (AD) / Lectin-chromatography / Mild cognitive impairment (MCI) / MS / Synaptic alterations 1 Introduction ized pathologically by the accumulation of senile plaques (SPs) and neurofibrillary tangles (NFTs). -
Targeted Genes and Methodology Details for Neuromuscular Genetic Panels
Targeted Genes and Methodology Details for Neuromuscular Genetic Panels Reference transcripts based on build GRCh37 (hg19) interrogated by Neuromuscular Genetic Panels Next-generation sequencing (NGS) and/or Sanger sequencing is performed Motor Neuron Disease Panel to test for the presence of a mutation in these genes. Gene GenBank Accession Number Regions of homology, high GC-rich content, and repetitive sequences may ALS2 NM_020919 not provide accurate sequence. Therefore, all reported alterations detected ANG NM_001145 by NGS are confirmed by an independent reference method based on laboratory developed criteria. However, this does not rule out the possibility CHMP2B NM_014043 of a false-negative result in these regions. ERBB4 NM_005235 Sanger sequencing is used to confirm alterations detected by NGS when FIG4 NM_014845 appropriate.(Unpublished Mayo method) FUS NM_004960 HNRNPA1 NM_031157 OPTN NM_021980 PFN1 NM_005022 SETX NM_015046 SIGMAR1 NM_005866 SOD1 NM_000454 SQSTM1 NM_003900 TARDBP NM_007375 UBQLN2 NM_013444 VAPB NM_004738 VCP NM_007126 ©2018 Mayo Foundation for Medical Education and Research Page 1 of 14 MC4091-83rev1018 Muscular Dystrophy Panel Muscular Dystrophy Panel Gene GenBank Accession Number Gene GenBank Accession Number ACTA1 NM_001100 LMNA NM_170707 ANO5 NM_213599 LPIN1 NM_145693 B3GALNT2 NM_152490 MATR3 NM_199189 B4GAT1 NM_006876 MYH2 NM_017534 BAG3 NM_004281 MYH7 NM_000257 BIN1 NM_139343 MYOT NM_006790 BVES NM_007073 NEB NM_004543 CAPN3 NM_000070 PLEC NM_000445 CAV3 NM_033337 POMGNT1 NM_017739 CAVIN1 NM_012232 POMGNT2 -
SETD1B-Associated Neurodevelopmental Disorder
Genotype- phenotype correlations J Med Genet: first published as 10.1136/jmedgenet-2019-106756 on 16 June 2020. Downloaded from Original research SETD1B- associated neurodevelopmental disorder Alexandra Roston ,1 Dan Evans,2 Harinder Gill,1,3 Margaret McKinnon,1 Bertrand Isidor,4 Benjamin Cogné ,4,5 Jill Mwenifumbo,1,6 Clara van Karnebeek,7,8 Jianghong An,9 Steven J M Jones,9 Matthew Farrer,2 Michelle Demos,10 Mary Connolly,10 William T Gibson ,1 CAUSES Study, EPGEN Study ► Additional material is ABSTRACT same gene allows causal inference for those geno- published online only. To view Background Dysfunction of histone methyltransferases type–phenotype correlations. This is especially true please visit the journal online (http:// dx. doi. org/ 10. 1136/ and chromatin modifiers has been implicated in complex when perturbation of the general biological process jmedgenet- 2019- 106756). neurodevelopmental syndromes and cancers. SETD1B has, in similar contexts, been shown reproducibly encodes a lysine- specific methyltransferase that assists to result in similar phenotypes. For numbered affiliations see in transcriptional activation of genes by depositing Individual case reports have appeared in the end of article. H3K4 methyl marks. Previous reports of patients with literature describing neurodevelopmental delays rare variants in SETD1B describe a distinctive phenotype associated with rare coding variants in SETD1B, Correspondence to Dr Alexandra Roston, that includes seizures, global developmental delay and and with hemizygosity for SETD1B due to CNVs. Department of Medical intellectual disability. Here we show that pathogenic variants within Genetics, The University of Methods Two of the patients described herein were SETD1B contribute to a conserved phenotype that British Columbia, Vancouver, BC identified via genome-wide and exome-wide testing, includes intellectual disability and childhood- onset, V6T 1Z4, Canada; with microarray and research- based exome, through treatment- refractory seizures. -
MRTF: Basic Biology and Role in Kidney Disease
International Journal of Molecular Sciences Review MRTF: Basic Biology and Role in Kidney Disease Maria Zena Miranda 1, Zsuzsanna Lichner 1, Katalin Szászi 1,2 and András Kapus 1,2,3,* 1 Keenan Research Centre for Biomedical Science of the St. Michael’s Hospital, Toronto, ON M5B 1W8, Canada; [email protected] (M.Z.M.); [email protected] (Z.L.); [email protected] (K.S.) 2 Department of Surgery, University of Toronto, Toronto, ON M5T 1P5, Canada 3 Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada * Correspondence: [email protected] Abstract: A lesser known but crucially important downstream effect of Rho family GTPases is the regulation of gene expression. This major role is mediated via the cytoskeleton, the organization of which dictates the nucleocytoplasmic shuttling of a set of transcription factors. Central among these is myocardin-related transcription factor (MRTF), which upon actin polymerization translocates to the nucleus and binds to its cognate partner, serum response factor (SRF). The MRTF/SRF complex then drives a large cohort of genes involved in cytoskeleton remodeling, contractility, extracellular matrix organization and many other processes. Accordingly, MRTF, activated by a variety of mechanical and chemical stimuli, affects a plethora of functions with physiological and pathological relevance. These include cell motility, development, metabolism and thus metastasis formation, inflammatory responses and—predominantly-organ fibrosis. The aim of this review is twofold: to provide an up- to-date summary about the basic biology and regulation of this versatile transcriptional coactivator; and to highlight its principal involvement in the pathobiology of kidney disease. -
Single-Cell Analysis Uncovers Fibroblast Heterogeneity
ARTICLE https://doi.org/10.1038/s41467-020-17740-1 OPEN Single-cell analysis uncovers fibroblast heterogeneity and criteria for fibroblast and mural cell identification and discrimination ✉ Lars Muhl 1,2 , Guillem Genové 1,2, Stefanos Leptidis 1,2, Jianping Liu 1,2, Liqun He3,4, Giuseppe Mocci1,2, Ying Sun4, Sonja Gustafsson1,2, Byambajav Buyandelger1,2, Indira V. Chivukula1,2, Åsa Segerstolpe1,2,5, Elisabeth Raschperger1,2, Emil M. Hansson1,2, Johan L. M. Björkegren 1,2,6, Xiao-Rong Peng7, ✉ Michael Vanlandewijck1,2,4, Urban Lendahl1,8 & Christer Betsholtz 1,2,4 1234567890():,; Many important cell types in adult vertebrates have a mesenchymal origin, including fibro- blasts and vascular mural cells. Although their biological importance is undisputed, the level of mesenchymal cell heterogeneity within and between organs, while appreciated, has not been analyzed in detail. Here, we compare single-cell transcriptional profiles of fibroblasts and vascular mural cells across four murine muscular organs: heart, skeletal muscle, intestine and bladder. We reveal gene expression signatures that demarcate fibroblasts from mural cells and provide molecular signatures for cell subtype identification. We observe striking inter- and intra-organ heterogeneity amongst the fibroblasts, primarily reflecting differences in the expression of extracellular matrix components. Fibroblast subtypes localize to discrete anatomical positions offering novel predictions about physiological function(s) and regulatory signaling circuits. Our data shed new light on the diversity of poorly defined classes of cells and provide a foundation for improved understanding of their roles in physiological and pathological processes. 1 Karolinska Institutet/AstraZeneca Integrated Cardio Metabolic Centre, Blickagången 6, SE-14157 Huddinge, Sweden. -
Tropomyosin Isoform Tpm2.1 Regulates Collective and Amoeboid Cell Migration and Cell Aggregation in Breast Epithelial Cells
www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 56), pp: 95192-95205 Research Paper Tropomyosin isoform Tpm2.1 regulates collective and amoeboid cell migration and cell aggregation in breast epithelial cells HyeRim Shin1, Dayoung Kim1 and David M. Helfman1 1Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea Correspondence to: David M. Helfman, email: [email protected] Keywords: collective cell migration, amoeboid migration, cell aggregation, AXL receptor tyrosine kinase, metastasis Received: November 17, 2016 Accepted: June 20, 2017 Published: July 12, 2017 Copyright: Shin et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Metastasis dissemination is the result of various processes including cell migration and cell aggregation. These processes involve alterations in the expression and organization of cytoskeletal and adhesion proteins in tumor cells. Alterations in actin filaments and their binding partners are known to be key players in metastasis. Downregulation of specific tropomyosin (Tpm) isoforms is a common characteristic of transformed cells. In this study, we examined the role of Tpm2.1 in non-transformed MCF10A breast epithelial cells in cell migration and cell aggregation, because this isoform is downregulated in primary and metastatic breast cancer as well as various breast cancer cell lines. Downregulation of Tpm2.1 using siRNA or shRNA resulted in retardation of collective cell migration but increase in single cell migration and invasion. -
Competing Endogenous RNA Network Analysis Reveals Pivotal Cernas in Bladder Urothelial Carcinoma
808 Original Article Competing endogenous RNA network analysis reveals pivotal ceRNAs in bladder urothelial carcinoma Yangle Li, Xiongbing Zu, Xiheng Hu, Cheng Zhao, Miao Mo, Benyi Fan Department of Urology, Xiangya Hospital, Central South University, Changsha, China Contributions: (I) Conception and design: All authors; (II) Administrative support: B Fan; (III) Provision of study materials or patients: None; (IV) Collection and assembly of data: Y Li, X Zu, X Hu; (V) Data analysis and interpretation: Y Li, X Zu, C Zhao, M Mo; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors. Correspondence to: Benyi Fan. 87 Xiangya Road, Changsha 410008, China. Email: [email protected]. Background: Bladder urothelial cancer (BUC) has become one of the most frequently occurring malignant tumors worldwide and it is of great importance to explore the molecular pathogenesis of bladder cancer. Emerging evidence has demonstrated that dysregulation of noncoding RNAs is critically involved in the tumorigenesis and progression of BUC. Long noncoding RNAs (lncRNAs) can act as microRNA (miRNA) sponges to regulate protein-coding gene expression and therefore form a competing endogenous RNA (ceRNA) network. ceRNA networks have been proven to play vital roles during tumorigenesis and progression. Elements involved in the ceRNA network have also been identified as potential therapeutic targets and prognostic biomarkers in various tumors. Understanding the regulatory mechanisms and functional roles of the ceRNA system will help understand tumorigenesis, progression mechanisms of BUC and develop therapeutics against cancer. Methods: In this study, we utilized the TCGA database and analyzed the multilevel expression profile of BUC. ceRNA regulatory networks were constructed by integrating tumor progression and prognosis information. -
Snapshot: Actin Regulators II Anosha D
SnapShot: Actin Regulators II Anosha D. Siripala and Matthew D. Welch Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA Representative Proteins Protein Family H. sapiens D. melanogaster C. elegans A. thaliana S. cerevisiae Endocytosis and Exocytosis ABP1/drebrin mABP1, drebrin, drebrin- †Q95RN0 †Q9XUT0 Abp1 like EPS15 EPS15 Eps-15 EHS-1 †Q56WL2 Pan1 HIP1R HIP1R †Q8MQK1 †O62142 Sla2 Synapsin synapsin Ia, Ib, IIa, IIb, III Synapsin SNN-1 Plasma Membrane Association Anillin anillin Scraps ANI-1, 2, 3 Annexins annexin A1–11, 13 (actin Annexin B9-11 NEX-1–4 ANN1-8 binding: 1, 2, 6) ERM proteins ezrin, radixin, moesin DMoesin ERM-1 MARCKS MARCKS, MRP/ Akap200 MACMARCKS/F52 Merlin *merlin/NF2 Merlin NFM-1 Protein 4.1 4.1R, G, N, B Coracle Spectrin α-spectrin (1–2), β-spectrin α-spectrin, β-spectrin, β heavy- SPC-1 (α-spectrin), UNC-70 (1–4), β heavy-spectrin/ spectrin/Karst (β-spectrin), SMA-1 (β heavy- karst spectrin) Identifi ed Cellular Role: X Membrane traffi cking and phagocytosis Cell-Cell Junctions X Cytokinesis α-catenin α-catenin 1–3 α-catenin HMP-1 X Cell surface organization and dynamics X Cell adhesion Afadin afadin/AF6 Canoe AFD-1 X Multiple functions ZO-1 ZO-1, ZO-2, ZO-3 ZO-1/Polychaetoid †Q56VX4 X Other/unknown Cell-Extracellular Matrix Junctions †UNIPROT database accession number *Mutation linked to human disease Dystrophin/utrophin *dystrophin, utrophin/ Dystrophin DYS-1 DRP1, DRP2 LASP LASP-1, LASP-2, LIM- Lasp †P34416 nebulette Palladin palladin Parvin α-, β-, χ-parvin †Q9VWD0 PAT-6 -
Identification of the Fatty Acid Synthase Interaction Network Via Itraq-Based Proteomics Indicates the Potential Molecular Mecha
Huang et al. Cancer Cell Int (2020) 20:332 https://doi.org/10.1186/s12935-020-01409-2 Cancer Cell International PRIMARY RESEARCH Open Access Identifcation of the fatty acid synthase interaction network via iTRAQ-based proteomics indicates the potential molecular mechanisms of liver cancer metastasis Juan Huang1, Yao Tang1, Xiaoqin Zou1, Yi Lu1, Sha She1, Wenyue Zhang1, Hong Ren1, Yixuan Yang1,2* and Huaidong Hu1,2* Abstract Background: Fatty acid synthase (FASN) is highly expressed in various types of cancer and has an important role in carcinogenesis and metastasis. To clarify the mechanisms of FASN in liver cancer invasion and metastasis, the FASN protein interaction network in liver cancer was identifed by targeted proteomic analysis. Methods: Wound healing and Transwell assays was performed to observe the efect of FASN during migration and invasion in liver cancer. Isobaric tags for relative and absolute quantitation (iTRAQ)-based mass spectrometry were used to identify proteins interacting with FASN in HepG2 cells. Diferential expressed proteins were validated by co-immunoprecipitation, western blot analyses and confocal microscopy. Western blot and reverse transcription- quantitative polymerase chain reaction (RT-qPCR) were performed to demonstrate the mechanism of FASN regulating metastasis. Results: FASN knockdown inhibited migration and invasion of HepG2 and SMMC7721 cells. A total of, 79 proteins interacting with FASN were identifed. Additionally, gene ontology term enrichment analysis indicated that the majority of biological regulation and cellular processes that the FASN-interacting proteins were associated with. Co- precipitation and co-localization of FASN with fascin actin-bundling protein 1 (FSCN1), signal-induced proliferation- associated 1 (SIPA1), spectrin β, non-erythrocytic 1 (SPTBN1) and CD59 were evaluated. -
Substrate Stiffness-Dependent Regulation of the SRF−Mkl1 Co-Activator Complex Requires the Inner Nuclear Membrane Protein Emerin Margaret K
© 2017. Published by The Company of Biologists Ltd | Journal of Cell Science (2017) 130, 2111-2118 doi:10.1242/jcs.197517 SHORT REPORT Substrate stiffness-dependent regulation of the SRF−Mkl1 co-activator complex requires the inner nuclear membrane protein Emerin Margaret K. Willer and Christopher W. Carroll* ABSTRACT transcription is thought to underlie persistent myofibroblast The complex comprising serum response factor (SRF) and activation (Zhou et al., 2013). Thus, determining how mechanical − megakaryoblastic leukemia 1 protein (Mkl1) promotes myofibroblast cues modulate SRF Mkl1-dependent gene expression is critical to differentiation during wound healing. SRF−Mkl1 is sensitive to the understand wound healing and pathologies caused by altered ECM mechanical properties of the extracellular environment; but how cells mechanics. sense and transduce mechanical cues to modulate SRF−Mkl1- The nuclear lamina is a network of nuclear envelope-associated dependent gene expression is not well understood. Here, we intermediate filaments and their associated proteins. Recently, the demonstrate that the nuclear lamina-associated inner nuclear nuclear lamina proteins Lamins A/C and Emerin were shown to − membrane protein Emerin stimulates SRF−Mkl1-dependent gene promote SRF Mkl1-dependent transcription (Ho et al., 2014). activity in a substrate stiffness-dependent manner. Specifically, Actin-generated forces regulate Lamins A/C and Emerin (Buxboim Emerin was required for Mkl1 nuclear accumulation and maximal et al., 2014; Guilluy et al., 2014; Swift et al., 2013), but whether the − SRF−Mkl1-dependent gene expression in response to serum nuclear lamina contributes to the mechanical control of SRF Mkl1- stimulation of cells grown on stiff substrates but was dispensable on dependent gene expression has not been tested. -
UC San Diego UC San Diego Electronic Theses and Dissertations
UC San Diego UC San Diego Electronic Theses and Dissertations Title Regulation of gene expression programs by serum response factor and megakaryoblastic leukemia 1/2 in macrophages Permalink https://escholarship.org/uc/item/8cc7d0t0 Author Sullivan, Amy Lynn Publication Date 2009 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Regulation of Gene Expression Programs by Serum Response Factor and Megakaryoblastic Leukemia 1/2 in Macrophages A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biomedical Sciences by Amy Lynn Sullivan Committee in charge: Professor Christopher K. Glass, Chair Professor Stephen M. Hedrick Professor Marc R. Montminy Professor Nicholas J. Webster Professor Joseph L. Witztum 2009 Copyright Amy Lynn Sullivan, 2009 All rights reserved. The Dissertation of Amy Lynn Sullivan is approved, and it is acceptable in quality and form for publication on microfilm and electronically: ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ Chair University of California, San Diego 2009 iii DEDICATION To my husband, Shane, for putting up with me through all of the long hours, last minute late nights, and for not letting me quit no matter how many times my projects fell apart. To my son, Tyler, for always making me smile and for making every day an adventure. To my gifted colleagues, for all of the thought-provoking discussions, technical help and moral support through the roller- coaster ride that has been my graduate career. To my family and friends, for all of your love and support. I couldn’t have done it without you! iv EPIGRAPH If at first you don’t succeed, try, try, again. -
Supplementary Material Contents
Supplementary Material Contents Immune modulating proteins identified from exosomal samples.....................................................................2 Figure S1: Overlap between exosomal and soluble proteomes.................................................................................... 4 Bacterial strains:..............................................................................................................................................4 Figure S2: Variability between subjects of effects of exosomes on BL21-lux growth.................................................... 5 Figure S3: Early effects of exosomes on growth of BL21 E. coli .................................................................................... 5 Figure S4: Exosomal Lysis............................................................................................................................................ 6 Figure S5: Effect of pH on exosomal action.................................................................................................................. 7 Figure S6: Effect of exosomes on growth of UPEC (pH = 6.5) suspended in exosome-depleted urine supernatant ....... 8 Effective exosomal concentration....................................................................................................................8 Figure S7: Sample constitution for luminometry experiments..................................................................................... 8 Figure S8: Determining effective concentration .........................................................................................................