Cerebral Cavernous Malformations: from Genes to Proteins to Disease
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Rala Requirement for V-Src- and V-Ras-Induced Tumorigenicity and Overproduction of Urokinase-Type Plasminogen Activator: Involvement of Metalloproteases
Oncogene (1999) 18, 4718 ± 4725 ã 1999 Stockton Press All rights reserved 0950 ± 9232/99 $15.00 http://www.stockton-press.co.uk/onc RalA requirement for v-Src- and v-Ras-induced tumorigenicity and overproduction of urokinase-type plasminogen activator: involvement of metalloproteases Julio A Aguirre-Ghiso*,1,4, Paul Frankel2, Eduardo F Farias1, Zhimin Lu2, Hong Jiang2,5, Amanda Olsen2, Larry A Feig3, Elisa Bal de Kier Joe1 and David A Foster2 1Cell Biology Department, Research Area, Institute of Oncology, `Angel H Roo', University of Buenos Aires, Buenos Aires 1417, Argentina; 2Department of Biological Sciences, Hunter College of The City University of New York, New York, NY 10021, USA; 3Department of Biochemistry, Tufts University School of Medicine, Boston, Massachusetts, MA 02111, USA Overproduction of urokinase-type plasminogen activator Introduction (uPA) and metalloproteases (MMPs) is strongly corre- lated with tumorigenicity and with invasive and meta- Metastasis is the last and most lethal stage of tumor static phenotypes of human and experimental tumors. progression. This process follows several steps including We demonstrated previously that overproduction of uPA the exit of tumor cells from the primary tumor, in tumor cells is mediated by a phospholipase D (PLD)- intravasation after degradation of the interstitial and and protein kinase C-dependent mechanism. The onco- the blood vessels extracellular matrix, dissemination genic stimulus of v-Src and v-Ras results in the through the lymphatic or arterial system, and ®nally activation of PLD, which is dependent upon the extravasation, settlement, and growth in a distant organ monomeric GTPase RalA. We have therefore investi- (Hart et al., 1989). -
Putting Rac1 on the Path to Glucose Uptake Assaf Rudich1 and Amira Klip2
COMMENTARY Putting Rac1 on the Path to Glucose Uptake Assaf Rudich1 and Amira Klip2 Rac1 is an obligatory element in the stimulation of glucose uptake by insulin in skeletal muscle. Insulin caused Rac1 n spite of numerous and key advances in our un- activation (GTP loading) in mouse muscle ex vivo, and derstanding of insulin signaling, the molecular basis muscles of mice conditionally lacking Rac1 in skeletal mus- for impaired insulin-stimulated glucose uptake un- cle, or treated with Rac inhibitors, showed reduced insulin- Iderlying insulin resistance remains unclear. Because simulated glucose uptake. Under these circumstances, skeletal muscle accounts for the majority of glucose utili- insulin-stimulated Akt was not affected. These data comple- zation in the postprandial insulin-regulated state, defects in ment a previous study with another muscle-specific Rac1- insulin action in muscle can determine whole-body glu- knockout mouse model, in which insulin-triggered GLUT4 cose utilization. In muscle and fat cells, overall similarities translocation was reduced (9). exist in the signals emanating from the insulin receptor Which Rac1 effectors are promoting glucose uptake? that mobilize glucose transporter GLUT4 to the membrane. The studies in cell culture have already revealed the acti- Importantly, defects in the signaling network connecting vation of three Rac-effector pathways: The aforementioned the activated insulin receptor to GLUT4 vesicles are of Arp2/3 (mediated by nucleating factors of the Wave family particular consequence to insulin resistance in muscle, where, and leading to actin remodeling) (4,10); the serine/threonine unlike the case of fat cells, GLUT4 expression is not sig- kinase PAK1 (7,11); and the small G protein Ral (12). -
Identification of Cis-Regulatory Sequence
Worsley-Hunt et al. Genome Medicine 2011, 3:65 http://genomemedicine.com/content/3/9/65 REVIEW Identication of cis-regulatory sequence variations in individual genome sequences Rebecca Worsley-Hunt1,2, Virginie Bernard1 and Wyeth W Wasserman1* Abstract for the appropriate patterning or magnitude of gene expression. Similarly, mutations can disrupt other sequence- Functional contributions of cis-regulatory sequence specific regulatory controls, such as elements regulating variations to human genetic disease are numerous. For RNA splicing or stability. Although much emphasis in the instance, disrupting variations in a HNF4A transcription age of exome sequencing has been placed on variation factor binding site upstream of the Factor IX gene within protein-encoding sequences, it is apparent that contributes causally to hemophilia B Leyden. Although regulatory sequence disruptions will become a key focus clinical genome sequence analysis currently focuses as full genome sequences become widely accessible for on the identication of protein-altering variation, the medical genetics research. impact of cis-regulatory mutations can be similarly e emerging collection of cis-regulatory variations strong. New technologies are now enabling genome that cause human disease or altered phenotype is grow- sequencing beyond exomes, revealing variation across ing [2-4]. Reports identify cis-acting, expression-altering the non-coding 98% of the genome responsible for mutations observed within introns, far upstream of developmental and physiological patterns of gene genes, at splicing sites or within microRNA target sites. activity. The capacity to identify causal regulatory For example, cis-regulatory mutations have roles in hemo- mutations is improving, but predicting functional philia, Gilbert’s syndrome, Bernard-Soulier syndrome, changes in regulatory DNA sequences remains a great irritable bowel syndrome, beta-thalassemia, cholesterol challenge. -
Transcriptome-Wide Profiling of Cerebral Cavernous Malformations
www.nature.com/scientificreports OPEN Transcriptome-wide Profling of Cerebral Cavernous Malformations Patients Reveal Important Long noncoding RNA molecular signatures Santhilal Subhash 2,8, Norman Kalmbach3, Florian Wegner4, Susanne Petri4, Torsten Glomb5, Oliver Dittrich-Breiholz5, Caiquan Huang1, Kiran Kumar Bali6, Wolfram S. Kunz7, Amir Samii1, Helmut Bertalanfy1, Chandrasekhar Kanduri2* & Souvik Kar1,8* Cerebral cavernous malformations (CCMs) are low-fow vascular malformations in the brain associated with recurrent hemorrhage and seizures. The current treatment of CCMs relies solely on surgical intervention. Henceforth, alternative non-invasive therapies are urgently needed to help prevent subsequent hemorrhagic episodes. Long non-coding RNAs (lncRNAs) belong to the class of non-coding RNAs and are known to regulate gene transcription and involved in chromatin remodeling via various mechanism. Despite accumulating evidence demonstrating the role of lncRNAs in cerebrovascular disorders, their identifcation in CCMs pathology remains unknown. The objective of the current study was to identify lncRNAs associated with CCMs pathogenesis using patient cohorts having 10 CCM patients and 4 controls from brain. Executing next generation sequencing, we performed whole transcriptome sequencing (RNA-seq) analysis and identifed 1,967 lncRNAs and 4,928 protein coding genes (PCGs) to be diferentially expressed in CCMs patients. Among these, we selected top 6 diferentially expressed lncRNAs each having signifcant correlative expression with more than 100 diferentially expressed PCGs. The diferential expression status of the top lncRNAs, SMIM25 and LBX2-AS1 in CCMs was further confrmed by qRT-PCR analysis. Additionally, gene set enrichment analysis of correlated PCGs revealed critical pathways related to vascular signaling and important biological processes relevant to CCMs pathophysiology. -
Methods in and Applications of the Sequencing of Short Non-Coding Rnas" (2013)
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2013 Methods in and Applications of the Sequencing of Short Non- Coding RNAs Paul Ryvkin University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Bioinformatics Commons, Genetics Commons, and the Molecular Biology Commons Recommended Citation Ryvkin, Paul, "Methods in and Applications of the Sequencing of Short Non-Coding RNAs" (2013). Publicly Accessible Penn Dissertations. 922. https://repository.upenn.edu/edissertations/922 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/922 For more information, please contact [email protected]. Methods in and Applications of the Sequencing of Short Non-Coding RNAs Abstract Short non-coding RNAs are important for all domains of life. With the advent of modern molecular biology their applicability to medicine has become apparent in settings ranging from diagonistic biomarkers to therapeutics and fields angingr from oncology to neurology. In addition, a critical, recent technological development is high-throughput sequencing of nucleic acids. The convergence of modern biotechnology with developments in RNA biology presents opportunities in both basic research and medical settings. Here I present two novel methods for leveraging high-throughput sequencing in the study of short non- coding RNAs, as well as a study in which they are applied to Alzheimer's Disease (AD). The computational methods presented here include High-throughput Annotation of Modified Ribonucleotides (HAMR), which enables researchers to detect post-transcriptional covalent modifications ot RNAs in a high-throughput manner. In addition, I describe Classification of RNAs by Analysis of Length (CoRAL), a computational method that allows researchers to characterize the pathways responsible for short non-coding RNA biogenesis. -
Individualized Systems Medicine Strategy to Tailor Treatments for Patients with Chemorefractory Acute Myeloid Leukemia
Published OnlineFirst September 20, 2013; DOI: 10.1158/2159-8290.CD-13-0350 RESEARCH ARTICLE Individualized Systems Medicine Strategy to Tailor Treatments for Patients with Chemorefractory Acute Myeloid Leukemia Tea Pemovska 1 , Mika Kontro 2 , Bhagwan Yadav 1 , Henrik Edgren 1 , Samuli Eldfors1 , Agnieszka Szwajda 1 , Henrikki Almusa 1 , Maxim M. Bespalov 1 , Pekka Ellonen 1 , Erkki Elonen 2 , Bjørn T. Gjertsen5 , 6 , Riikka Karjalainen 1 , Evgeny Kulesskiy 1 , Sonja Lagström 1 , Anna Lehto 1 , Maija Lepistö1 , Tuija Lundán 3 , Muntasir Mamun Majumder 1 , Jesus M. Lopez Marti 1 , Pirkko Mattila 1 , Astrid Murumägi 1 , Satu Mustjoki 2 , Aino Palva 1 , Alun Parsons 1 , Tero Pirttinen 4 , Maria E. Rämet 4 , Minna Suvela 1 , Laura Turunen 1 , Imre Västrik 1 , Maija Wolf 1 , Jonathan Knowles 1 , Tero Aittokallio 1 , Caroline A. Heckman 1 , Kimmo Porkka 2 , Olli Kallioniemi 1 , and Krister Wennerberg 1 ABSTRACT We present an individualized systems medicine (ISM) approach to optimize cancer drug therapies one patient at a time. ISM is based on (i) molecular profi ling and ex vivo drug sensitivity and resistance testing (DSRT) of patients’ cancer cells to 187 oncology drugs, (ii) clinical implementation of therapies predicted to be effective, and (iii) studying consecutive samples from the treated patients to understand the basis of resistance. Here, application of ISM to 28 samples from patients with acute myeloid leukemia (AML) uncovered fi ve major taxonomic drug-response sub- types based on DSRT profi les, some with distinct genomic features (e.g., MLL gene fusions in subgroup IV and FLT3 -ITD mutations in subgroup V). Therapy based on DSRT resulted in several clinical responses. -
Mirna‑26A‑5P and Mir‑26B‑5P Inhibit the Proliferation of Bladder Cancer Cells by Regulating PDCD10
ONCOLOGY REPORTS 40: 3523-3532, 2018 miRNA‑26a‑5p and miR‑26b‑5p inhibit the proliferation of bladder cancer cells by regulating PDCD10 KE WU1*, XING-YU MU1*, JUN-TAO JIANG1, MING-YUE TAN1, REN-JIE WANG1, WEN-JIE ZHOU2, XIANG WANG1, YIN-YAN HE3, MING-QING LI2 and ZHI-HONG LIU1 1Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080; 2Laboratory for Reproductive Immunology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai 200011; 3Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China Received October 11, 2017; Accepted September 4, 2018 DOI: 10.3892/or.2018.6734 Abstract. MicroRNA (miR)-26a-5p and miR-26b-5p consis- and miR-26b-5p were pivotal regulators in BC progression tently play an antitumor role in many types of cancers, but the by targeting the proliferation-related protein, PDCD10. The underlying mechanism remains unclear in bladder cancer (BC). miR-26-5p/PDCD10 interaction may provide important In the present study, we found that, in BC tissues, the levels of insight into the pathway of BC progression and present novel miR-26a-5p and miR-26b-5p were lower than in paired normal opportunities for future diagnosis and treatment strategies, tissues. The upregulation of miR‑26‑5p significantly inhibited especially for patients with high levels of PDCD10. the proliferation of BC cell lines (T24 and 5637). Bioinformatics analysis indicated that Programmed Cell Death 10 (PDCD10) Introduction was the downstream target gene of miR-26a-5p/miR-26b-5p, and this was ascertained by western blotting and quantitative Bladder cancer (BC) is one of the most important urinary real-time reverse transcription PCR (RT-qPCR). -
Mir-17-92 Fine-Tunes MYC Expression and Function to Ensure
ARTICLE Received 31 Mar 2015 | Accepted 22 Sep 2015 | Published 10 Nov 2015 DOI: 10.1038/ncomms9725 OPEN miR-17-92 fine-tunes MYC expression and function to ensure optimal B cell lymphoma growth Marija Mihailovich1, Michael Bremang1, Valeria Spadotto1, Daniele Musiani1, Elena Vitale1, Gabriele Varano2,w, Federico Zambelli3, Francesco M. Mancuso1,w, David A. Cairns1,w, Giulio Pavesi3, Stefano Casola2 & Tiziana Bonaldi1 The synergism between c-MYC and miR-17-19b, a truncated version of the miR-17-92 cluster, is well-documented during tumor initiation. However, little is known about miR-17-19b function in established cancers. Here we investigate the role of miR-17-19b in c-MYC-driven lymphomas by integrating SILAC-based quantitative proteomics, transcriptomics and 30 untranslated region (UTR) analysis upon miR-17-19b overexpression. We identify over one hundred miR-17-19b targets, of which 40% are co-regulated by c-MYC. Downregulation of a new miR-17/20 target, checkpoint kinase 2 (Chek2), increases the recruitment of HuR to c- MYC transcripts, resulting in the inhibition of c-MYC translation and thus interfering with in vivo tumor growth. Hence, in established lymphomas, miR-17-19b fine-tunes c-MYC activity through a tight control of its function and expression, ultimately ensuring cancer cell homeostasis. Our data highlight the plasticity of miRNA function, reflecting changes in the mRNA landscape and 30 UTR shortening at different stages of tumorigenesis. 1 Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy. 2 Units of Genetics of B cells and lymphomas, IFOM, FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy. -
Structural Basis of the Interaction Between Rala and Sec5, a Subunit of the Sec6/8 Complex
The EMBO Journal Vol. 22 No. 13 pp. 3267±3278, 2003 Structural basis of the interaction between RalA and Sec5, a subunit of the sec6/8 complex Shuya Fukai, Hugo T.Matern1, membrane fusion. The tethering step is de®ned as the Junutula R.Jagath1, Richard H.Scheller1 and initial contact of the vesicle via a protein bridge with its Axel T.Brunger2 target compartment and is the critical determinant in the speci®city of membrane fusion. Essential for this tethering Howard Hughes Medical Institute and Departments of Molecular and are multimeric protein complexes that have been shown to Cellular Physiology, Neurology and Neurological Sciences and Stanford Synchrotron Radiation Laboratory, Stanford University, be involved in most, if not all, intracellular traf®cking James H.Clark Center, E300C, 318 Campus Drive, Stanford, CA events (Whyte and Munro, 2002). 94305-5432 and 1Genentech Inc., 1 DNA Way, South San Francisco, The tethering complex for exocytosis at the plasma CA 94080, USA membrane is referred to as the sec6/8 complex or exocyst 2Corresponding author in yeast (TerBush et al., 1996; Kee et al., 1997). This e-mail: [email protected] hetero-octameric protein complex is composed of the original SEC gene products (Sec3, Sec5, Sec6, Sec8, The sec6/8 complex or exocyst is an octameric protein Sec10, Sec15), plus Exo70 and Exo84. The exocyst complex that functions during cell polarization by components were originally identi®ed in a yeast genetic regulating the site of exocytic vesicle docking to the screen for mutants that are de®cient in the fusion of plasma membrane, in concert with small GTP-binding secretory vesicles with the plasma membrane (TerBush proteins. -
CCM1 and CCM2 Variants in Patients with Cerebral Cavernous
www.nature.com/scientificreports OPEN CCM1 and CCM2 variants in patients with cerebral cavernous malformation in an ethnically Received: 19 January 2018 Accepted: 11 July 2019 Chinese population in Taiwan Published: xx xx xxxx Chun-Wei Chang 1, Peng-Wei Hsu2,3, Kuo-Chen Wei2,3, Chia-Wen Chang1, Hon-Chung Fung1, Mo-Song Hsih1, Wen-Chuin Hsu1,3, Long-Sun Ro1,3, Chen-Nen Chang2,4, Jiun-Jie Wang5,6, Yih-Ru Wu1,3 & Sien-Tsong Chen1 Cerebral cavernous malformation (CCM) is a vascular malformation characterized by clustered enlarged capillary-like channels in the central nervous system. The genes harboring variants in patients with CCM include CCM1/Krev interaction trapped-1, CCM2/MGC4607, and CCM3/programmed cell death protein 10. We aimed to identify pathogenic variants in an ethnic Chinese population in Taiwan. We recruited 95 patients with multiple CCMs or a single lesion with a relevant family history. Sanger sequencing was performed for 41 patients. Variants were identifed using sequence alignment tools, and the clinical signifcance of these variants was determined using American College of Medical Genetics and Genomics standards and guidelines. Several pathogenic variants were found in six patients, including three unrelated patients and three afected members of one family. Two novel pathogenic variants leading to early truncation comprised a deletion variant in exon 18 of CCM1 (c.1846delA; p.Glu617LysfsTer44) and an insertion variant in exon 4 of CCM2 (c.401_402insGCCC; p.Ile136AlafsTer4). One novel pathogenic splice site variant was c.485 + 1G > C at the beginning of intron 8 of CCM1. In this study, we identifed novel variants related to CCM in an ethnically Chinese population in Taiwan. -
Human Cumulus Cells in Long-Term in Vitro Culture Reflect Differential
cells Article Human Cumulus Cells in Long-Term In Vitro Culture Reflect Differential Expression Profile of Genes Responsible for Planned Cell Death and Aging—A Study of New Molecular Markers Bła˙zejChermuła 1, Wiesława Kranc 2 , Karol Jopek 3, Joanna Budna-Tukan 3 , Greg Hutchings 2,4, Claudia Dompe 3,4, Lisa Moncrieff 3,4 , Krzysztof Janowicz 2,4, Małgorzata Józkowiak 5, Michal Jeseta 6 , Jim Petitte 7 , Paul Mozdziak 8 , Leszek Pawelczyk 1, Robert Z. Spaczy ´nski 1 and Bartosz Kempisty 2,3,6,9,* 1 Division of Infertility and Reproductive Endocrinology, Department of Gynecology, Obstetrics and Gynecological Oncology, Poznan University of Medical Sciences, 33 Polna St., 60-535 Poznan, Poland; [email protected] (B.C.); [email protected] (L.P.); [email protected] (R.Z.S.) 2 Department of Anatomy, Poznan University of Medical Sciences, 6 Swiecickiego St., 60-781 Poznan, Poland; [email protected] (W.K.); [email protected] (G.H.); [email protected] (K.J.) 3 Department of Histology and Embryology, Poznan University of Medical Sciences, 6 Swiecickiego St., 60-781 Poznan, Poland; [email protected] (K.J.); [email protected] (J.B.-T.); [email protected] (C.D.); l.moncrieff[email protected] (L.M.) 4 The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK 5 Department of Toxicology, Poznan University of Medical Sciences, 30 Dojazd St., 60-631 Poznan, Poland; [email protected] 6 Department of Obstetrics and Gynecology, University Hospital and -
The Dual Role of Filamin a in Cancer: Can't Live with (Too Much
R M Savoy and P M Ghosh Dual role of filamin A in cancer 20:6 R341–R356 Review The dual role of filamin A in cancer: can’t live with (too much of) it, can’t live without it Correspondence 1 1,2 Rosalinda M Savoy and Paramita M Ghosh should be addressed to P M Ghosh 1Department of Urology, University of California Davis School of Medicine, University of California, 4860 Y Street, Email Suite 3500, Sacramento, California 95817, USA Paramita.Ghosh@ 2VA Northern California Health Care System, Mather, California, USA ucdmc.ucdavis.edu Abstract Filamin A (FlnA) has been associated with actin as cytoskeleton regulator. Recently its role in Key Words the cell has come under scrutiny for FlnA’s involvement in cancer development. FlnA was " filamin A originally revealed as a cancer-promoting protein, involved in invasion and metastasis. " metastasis However, recent studies have also found that under certain conditions, it prevented tumor " cancer formation or progression, confusing the precise function of FlnA in cancer development. " transcription Here, we try to decipher the role of FlnA in cancer and the implications for its dual role. We " nucleus propose that differences in subcellular localization of FlnA dictate its role in cancer " cytoplasm development. In the cytoplasm, FlnA functions in various growth signaling pathways, such as " localization vascular endothelial growth factor, in addition to being involved in cell migration and adhesion pathways, such as R-Ras and integrin signaling. Involvement in these pathways and Endocrine-Related Cancer various others has shown a correlation between high cytoplasmic FlnA levels and invasive cancers.