1 Gα13 Loss Promotes Tumor Progression in the KPC Transgenic
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The Rac Gtpase in Cancer: from Old Concepts to New Paradigms Marcelo G
Published OnlineFirst August 14, 2017; DOI: 10.1158/0008-5472.CAN-17-1456 Cancer Review Research The Rac GTPase in Cancer: From Old Concepts to New Paradigms Marcelo G. Kazanietz1 and Maria J. Caloca2 Abstract Rho family GTPases are critical regulators of cellular func- mislocalization of Rac signaling components. The unexpected tions that play important roles in cancer progression. Aberrant pro-oncogenic functions of Rac GTPase-activating proteins also activity of Rho small G-proteins, particularly Rac1 and their challenged the dogma that these negative Rac regulators solely regulators, is a hallmark of cancer and contributes to the act as tumor suppressors. The potential contribution of Rac tumorigenic and metastatic phenotypes of cancer cells. This hyperactivation to resistance to anticancer agents, including review examines the multiple mechanisms leading to Rac1 targeted therapies, as well as to the suppression of antitumor hyperactivation, particularly focusing on emerging paradigms immune response, highlights the critical need to develop ther- that involve gain-of-function mutations in Rac and guanine apeutic strategies to target the Rac pathway in a clinical setting. nucleotide exchange factors, defects in Rac1 degradation, and Cancer Res; 77(20); 5445–51. Ó2017 AACR. Introduction directed toward targeting Rho-regulated pathways for battling cancer. Exactly 25 years ago, two seminal papers by Alan Hall and Nearly all Rho GTPases act as molecular switches that cycle colleagues illuminated us with one of the most influential dis- between GDP-bound (inactive) and GTP-bound (active) forms. coveries in cancer signaling: the association of Ras-related small Activation is promoted by guanine nucleotide exchange factors GTPases of the Rho family with actin cytoskeleton reorganization (GEF) responsible for GDP dissociation, a process that normally (1, 2). -
A GTP-State Specific Cyclic Peptide Inhibitor of the Gtpase Gαs
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.25.054080; this version posted April 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-ND 4.0 International license. A GTP-state specific cyclic peptide inhibitor of the GTPase Gαs Shizhong A. Dai1,2†, Qi Hu1,2†, Rong Gao3†, Andre Lazar1,4†, Ziyang Zhang1,2, Mark von Zastrow1,4, Hiroaki Suga3*, Kevan M. Shokat1,2* 5 1Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA 2Howard Hughes Medical Institute 3Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan 10 4Department of Psychiatry, University of California, San Francisco, San Francisco, CA, 94158, USA *Correspondence to: [email protected], [email protected] †These authors contributed equally. 15 20 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.25.054080; this version posted April 27, 2020. 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-ND 4.0 International license. Abstract: The G protein-coupled receptor (GPCR) cascade leading to production of the second messenger cAMP is replete with pharmacologically targetable receptors and enzymes with the exception of the stimulatory G protein α subunit, Gαs. -
Clinical Utility of Recently Identified Diagnostic, Prognostic, And
Modern Pathology (2017) 30, 1338–1366 1338 © 2017 USCAP, Inc All rights reserved 0893-3952/17 $32.00 Clinical utility of recently identified diagnostic, prognostic, and predictive molecular biomarkers in mature B-cell neoplasms Arantza Onaindia1, L Jeffrey Medeiros2 and Keyur P Patel2 1Instituto de Investigacion Marques de Valdecilla (IDIVAL)/Hospital Universitario Marques de Valdecilla, Santander, Spain and 2Department of Hematopathology, MD Anderson Cancer Center, Houston, TX, USA Genomic profiling studies have provided new insights into the pathogenesis of mature B-cell neoplasms and have identified markers with prognostic impact. Recurrent mutations in tumor-suppressor genes (TP53, BIRC3, ATM), and common signaling pathways, such as the B-cell receptor (CD79A, CD79B, CARD11, TCF3, ID3), Toll- like receptor (MYD88), NOTCH (NOTCH1/2), nuclear factor-κB, and mitogen activated kinase signaling, have been identified in B-cell neoplasms. Chronic lymphocytic leukemia/small lymphocytic lymphoma, diffuse large B-cell lymphoma, follicular lymphoma, mantle cell lymphoma, Burkitt lymphoma, Waldenström macroglobulinemia, hairy cell leukemia, and marginal zone lymphomas of splenic, nodal, and extranodal types represent examples of B-cell neoplasms in which novel molecular biomarkers have been discovered in recent years. In addition, ongoing retrospective correlative and prospective outcome studies have resulted in an enhanced understanding of the clinical utility of novel biomarkers. This progress is reflected in the 2016 update of the World Health Organization classification of lymphoid neoplasms, which lists as many as 41 mature B-cell neoplasms (including provisional categories). Consequently, molecular genetic studies are increasingly being applied for the clinical workup of many of these neoplasms. In this review, we focus on the diagnostic, prognostic, and/or therapeutic utility of molecular biomarkers in mature B-cell neoplasms. -
Predicting Coupling Probabilities of G-Protein Coupled Receptors Gurdeep Singh1,2,†, Asuka Inoue3,*,†, J
Published online 30 May 2019 Nucleic Acids Research, 2019, Vol. 47, Web Server issue W395–W401 doi: 10.1093/nar/gkz392 PRECOG: PREdicting COupling probabilities of G-protein coupled receptors Gurdeep Singh1,2,†, Asuka Inoue3,*,†, J. Silvio Gutkind4, Robert B. Russell1,2,* and Francesco Raimondi1,2,* 1CellNetworks, Bioquant, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany, 2Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany, 3Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan and 4Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA Received February 10, 2019; Revised April 13, 2019; Editorial Decision April 24, 2019; Accepted May 01, 2019 ABSTRACT great use in tinkering with signalling pathways in living sys- tems (5). G-protein coupled receptors (GPCRs) control multi- Ligand binding to GPCRs induces conformational ple physiological states by transducing a multitude changes that lead to binding and activation of G-proteins of extracellular stimuli into the cell via coupling to situated on the inner cell membrane. Most of mammalian intra-cellular heterotrimeric G-proteins. Deciphering GPCRs couple with more than one G-protein giving each which G-proteins couple to each of the hundreds receptor a distinct coupling profile (6) and thus specific of GPCRs present in a typical eukaryotic organism downstream cellular responses. Determining these coupling is therefore critical to understand signalling. Here, profiles is critical to understand GPCR biology and phar- we present PRECOG (precog.russelllab.org): a web- macology. Despite decades of research and hundreds of ob- server for predicting GPCR coupling, which allows served interactions, coupling information is still missing for users to: (i) predict coupling probabilities for GPCRs many receptors and sequence determinants of coupling- specificity are still largely unknown. -
Tumor Markers
Tumor Markers Alan H.B. Wu, Ph.D. Professor, Laboratory Medicine, UCSF Section Chief, Clinical Chemistry, Toxicology, Pharmacogenomics Laboratory, SFGH Learning objectives • Know the ideal characteristics of a tumor marker • Understand the role of tumor markers for diagnosis and management of patients with cancer. • Know the emerging technologies for tumor markers • Understand the role of tumor markers for therapeutic selection How do we diagnose cancer today? Physical Examination Blood tests CT scans Biopsy Human Prostate Cancer Normal Blood Smear Chronic Myeloid Leukemia Death rates for cancer vs. heart disease New cancer cases per year Cancer Site or Type New Cases Prostate 218,000 Lung 222,500 Breast 207,500 Colorectal 149,000 Urinary system 131,500 Skin 68,770 Pancreas 43,100 Ovarian 22,000 Myeloma 20,200 Thyroid 44,700 Germ Cell 9,000 Types of Tumor Markers • Hormones (hCG; calcitonin; gastrin; prolactin;) • Enzymes (acid phosphatase; alkaline phosphatase; PSA) • Cancer antigen proteins & glycoproteins (CA125; CA 15.3; CA19.9) • Metabolites (norepinephrine, epinephrine) • Normal proteins (thyroglobulin) • Oncofetal antigens (CEA, AFP) • Receptors (ER, PR, EGFR) • Genetic changes (mutations/translocations, etc.) Characteristics of an ideal tumor marker • Specificity for a single type of cancer • High sensitivity and specificity for cancerous growth • Correlation of marker level with tumor size • Homogeneous (i.e., minimal post-translational modifications) • Short half-life in circulation Roles for tumor markers • Determine risk (PSA) -
Recurrent GNAQ Mutation Encoding T96S in Natural Killer/T Cell Lymphoma
ARTICLE https://doi.org/10.1038/s41467-019-12032-9 OPEN Recurrent GNAQ mutation encoding T96S in natural killer/T cell lymphoma Zhaoming Li 1,2,9, Xudong Zhang1,2,9, Weili Xue1,3,9, Yanjie Zhang1,3,9, Chaoping Li1,3, Yue Song1,3, Mei Mei1,3, Lisha Lu1,3, Yingjun Wang1,3, Zhiyuan Zhou1,3, Mengyuan Jin1,3, Yangyang Bian4, Lei Zhang1,2, Xinhua Wang1,2, Ling Li1,2, Xin Li1,2, Xiaorui Fu1,2, Zhenchang Sun1,2, Jingjing Wu1,2, Feifei Nan1,2, Yu Chang1,2, Jiaqin Yan1,2, Hui Yu1,2, Xiaoyan Feng1,2, Guannan Wang5, Dandan Zhang5, Xuefei Fu6, Yuan Zhang7, Ken H. Young8, Wencai Li5 & Mingzhi Zhang1,2 1234567890():,; Natural killer/T cell lymphoma (NKTCL) is a rare and aggressive malignancy with a higher prevalence in Asia and South America. However, the molecular genetic mechanisms underlying NKTCL remain unclear. Here, we identify somatic mutations of GNAQ (encoding the T96S alteration of Gαq protein) in 8.7% (11/127) of NKTCL patients, through whole- exome/targeted deep sequencing. Using conditional knockout mice (Ncr1-Cre-Gnaqfl/fl), we demonstrate that Gαqdeficiency leads to enhanced NK cell survival. We also find that Gαq suppresses tumor growth of NKTCL via inhibition of the AKT and MAPK signaling pathways. Moreover, the Gαq T96S mutant may act in a dominant negative manner to promote tumor growth in NKTCL. Clinically, patients with GNAQ T96S mutations have inferior survival. Taken together, we identify recurrent somatic GNAQ T96S mutations that may contribute to the pathogenesis of NKTCL. Our work thus has implications for refining our understanding of the genetic mechanisms of NKTCL and for the development of therapies. -
ANALYSIS Doi:10.1038/Nature14663
ANALYSIS doi:10.1038/nature14663 Universal allosteric mechanism for Ga activation by GPCRs Tilman Flock1, Charles N. J. Ravarani1*, Dawei Sun2,3*, A. J. Venkatakrishnan1{, Melis Kayikci1, Christopher G. Tate1, Dmitry B. Veprintsev2,3 & M. Madan Babu1 G protein-coupled receptors (GPCRs) allosterically activate heterotrimeric G proteins and trigger GDP release. Given that there are 800 human GPCRs and 16 different Ga genes, this raises the question of whether a universal allosteric mechanism governs Ga activation. Here we show that different GPCRs interact with and activate Ga proteins through a highly conserved mechanism. Comparison of Ga with the small G protein Ras reveals how the evolution of short segments that undergo disorder-to-order transitions can decouple regions important for allosteric activation from receptor binding specificity. This might explain how the GPCR–Ga system diversified rapidly, while conserving the allosteric activation mechanism. proteins bind guanine nucleotides and act as molecular switches almost 30 A˚ away from the GDP binding region5 and allosterically trig- in a number of signalling pathways by interconverting between ger GDP release to activate them. 1,2 G a GDP-bound inactive and a GTP-bound active state . They The high-resolution structure of the Gas-bound b2-adrenergic recep- 3 5 consist of two major classes: monomeric small G proteins and hetero- tor (b2AR) provided crucial insights into the receptor–G protein inter- trimeric G proteins4. While small G proteins and the a-subunit (Ga)of face and conformational changes in Ga upon receptor binding6,7. Recent 6 8 heterotrimeric G proteins both contain a GTPase domain (G-domain), studies described dynamic regions in Gas and Gai , the importance of ˚ Ga contains an additional helical domain (H-domain) and also forms a displacement of helix 5 (H5) of Gas and Gat by up to 6 A into the complex with the Gb and Gc subunits. -
Screening of Potential Genes and Transcription Factors Of
ANIMAL STUDY e-ISSN 1643-3750 © Med Sci Monit, 2018; 24: 503-510 DOI: 10.12659/MSM.907445 Received: 2017.10.08 Accepted: 2018.01.01 Screening of Potential Genes and Transcription Published: 2018.01.25 Factors of Postoperative Cognitive Dysfunction via Bioinformatics Methods Authors’ Contribution: ABE 1 Yafeng Wang 1 Department of Anesthesiology, The First Affiliated Hospital of Guangxi Medical Study Design A AB 1 Ailan Huang University, Nanning, Guangxi, P.R. China Data Collection B 2 Department of Gynecology, People’s Hospital of Guangxi Zhuang Autonomous Statistical Analysis C BEF 1 Lixia Gan Region, The First Affiliated Hospital of Guangxi Medical University, Nanning, Data Interpretation D BCF 1 Yanli Bao Guangxi, P.R. China Manuscript Preparation E BDF 1 Weilin Zhu 3 Department of Anesthesiology, The First Affiliated Hospital of Guangxi Medical Literature Search F University, Nanning, Guangxi, P.R. China Funds Collection G EF 1 Yanyan Hu AE 1 Li Ma CF 2 Shiyang Wei DE 3 Yuyan Lan Corresponding Author: Yafeng Wang, e-mail: [email protected] Source of support: Departmental sources Background: The aim of this study was to explore the potential genes and transcription factors involved in postoperative cognitive dysfunction (POCD) via bioinformatics analysis. Material/Methods: GSE95070 miRNA expression profiles were downloaded from Gene Expression Omnibus database, which in- cluded five hippocampal tissues from POCD mice and controls. Moreover, the differentially expressed miRNAs (DEMs) between the two groups were identified. In addition, the target genes of DEMs were predicted using Targetscan 7.1, followed by protein-protein interaction (PPI) network construction, functional enrichment anal- ysis, pathway analysis, and prediction of transcription factors (TFs) targeting the potential targets. -
Screening for Tumor Suppressors: Loss of Ephrin PNAS PLUS Receptor A2 Cooperates with Oncogenic Kras in Promoting Lung Adenocarcinoma
Screening for tumor suppressors: Loss of ephrin PNAS PLUS receptor A2 cooperates with oncogenic KRas in promoting lung adenocarcinoma Narayana Yeddulaa, Yifeng Xiaa, Eugene Kea, Joep Beumera,b, and Inder M. Vermaa,1 aLaboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037; and bHubrecht Institute, Utrecht, The Netherlands Contributed by Inder M. Verma, October 12, 2015 (sent for review July 28, 2015; reviewed by Anton Berns, Tyler Jacks, and Frank McCormick) Lung adenocarcinoma, a major form of non-small cell lung cancer, injections in embryonic skin cells identified several potential tu- is the leading cause of cancer deaths. The Cancer Genome Atlas morigenic factors (14–16). None of the reported studies have analysis of lung adenocarcinoma has identified a large number of performed direct shRNA-mediated high-throughput approaches previously unknown copy number alterations and mutations, re- in adult mice recapitulating the mode of tumorigenesis in humans. quiring experimental validation before use in therapeutics. Here, we Activating mutations at positions 12, 13, and 61 amino acids in describe an shRNA-mediated high-throughput approach to test a set Kirsten rat sarcoma viral oncogene homolog (KRas) contributes of genes for their ability to function as tumor suppressors in the to tumorigenesis in 32% of lung adenocarcinoma patients (2) by background of mutant KRas and WT Tp53. We identified several activating downstream signaling cascades. Mice with the KRasG12D candidate genes from tumors originated from lentiviral delivery of allele develop benign adenomatous lesions with long latency to shRNAs along with Cre recombinase into lungs of Loxp-stop-Loxp- develop adenocarcinoma (17, 18). -
Investigating the Mechanism of Hepatocellular Carcinoma Progression by Constructing Genetic and Epigenetic Networks Using NGS Data Identification and Big Database Mining Method
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 7, No. 48 Research Paper Investigating the mechanism of hepatocellular carcinoma progression by constructing genetic and epigenetic networks using NGS data identification and big database mining method Cheng-Wei Li1, Ping-Yao Chang1, Bor-Sen Chen1 1Laboratory of Control and Systems Biology, National Tsing Hua University, Hsinchu, Taiwan Correspondence to: Bor-Sen Chen, email: [email protected] Keywords: DNA methylation, multiple potential drugs, hepatocarcinogenesis, miRNAs, principal network projection Received: February 19, 2016 Accepted: October 26, 2016 Published: November 04, 2016 ABSTRACT The mechanisms leading to the development and progression of hepatocellular carcinoma (HCC) are complicated and regulated genetically and epigenetically. The recent advancement in high-throughput sequencing has facilitated investigations into the role of genetic and epigenetic regulations in hepatocarcinogenesis. Therefore, we used systems biology and big database mining to construct genetic and epigenetic networks (GENs) using the information about mRNA, miRNA, and methylation profiles of HCC patients. Our approach involves analyzing gene regulatory networks (GRNs), protein-protein networks (PPINs), and epigenetic networks at different stages of hepatocarcinogenesis. The core GENs, influencing each stage of HCC, were extracted via principal network projection (PNP). The pathways during different stages of HCC were compared. We observed that extracellular signals were further transduced to -
The Effects of Oncogenic G12d Mutation on K-Ras Structure, Conformation and Dynamics
bioRxiv preprint doi: https://doi.org/10.1101/178483; this version posted August 19, 2017. 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. THE EFFECTS OF ONCOGENIC G12D MUTATION ON K-RAS STRUCTURE, CONFORMATION AND DYNAMICS Sezen Vatansever1, 2, 3, Zeynep H. Gümüş2, 3*, Burak Erman1* 1Department of Chemical and Biological Engineering, College of Engineering, Koç University, Rumelifeneri Yolu, 34450, Sarıyer, Istanbul, Turkey 2Department of Genetics and Genomics, 3Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 *Correspondence: [email protected] (B.E.) and [email protected] (Z.H.G.) ABSTRACT K-Ras is the most frequently mutated protein in human tumors. Activating K-Ras mutations drive cancer initiation, progression and drug resistance, directly leading to nearly a million deaths per year. To understand the mechanisms by which mutations alter K-Ras function, we need to understand their effects on protein dynamics. However, despite decades of research, how oncogenic mutations in K-Ras alter its conformation and dynamics remain to be understood. Here, we present how the most recurrent K-Ras oncogenic mutation, G12D, leads to structural, conformational and dynamical changes that lead to constitutively active K- Ras. We have developed a new integrated MD simulation data analysis approach to quantify such changes in a protein and applied it to K-Ras. Our results show that G12D mutation induces strong negative correlations between the fluctuations of SII and those of the P-loop, Switch I (SI) and α3 regions in K-RasG12D. -
4 Understanding the Role of GNA13 Deregulation in Lymphomagenesis
Integrative Genomics Reveals a Role for GNA13 in Lymphomagenesis by Adrienne Greenough University Program in Genetics and Genomics Duke University Approved: ___________________________ Sandeep Dave, Supervisor ___________________________ Fred Dietrich ___________________________ Jack Keene ___________________________ Yuan Zhuang Dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the University Program in Genetics and Genomics in the Graduate School of Duke University 2014 i v ABSTRACT Integrative Genomics Reveals a Role for GNA13 in Lymphomagenesis by Adrienne Greenough University Program in Genetics and Genomics Duke University Approved: ___________________________ Sandeep Dave, Supervisor ___________________________ Fred Dietrich ___________________________ Jack Keene ___________________________ Yuan Zhuang An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the University Program in Genetics and Genomics in the Graduate School of Duke University 2014 Copyright by Adrienne Greenough 2014 Abstract Lymphomas comprise a diverse group of malignancies derived from immune cells. High throughput sequencing has recently emerged as a powerful and versatile method for analysis of the cancer genome and transcriptome. As these data continue to emerge, the crucial work lies in sorting through the wealth of information to hone in on the critical aspects that will give us a better understanding of biology and new insight for how to treat disease. Finding the important signals within these large data sets is one of the major challenges of next generation sequencing. In this dissertation, I have developed several complementary strategies to describe the genetic underpinnings of lymphomas. I begin with developing a better method for RNA sequencing that enables strand-specific total RNA sequencing and alternative splicing profiling in the same analysis.