Wingless Signaling: a Genetic Journey from Morphogenesis to Metastasis
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A Novel Ve-Zinc Nger-Related-Gene Signature Related to Tumor Immune
A novel ve-zinc nger-related-gene signature related to tumor immune microenvironment allows for treatment stratication and predicts prognosis in clear cell renal cell carcinoma patients Feilong Zhang Beijing Chaoyang Hospital Jiyue Wu Beijing Chaoyang Hospital Jiandong Zhang Beijing Chaoyang Hospital Peng Cao Beijing Chaoyang Hospital Zejia Sun Beijing Chaoyang Hospital Wei Wang ( [email protected] ) Beijing Chaoyang Hospital https://orcid.org/0000-0003-2642-3338 Research Keywords: Posted Date: February 23rd, 2021 DOI: https://doi.org/10.21203/rs.3.rs-207677/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/25 Abstract Background Clear cell renal cell carcinoma (ccRCC) is one of the most prevalent renal malignant tumors, which survival rate and quality of life of ccRCC patients are not satisfactory. Therefore, identication of prognostic biomarkers of ccRCC patients will contribute to early and accurate clinical intervention and treatment, and then improve their prognosis. Methods We downloaded the original expression data of mRNAs from The Cancer Genome Atlas database and the zinc nger(ZNF)-related genes (ZRGs) from UniProt online database. Differentially expressed ZRGs (DE- ZRGs) was screened from tumor and adjacent nontumor tissues and functional enrichment analysis was conducted out. A ve-ZRG signature were constructed by univariate Cox regression, least absolute shrinkage and selection operator and multivariate Cox regression. Furthermore, we screened out independent prognosis-related factors to build a nomogram by univariate and multivariate Cox regression. Potential biological pathways of ve ZRGs were analyzed by Gene Set Enrichment Analysis (GSEA). Then, we further quantitatively analyze immune inltration and evaluate tumor microenvironment by single sample GSEA. -
Genetic Variants in WNT2B and BTRC Predict Melanoma Survival
ACCEPTED MANUSCRIPT Genetic Variants in WNT2B and BTRC Predict Melanoma Survival Qiong Shi1, 2, 3, 9, Hongliang Liu2, 3, 9, Peng Han2, 3, 4, 9, Chunying Li1, Yanru Wang2, 3, Wenting Wu5, Dakai Zhu6, Christopher I. Amos6, Shenying Fang7, Jeffrey E. Lee7, Jiali Han5, 8* and Qingyi Wei2, 3* 1Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi 710032, China; 2Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA, 3Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA, 4Department of Otorhinolaryngology Head and Neck Surgery, First Affiliated Hospital, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi 710061, China; 5Department of Epidemiology, Fairbanks School of Public Health, Indiana University Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis,MANUSCRIPT IN 46202, USA 6Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA; 7Department of Surgical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA. 8Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA 9These authors contributed equally to this work. ACCEPTED *Correspondence: Qingyi Wei, M.D., Ph.D., Duke Cancer Institute, Duke University Medical Center and Department of Medicine, Duke School of Medicine, 905 S LaSalle Street, Durham, NC 27710, USA, Tel.: (919) 660-0562, E-mail: [email protected] and Jiali Han, M.D., Ph.D., 1 _________________________________________________________________________________ This is the author's manuscript of the article published in final edited form as: Shi, Q., Liu, H., Han, P., Li, C., Wang, Y., Wu, W., … Wei, Q. -
Long Noncoding Rnas: Functional Surprises from the RNA World
Downloaded from genesdev.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Long noncoding RNAs: functional surprises from the RNA world Jeremy E. Wilusz,1 Hongjae Sunwoo,2 and David L. Spector1,3 1Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; 2Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York 11794 Most of the eukaryotic genome is transcribed, yielding complexity. In addition, there has been an explosion of a complex network of transcripts that includes tens of research addressing possible functional roles for the thousands of long noncoding RNAs with little or no other 98% of the human genome that does not encode protein-coding capacity. Although the vast majority of proteins. Rather unexpectedly, transcription is not lim- long noncoding RNAs have yet to be characterized thor- ited to protein-coding regions, but is instead pervasive oughly, many of these transcripts are unlikely to represent throughout the mammalian genome as demonstrated by transcriptional ‘‘noise’’ as a significant number have been large-scale cDNA cloning projects (Carninci et al. 2005; shown to exhibit cell type-specific expression, localiza- Katayama et al. 2005) and genomic tiling arrays (Bertone tion to subcellular compartments, and association with et al. 2004; Cheng et al. 2005; Birney et al. 2007; Kapranov human diseases. Here, we highlight recent efforts that et al. 2007a). In fact, >90% of the human genome is likely have identified a myriad of molecular functions for long to be transcribed (Birney et al. 2007), yielding a complex noncoding RNAs. -
Perspectives
Copyright 0 1994 by the Genetics Society of America Perspectives Anecdotal, Historical and Critical Commentaries on Genetics Edited by James F. Crow and William F. Dove A Century of Homeosis, A Decade of Homeoboxes William McGinnis Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114 NE hundred years ago, while the science of genet- ing mammals, and were proposed to encode DNA- 0 ics still existed only in the yellowing reprints of a binding homeodomainsbecause of a faint resemblance recently deceased Moravian abbot, WILLIAMBATESON to mating-type transcriptional regulatory proteins of (1894) coined the term homeosis to define a class of budding yeast and an even fainter resemblance to bac- biological variations in whichone elementof a segmen- terial helix-turn-helix transcriptional regulators. tally repeated array of organismal structures is trans- The initial stream of papers was a prelude to a flood formed toward the identity of another. After the redis- concerning homeobox genes and homeodomain pro- coveryof MENDEL’Sgenetic principles, BATESONand teins, a flood that has channeled into a steady river of others (reviewed in BATESON1909) realized that some homeo-publications, fed by many tributaries. A major examples of homeosis in floral organs and animal skel- reason for the continuing flow of studies is that many etons could be attributed to variation in genes. Soon groups, working on disparate lines of research, have thereafter, as the discipline of Drosophila genetics was found themselves swept up in the currents when they born and was evolving into a formidable intellectual found that their favorite protein contained one of the force enriching many biologicalsubjects, it gradually be- many subtypes of homeodomain. -
Three Dact Gene Family Members Are Expressed During Embryonic Development
Three Dact Gene Family Members are Expressed During Embryonic Development and in the Adult Brains of Mice Daniel A Fisher, Saul Kivimäe, Jun Hoshino, Rowena Suriben, Pierre -Marie Martin, Nichol Baxter, Benjamin NR Cheyette Department of Psychiatry & Gra duate Programs in Developmental Biology and Neuroscience, University of California, San Francisco, 94143-2611 Correspondence: Benjamin NR Cheyette [email protected] 415.476.7826 Running Title: Mouse Dact Gene Family Expression Key Words: mouse, Dpr, Frodo, Thyex, Dact, Wnt, Dvl, expression, embryo, brain Supported by: NIH: MH01750 K08; NARSAD Young Investigator Award; NAAR award #551. Abstract Members of the Dact protein family were initially identified through binding to Dishevelled (Dvl), a cytoplasmic protein central to Wnt signaling. During mouse development, Dact1 is detected in the presomitic mesoderm and somites during segmentation, in the limb bud mesenchyme and other mesoderm-derived tissues, and in the central nervous system (CNS). Dact2 expression is most prominent during organogenesis of the thymus, kidneys, and salivary glands, with much lower levels in the somites and in the developing CNS. Dact3, not previously described in any organism, is expressed in the ventral region of maturing somites, limb bud and branchial arch mesenchyme, and in the embryonic CNS; of the three paralogs it is the most highly expressed in the adult cerebral cortex. These data are consistent with studies in other vertebrates showing that Dact paralogs have distinct signaling and developmental roles, and suggest they may differentially contribute to postnatal brain physiology. Introduction Signaling downstream of secreted Wnt ligands is a conserved process in multicellular animals that plays important roles during development and, when misregulated, contributes to cancer and other diseases (Polakis, 2000; Moon et al., 2002). -
Substrate Trapping Proteomics Reveals Targets of the Trcp2
Substrate Trapping Proteomics Reveals Targets of the TrCP2/FBXW11 Ubiquitin Ligase Tai Young Kim,a,b* Priscila F. Siesser,a,b Kent L. Rossman,b,c Dennis Goldfarb,a,d Kathryn Mackinnon,a,b Feng Yan,a,b XianHua Yi,e Michael J. MacCoss,e Randall T. Moon,f Channing J. Der,b,c Michael B. Majora,b,d Department of Cell Biology and Physiology,a Lineberger Comprehensive Cancer Center,b Department of Pharmacology,c and Department of Computer Science,d University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Genome Sciencese and Department of Pharmacology and HHMI,f University of Washington, Seattle, Washington, USA Defining the full complement of substrates for each ubiquitin ligase remains an important challenge. Improvements in mass spectrometry instrumentation and computation and in protein biochemistry methods have resulted in several new methods for ubiquitin ligase substrate identification. Here we used the parallel adapter capture (PAC) proteomics approach to study TrCP2/FBXW11, a substrate adaptor for the SKP1–CUL1–F-box (SCF) E3 ubiquitin ligase complex. The processivity of the ubiquitylation reaction necessitates transient physical interactions between FBXW11 and its substrates, thus making biochemi- cal purification of FBXW11-bound substrates difficult. Using the PAC-based approach, we inhibited the proteasome to “trap” ubiquitylated substrates on the SCFFBXW11 E3 complex. Comparative mass spectrometry analysis of immunopurified FBXW11 protein complexes before and after proteasome inhibition revealed 21 known and 23 putatively novel substrates. In focused studies, we found that SCFFBXW11 bound, polyubiquitylated, and destabilized RAPGEF2, a guanine nucleotide exchange factor that activates the small GTPase RAP1. -
Systematic Cpg Islands Methylation Profiling of Genes in the Wnt Pathway in Epithelial Ovarian Cancer Identifies Biomarkers of Progression-Free Survival
Published OnlineFirst April 1, 2011; DOI: 10.1158/1078-0432.CCR-10-3021 Clinical Cancer Imaging, Diagnosis, Prognosis Research Systematic CpG Islands Methylation Profiling of Genes in the Wnt Pathway in Epithelial Ovarian Cancer Identifies Biomarkers of Progression-Free Survival Wei Dai1, Jens M. Teodoridis1, Constanze Zeller1, Janet Graham1, Jenny Hersey3, James M. Flanagan1, Euan Stronach2, David W. Millan4, Nadeem Siddiqui5, Jim Paul6, and Robert Brown1,3 Abstract Purpose: Wnt pathways control key biological processes that potentially impact on tumor progression and patient survival. We aimed to evaluate DNA methylation at promoter CpG islands (CGI) of Wnt pathway genes in ovarian tumors at presentation and identify biomarkers of patient progression-free survival (PFS). Experimental Design: Epithelial ovarian tumors (screening study n ¼ 120, validation study n ¼ 61), prospectively collected through a cohort study, were analyzed by differential methylation hybridization at 302 loci spanning 189 promoter CGIs at 137 genes in Wnt pathways. The association of methylation and PFS was examined by Cox proportional hazards model. Results: DNA methylation is associated with PFS at 20 of 302 loci (P < 0.05, n ¼ 111), with 5 loci significant at false discovery rate (FDR) less than 10%. A total of 11 of 20 loci retain significance in an independent validation cohort (n ¼ 48, P 0.05, FDR 10%), and 7 of these loci, at FZD4, DVL1, NFATC3, ROCK1, LRP5, AXIN1, and NKD1 genes, are independent from clinical parameters (adjusted P < 0.05). Increased methylation at these loci associates with increased hazard of disease progression. A multivariate Cox model incorporates only NKD1 and DVL1, identifying two groups differing in PFS [HR ¼ 2.09; 95% CI (1.39–3.15); permutation test P < 0.005]. -
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. -
Phosphorylation, Expression and Function of the Ultrabithorax Protein Family in Drosophila Melanogaster
Development 112, 1077-1093 (1991) 1077 Printed in Great Britain © The Company of Biologists Limited 1991 Phosphorylation, expression and function of the Ultrabithorax protein family in Drosophila melanogaster ELIZABETH R. GAVIS* and DAVID S. HOGNESSt't Department of Biochemistry, Beckman Center, Stanford University School of Medicine, Stanford, California 94305 USA * Present address: Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142 USA t Present address: Department of Developmental Biology, Beckman Center, Stanford University School of Medicine, Stanford, California, 94305 USA $ Author for correspondence Summary Alternative splicing of the Ultrabithorax homeotic gene parallel those for the respective mRNAs, and all transcript generates a family of five proteins (UBX isoforms are similarly phosphorylated throughout em- isoforms) that function as transcription factors. All bryogenesis. Analysis by cotransfection assays of the isoforms contain a homeodomain within a common 99 aa promoter activation and repression functions of mutant C-terminal region (C-constant region) which is joined to UBX proteins with various deletions in the N-constant a common 247 aa N-terminal (N-constant) region by region shows that repression is generally insensitive to different combinations of three small optional elements. deletion and, hence, presumably to phosphorylation. By Unlike the UBX proteins expressed in E. coli, UBX contrast, the activation function is differentially sensitive isoforms expressed in D. melanogaster cells are phos- to the different deletions in a manner indicating the phorylated on serine and threonine residues, located absence of a discrete activating domain and instead, the primarily within a 53 aa region near the middle of the presence of multiple activating sequences spread N-constant region, to form at least five phosphorylated throughout the region. -
Identification of Ovarian Cancer Gene Expression Patterns Associated
ORIG I NAL AR TI CLE JOURNALSECTION IdentifiCATION OF Ovarian Cancer Gene Expression PATTERNS Associated WITH Disease Progression AND Mortality Md. Ali Hossain1,2 | Sheikh Muhammad Saiful Islam3 | Julian Quinn4 | Fazlul Huq5 | Mohammad Ali Moni4,5 1Dept OF CSE, ManarAT International UnivERSITY, Dhaka-1212, Bangladesh Ovarian CANCER (OC) IS A COMMON CAUSE OF DEATH FROM can- 2Dept OF CSE, Jahangirnagar UnivERSITY, CER AMONG WOMEN worldwide, SO THERE IS A PRESSING NEED SaVAR, Dhaka, Bangladesh TO IDENTIFY FACTORS INflUENCING MORTALITY. Much OC PATIENT 3Dept. OF Pharmacy, ManarAT International UnivERSITY, Dhaka-1212, Bangladesh CLINICAL DATA IS NOW PUBLICALLY ACCESSIBLE (including PATIENT 4Bone BIOLOGY divisions, Garvan Institute OF age, CANCER SITE STAGE AND SUBTYPE), AS ARE LARGE DATASETS OF Medical Research, SyDNEY, NSW 2010, OC GENE TRANSCRIPTION PROfiles. These HAVE ENABLED STUDIES AustrALIA CORRELATING OC PATIENT SURVIVAL WITH CLINICAL VARIABLES AND 5The UnivERSITY OF SyDNEY, SyDNEY Medical School, School OF Medical Science, WITH GENE EXPRESSION BUT IT IS NOT WELL UNDERSTOOD HOW THESE Discipline OF Biomedical Sciences, NSW TWO ASPECTS INTERACT TO INflUENCE MORTALITY. TO STUDY THIS 1825, AustrALIA WE INTEGRATED CLINICAL AND TISSUE TRANSCRIPTOME DATA FROM Correspondence THE SAME PATIENTS AVAILABLE FROM THE Broad Institute Cancer Dept OF CSE, Jahangirnagar UnivERSITY, Dhaka, Bangladesh Genome Atlas (TCGA) portal. WE INVESTIGATED OC mRNA The UnivERSITY OF SyDNEY, SyDNEY Medical EXPRESSION LEVELS (relativE TO NORMAL PATIENT TISSUE) OF 26 School, School OF Medical Science, Discipline OF Biomedical Sciences, NSW GENES ALREADY STRONGLY IMPLICATED IN OC, ASSESSED HOW THEIR 1825, AustrALIA EXPRESSION IN OC TISSUE PREDICTS PATIENT SURVIVAL THEN em- Email: al i :hossai n@manarat :ac:bd , mohammad :moni @sydney :eduau PLOYED CoX Proportional Hazard REGRESSION MODELS TO anal- YSE BOTH CLINICAL FACTORS AND TRANSCRIPTOMIC INFORMATION TO FUNDING INFORMATION DETERMINE RELATIVE RISK OF DEATH ASSOCIATED WITH EACH FACTOR. -
Mechanisms of Wnt Signaling in Development
P1: APR/ary P2: ARS/dat QC: ARS/APM T1: ARS August 29, 1998 9:42 Annual Reviews AR066-03 Annu. Rev. Cell Dev. Biol. 1998. 14:59–88 Copyright c 1998 by Annual Reviews. All rights reserved MECHANISMS OF WNT SIGNALING IN DEVELOPMENT Andreas Wodarz Institut f¨ur Genetik, Universit¨at D¨usseldorf, Universit¨atsstrasse 1, 40225 D¨usseldorf, Germany; e-mail: [email protected] Roel Nusse Howard Hughes Medical Institute and Department of Developmental Biology, Stanford University, Stanford, CA 94305-5428; e-mail: [email protected] KEY WORDS: Wnt, wingless, frizzled, catenin, signal transduction ABSTRACT Wnt genes encode a large family of secreted, cysteine-rich proteins that play key roles as intercellular signaling molecules in development. Genetic studies in Drosophila and Caenorhabditis elegans, ectopic gene expression in Xenopus, and gene knockouts in the mouse have demonstrated the involvement of Wnts in pro- cesses as diverse as segmentation, CNS patterning, and control of asymmetric cell divisions. The transduction of Wnt signals between cells proceeds in a complex series of events including post-translational modification and secretion of Wnts, binding to transmembrane receptors, activation of cytoplasmic effectors, and, finally, transcriptional regulation of target genes. Over the past two years our understanding of Wnt signaling has been substantially improved by the identifi- cation of Frizzled proteins as cell surface receptors for Wnts and by the finding that -catenin, a component downstream of the receptor, can translocate to the nucleus and function as a transcriptional activator. Here we review recent data that have started to unravel the mechanisms of Wnt signaling. -
Identification of Genomic Organisation, Sequence Variants and Analysis of the Role of the Human Dishevelled 1 Gene in Late Onset Alzheimer's Disease
Molecular Psychiatry (2002) 7, 104–109 2002 Nature Publishing Group All rights reserved 1359-4184/02 $15.00 www.nature.com/mp ORIGINAL RESEARCH ARTICLE Identification of genomic organisation, sequence variants and analysis of the role of the human dishevelled 1 gene in late onset Alzheimer’s disease C Russ, S Lovestone and JF Powell Department of Neuroscience, Institute of Psychiatry, London SE5 8AF, UK Keywords: polymorphism; genomic; DVL1; association; kinases, such as c-Jun N-terminal kinase (JNK), and SNP glycogen synthase kinase 3 beta (GSK3) have been Alzheimer’s disease (AD) is a disorder characterised by shown to phosphorylate tau in vitro, in cell at sites that a progressive deterioration in memory and other cogni- are phosphorylated in PHF.4–7 JNK and GSK3 are tive functions. Neurofibrillary tangles (NFT) are a major regulated by the dishevelled 1 gene (DVL1), the latter pathological hallmark of AD, these are aggregations of as part of the wnt signalling pathways.8–11 Activation paired helical filaments (PHF) comprised of the hyper- of the wnt signalling pathway is thought to cause DVL1 phosphorylated microtubule associated protein tau. to inactivate GSK3 through complex-formation with Several kinases, such as glycogen synthase kinase 3   adenomatous poliposis coli (APC), axin and -catenin beta (GSK3 ) and c-Jun N-terminal kinase (JNK), phos- proteins,8 whereas JNK is activated by DVL1.10,11 The phorylate tau at sites that are phosphorylated in PHF. Dishevelled 1 (DVL1) is thought to act as a positive mechanism by which this JNK activation occurs is regulator of the wnt signalling pathway, and inhibits unclear, however, it has been demonstrated that a DEP GSK3 activity preventing -catenin degradation and (dishevelled, egl-10 and pleckstrin) protein binding thus allowing wnt target gene expression.