Number 2 February 2017 Atlas of Genetics and Cytogenetics in Oncology and Haematology
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Redefining the Specificity of Phosphoinositide-Binding by Human
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.20.163253; this version posted June 21, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 4.0 International license. Redefining the specificity of phosphoinositide-binding by human PH domain-containing proteins Nilmani Singh1†, Adriana Reyes-Ordoñez1†, Michael A. Compagnone1, Jesus F. Moreno Castillo1, Benjamin J. Leslie2, Taekjip Ha2,3,4,5, Jie Chen1* 1Department of Cell & Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801; 2Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205; 3Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218; 4Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205; 5Howard Hughes Medical Institute, Baltimore, MD 21205, USA †These authors contributed equally to this work. *Correspondence: [email protected]. bioRxiv preprint doi: https://doi.org/10.1101/2020.06.20.163253; this version posted June 21, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 4.0 International license. ABSTRACT Pleckstrin homology (PH) domains are presumed to bind phosphoinositides (PIPs), but specific interaction with and regulation by PIPs for most PH domain-containing proteins are unclear. Here we employed a single-molecule pulldown assay to study interactions of lipid vesicles with full-length proteins in mammalian whole cell lysates. -
HOXD8 Exerts a Tumor-Suppressing Role in Colorectal Cancer As an Apoptotic Inducer
HOXD8 exerts a tumor-suppressing role in colorectal cancer as an apoptotic inducer Mohammed A. Mansour1, Takeshi Senga2 1Biochemistry Division, Department of Chemistry, Faculty of Science, Tanta University, Tanta 31527, Egypt 2Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa, Nagoya, 466-8550 Japan Address correspondence to: Mohammed A. Mansour; Biochemistry division, Department of Chemistry, Faculty of Science, Tanta University, Tanta 31527, Egypt; E-mail: [email protected] Running title: HOXD8 suppresses colorectal cancer progression Keywords: Colorectal Cancer; HOXD8; homology modeling; TCGA; STK38; MYC; Apoptosis Conflict-of-interest statement: The authors declare that they have no conflict of interest. The data sharing statement: No additional data are available. Abstract Homeobox (HOX) genes are conserved transcription factors which determine the anterior- posterior body axis patterning. HOXD8 is a member of HOX genes deregulated in several tumors such as lung carcinoma, neuroblastoma, glioma and colorectal cancer (CRC) in a context-dependent manner. In CRC, HOXD8 is downregulated in cancer tissues and metastatic foci as compared to normal tissues. Whether HOXD8 acts as a tumor suppressor of malignant progression and metastasis is still unclear. Also, the underlying mechanism of its function including the downstream targets is totally unknown. Here, we clarified the lower expression of HOXD8 in clinical colorectal cancer vs. normal colon tissues. Also, we showed that stable expression of HOXD8 in colorectal cancer cells significantly reduced the cell proliferation, anchorage-independent growth and invasion. Further, using The Cancer Genome Atlas (TCGA), we identified the genes associated with HOXD8 in order to demonstrate its function as a suppressor or a promoter of colorectal carcinoma. -
Open Data for Differential Network Analysis in Glioma
International Journal of Molecular Sciences Article Open Data for Differential Network Analysis in Glioma , Claire Jean-Quartier * y , Fleur Jeanquartier y and Andreas Holzinger Holzinger Group HCI-KDD, Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Auenbruggerplatz 2/V, 8036 Graz, Austria; [email protected] (F.J.); [email protected] (A.H.) * Correspondence: [email protected] These authors contributed equally to this work. y Received: 27 October 2019; Accepted: 3 January 2020; Published: 15 January 2020 Abstract: The complexity of cancer diseases demands bioinformatic techniques and translational research based on big data and personalized medicine. Open data enables researchers to accelerate cancer studies, save resources and foster collaboration. Several tools and programming approaches are available for analyzing data, including annotation, clustering, comparison and extrapolation, merging, enrichment, functional association and statistics. We exploit openly available data via cancer gene expression analysis, we apply refinement as well as enrichment analysis via gene ontology and conclude with graph-based visualization of involved protein interaction networks as a basis for signaling. The different databases allowed for the construction of huge networks or specified ones consisting of high-confidence interactions only. Several genes associated to glioma were isolated via a network analysis from top hub nodes as well as from an outlier analysis. The latter approach highlights a mitogen-activated protein kinase next to a member of histondeacetylases and a protein phosphatase as genes uncommonly associated with glioma. Cluster analysis from top hub nodes lists several identified glioma-associated gene products to function within protein complexes, including epidermal growth factors as well as cell cycle proteins or RAS proto-oncogenes. -
NUDT21-Spanning Cnvs Lead to Neuropsychiatric Disease And
Vincenzo A. Gennarino1,2†, Callison E. Alcott2,3,4†, Chun-An Chen1,2, Arindam Chaudhury5,6, Madelyn A. Gillentine1,2, Jill A. Rosenfeld1, Sumit Parikh7, James W. Wheless8, Elizabeth R. Roeder9,10, Dafne D. G. Horovitz11, Erin K. Roney1, Janice L. Smith1, Sau W. Cheung1, Wei Li12, Joel R. Neilson5,6, Christian P. Schaaf1,2 and Huda Y. Zoghbi1,2,13,14. 1Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA. 2Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, Texas, 77030, USA. 3Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, 77030, USA. 4Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas, 77030, USA. 5Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, 77030, USA. 6Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, 77030, USA. 7Center for Child Neurology, Cleveland Clinic Children's Hospital, Cleveland, OH, United States. 8Department of Pediatric Neurology, Neuroscience Institute and Tuberous Sclerosis Clinic, Le Bonheur Children's Hospital, University of Tennessee Health Science Center, Memphis, TN, USA. 9Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas, USA. 10Department of Molecular and Human Genetics, Baylor College of Medicine, San Antonio, Texas, USA. 11Instituto Nacional de Saude da Mulher, da Criança e do Adolescente Fernandes Figueira - Depto de Genetica Medica, Rio de Janeiro, Brazil. 12Division of Biostatistics, Dan L Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA. 13Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, 77030, USA. -
Altered Gene Expression in Circulating Immune Cells Following a 24-Hour Passive Dehydration
University of Connecticut OpenCommons@UConn Master's Theses University of Connecticut Graduate School 5-10-2020 Altered Gene Expression in Circulating Immune Cells Following a 24-Hour Passive Dehydration Aidan Fiol [email protected] Follow this and additional works at: https://opencommons.uconn.edu/gs_theses Recommended Citation Fiol, Aidan, "Altered Gene Expression in Circulating Immune Cells Following a 24-Hour Passive Dehydration" (2020). Master's Theses. 1480. https://opencommons.uconn.edu/gs_theses/1480 This work is brought to you for free and open access by the University of Connecticut Graduate School at OpenCommons@UConn. It has been accepted for inclusion in Master's Theses by an authorized administrator of OpenCommons@UConn. For more information, please contact [email protected]. Altered Gene Expression in Circulating Immune Cells Following a 24- Hour Passive Dehydration Aidan Fiol B.S., University of Connecticut, 2018 A Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of Master of Science At the University of Connecticut 2020 i copyright by Aidan Fiol 2020 ii APPROVAL PAGE Master of Science Thesis Altered Gene Expression in Circulating Immune Cells Following a 24- Hour Passive Dehydration Presented by Aidan Fiol, B.S. Major Advisor__________________________________________________________________ Elaine Choung-Hee Lee, Ph.D. Associate Advisor_______________________________________________________________ Douglas J. Casa, Ph.D. Associate Advisor_______________________________________________________________ Robert A. Huggins, Ph.D. University of Connecticut 2020 iii ACKNOWLEDGEMENTS I’d like to thank my committee members. Dr. Lee, you have been an amazing advisor, mentor and friend to me these past few years. Your advice, whether it was how to be a better writer or scientist, or just general life advice given on our way to get coffee, has helped me grow as a researcher and as a person. -
Missing Proteins in Chromosome 16
Missing proteins in Chromosome 16 - Spanish HPP Manuel Fuentes1, Noelia Dasilva1, Felipe Clemente2, María Luisa Hernáez2, Paula Díez1, Maria Gonzalez-Gonzalez1, Alberto Orfao1, Felix Elortza5, Fernando Corrales4, Juan Pablo Albar3, Concha Gil2. 1Cancer Research Center. University of Salamanca-CSIC, IBSAL. Campus Miguel de Unamuno s/n. 37007 Salamanca. Spain. 2ProteoRed-ISCIII. Dpt. Microbiology & Proteomics Unit. University Complutense. Madrid. Spain. 3 ProteoRed-ISCIII. National Center of Biotechnology. CSIC. Madrid. Spain. 4ProteoRed-ISCIII. Center for Applied Medical Research (CIMA), Spain. 5ProteoRed-ISCIII. CIC bioGUNE. Bilbao. Spain. AIM In the scope of the HPP project, there is a special situation for the proteins that had not spectral and/or expression evidence, those are called "Unknown proteins".These proteins must be studied specifically to get enough information to build MRM quantitation methods. The Spanish HPP consortium has developed a specific protocol for unknown proteins in order to get MSMS information for the MRM method. MATERIALS AND METHODS Clones and plasmids All the clones used are from pANT7_cGST clone collection distributed by Plasmid repository at Arizona State University Biodesign Institute. Each clone contains an in-frame fused C-terminal GST tag. Each bacterial clone was grown overnight in 5 mL of Luria broth with 100 µg/mL ampicillin. Plasmid DNA was extracted using Mini- Prep Kit from Promega, following manufacture instructions. All plasmids were sequence to confirm the identity of the insert. DNA isolation and sequence verification Protein IVVT production Proteins were synthesized from plasmid DNA using Human In vitro Protein Expression kit (Thermo) following manufacture s protocol with a few minimal modifications in order to adapt for 1.5 mL eppendorf tubes. -
HOXD8 Exerts a Tumor-Suppressing Role in Colorectal Cancer As an Apoptotic Inducer
Mansour, M. A. and Senga, T. (2017) HOXD8 exerts a tumor-suppressing role in colorectal cancer as an apoptotic inducer. International Journal of Biochemistry and Cell Biology, 88, pp. 1-13. There may be differences between this version and the published version. You are advised to consult the publisher’s version if you wish to cite from it. http://eprints.gla.ac.uk/140905/ Deposited on: 30 May 2017 Enlighten – Research publications by members of the University of Glasgow http://eprints.gla.ac.uk HOXD8 exerts a tumor-suppressing role in colorectal cancer as an apoptotic inducer Mohammed A. Mansour1,2,3, Takeshi Senga4 1Biochemistry Division, Department of Chemistry, Faculty of Science, Tanta University, Tanta 31527, Egypt 2Cancer Research UK Beatson Institute, Switchback Road, Glasgow, G61 1BD, UK 3Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK 4Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa, Nagoya, 466-8550 Japan Address correspondence to: Mohammed A. Mansour; Biochemistry division, Department of Chemistry, Faculty of Science, Tanta University, Tanta 31527, Egypt; E-mail: [email protected] Running title: HOXD8 suppresses colorectal cancer progression Keywords: Colorectal Cancer; HOXD8; homology modeling; TCGA; STK38; MYC; Apoptosis Conflict-of-interest statement: The authors declare that they have no conflict of interest. The data sharing statement: No additional data are available. Abstract Homeobox (HOX) genes are conserved transcription factors which determine the anterior- posterior body axis patterning. HOXD8 is a member of HOX genes deregulated in several tumors such as lung carcinoma, neuroblastoma, glioma and colorectal cancer (CRC) in a context-dependent manner. -
Phenotype Informatics
Freie Universit¨atBerlin Department of Mathematics and Computer Science Phenotype informatics: Network approaches towards understanding the diseasome Sebastian Kohler¨ Submitted on: 12th September 2012 Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) am Fachbereich Mathematik und Informatik der Freien Universitat¨ Berlin ii 1. Gutachter Prof. Dr. Martin Vingron 2. Gutachter: Prof. Dr. Peter N. Robinson 3. Gutachter: Christopher J. Mungall, Ph.D. Tag der Disputation: 16.05.2013 Preface This thesis presents research work on novel computational approaches to investigate and characterise the association between genes and pheno- typic abnormalities. It demonstrates methods for organisation, integra- tion, and mining of phenotype data in the field of genetics, with special application to human genetics. Here I will describe the parts of this the- sis that have been published in peer-reviewed journals. Often in modern science different people from different institutions contribute to research projects. The same is true for this thesis, and thus I will itemise who was responsible for specific sub-projects. In chapter 2, a new method for associating genes to phenotypes by means of protein-protein-interaction networks is described. I present a strategy to organise disease data and show how this can be used to link diseases to the corresponding genes. I show that global network distance measure in interaction networks of proteins is well suited for investigat- ing genotype-phenotype associations. This work has been published in 2008 in the American Journal of Human Genetics. My contribution here was to plan the project, implement the software, and finally test and evaluate the method on human genetics data; the implementation part was done in close collaboration with Sebastian Bauer. -
Table S1. 103 Ferroptosis-Related Genes Retrieved from the Genecards
Table S1. 103 ferroptosis-related genes retrieved from the GeneCards. Gene Symbol Description Category GPX4 Glutathione Peroxidase 4 Protein Coding AIFM2 Apoptosis Inducing Factor Mitochondria Associated 2 Protein Coding TP53 Tumor Protein P53 Protein Coding ACSL4 Acyl-CoA Synthetase Long Chain Family Member 4 Protein Coding SLC7A11 Solute Carrier Family 7 Member 11 Protein Coding VDAC2 Voltage Dependent Anion Channel 2 Protein Coding VDAC3 Voltage Dependent Anion Channel 3 Protein Coding ATG5 Autophagy Related 5 Protein Coding ATG7 Autophagy Related 7 Protein Coding NCOA4 Nuclear Receptor Coactivator 4 Protein Coding HMOX1 Heme Oxygenase 1 Protein Coding SLC3A2 Solute Carrier Family 3 Member 2 Protein Coding ALOX15 Arachidonate 15-Lipoxygenase Protein Coding BECN1 Beclin 1 Protein Coding PRKAA1 Protein Kinase AMP-Activated Catalytic Subunit Alpha 1 Protein Coding SAT1 Spermidine/Spermine N1-Acetyltransferase 1 Protein Coding NF2 Neurofibromin 2 Protein Coding YAP1 Yes1 Associated Transcriptional Regulator Protein Coding FTH1 Ferritin Heavy Chain 1 Protein Coding TF Transferrin Protein Coding TFRC Transferrin Receptor Protein Coding FTL Ferritin Light Chain Protein Coding CYBB Cytochrome B-245 Beta Chain Protein Coding GSS Glutathione Synthetase Protein Coding CP Ceruloplasmin Protein Coding PRNP Prion Protein Protein Coding SLC11A2 Solute Carrier Family 11 Member 2 Protein Coding SLC40A1 Solute Carrier Family 40 Member 1 Protein Coding STEAP3 STEAP3 Metalloreductase Protein Coding ACSL1 Acyl-CoA Synthetase Long Chain Family Member 1 Protein -
The Genetic Architecture Underlying Ecological Adaptation in Atlantic
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.15.204214; this version posted July 15, 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 The genetic architecture underlying ecological adaptation in 2 Atlantic herring is not consistent with the infinitesimal model 3 4 Fan Han1, Minal Jamsandekar2, Mats E. Pettersson1, Leyi Su1, Angela Fuentes-Pardo1, Brian 5 Davis2, Dorte Bekkevold3, Florian Berg4,5, Michele Cassini6,7, Geir Dahle5, Edward D. 6 Farell8, Arild Folkvord4,5, Leif Andersson1,2,9,* 7 8 1Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 9 Sweden. 10 2Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, 11 USA. 12 3National Institute of Aquatic Resources, Technical University of Denmark. 13 4Department of Biological Sciences, University of Bergen, Bergen, Norway. 14 5Institute of Marine Research, Bergen, Norway. 15 6Department of Aquatic Resources, Institute of Marine Research, Swedish University of 16 Agricultural Sciences, Lysekil, Sweden. 17 7Department of Biological, Geological and Environmental Sciences, University of Bologna, 18 Bologna, Italy.8School of Biology and Environmental Science, Science Centre West, 19 University College Dublin, Belfield, Dublin 4, Ireland.9Department of Animal Breeding and 20 Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden. 21 *Corresponding author: Email:[email protected] 22 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.15.204214; this version posted July 15, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
Redefining the Specificity of Phosphoinositide-Binding By
ARTICLE https://doi.org/10.1038/s41467-021-24639-y OPEN Redefining the specificity of phosphoinositide- binding by human PH domain-containing proteins Nilmani Singh 1,6, Adriana Reyes-Ordoñez1,6, Michael A. Compagnone1, Jesus F. Moreno1, Benjamin J. Leslie2, ✉ Taekjip Ha 2,3,4,5 & Jie Chen 1 Pleckstrin homology (PH) domains are presumed to bind phosphoinositides (PIPs), but specific interaction with and regulation by PIPs for most PH domain-containing proteins are 1234567890():,; unclear. Here we employ a single-molecule pulldown assay to study interactions of lipid vesicles with full-length proteins in mammalian whole cell lysates. Of 67 human PH domain- containing proteins initially examined, 36 (54%) are found to have affinity for PIPs with various specificity, the majority of which have not been reported before. Further investigation of ARHGEF3 reveals distinct structural requirements for its binding to PI(4,5)P2 and PI(3,5) P2, and functional relevance of its PI(4,5)P2 binding. We generate a recursive-learning algorithm based on the assay results to analyze the sequences of 242 human PH domains, predicting that 49% of them bind PIPs. Twenty predicted binders and 11 predicted non- binders are assayed, yielding results highly consistent with the prediction. Taken together, our findings reveal unexpected lipid-binding specificity of PH domain-containing proteins. 1 Department of Cell & Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. 2 Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA. 3 Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA. 4 Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. -
Spotlight on Clinical Response
Published OnlineFirst April 29, 2008; DOI: 10.1158/1535-7163.MCT-07-2422 1001 Spotlight on Clinical Response Medullary thyroid cancer: targeting the RET kinase pathway with sorafenib/tipifarnib David Hong,1 Lei Ye,2 Robert Gagel,2 marfanoid habitus), and familial MTC. The RET proto- Lakshmi Chintala,1 Adel K. El Naggar,3 oncogene, located at chromosome 10q11.2, has been John Wright,4 and Razelle Kurzrock1 implicated in the pathogenesis of familial MTC and in as many as 50% of cases of sporadic MTC (2). 1Department of Investigational Cancer Therapeutics (Phase I Surgical resection is the mainstay of treatment; however, 2 Program), Division of Cancer Medicine, Department of Internal once MTC becomes unresectable, neither radiotherapy nor Medicine, and 3Pathology, M.D.Anderson Cancer Center, Houston, Texas; and 4Cancer Therapy Evaluation Program, systemic chemotherapeutic regimens have proved effective National Cancer Institute, Bethesda, Maryland in prolonging survival. Therefore, investigational therapies directed at molecularly defined etiologies of MTC are being pursued (3). Here we describe the rapid response of a Abstract patient with spontaneous MTC, who had aggressive Medullary thyroid carcinoma (MTC) is an uncommon disease and had progressed on conventional therapies. malignancy of hereditary and sporadic presentation. The patient’s tumor had an aberrant RET kinase gene and Mutations in the RET proto-oncogene are involved in the was treated with a combination of sorafenib (RET and RAF pathogenesis of familial MTC and >50% of the sporadic kinase and vascular endothelial growth factor receptor cases.Currently, there is no effective treatment for inhibitor) and tipifarnib (a farnesyltransferase inhibitor), recurrent or metastatic MTC.We report here a rapid targeted therapies that would disrupt RET-mediated signal response to a sorafenib (RET and RAF kinase and vascular transduction.