DOCSLIB.ORG

FACULDADE INFÓRIUM Diego Vinícius De Castro Pereira

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
FACULDADE INFÓRIUM Diego Vinícius De Castro Pereira FACULDADE INFÓRIUM Diego Vinícius de Castro Pereira IDENTIFICAÇÃO E ANÁLISE DE REDE DE GENES ENVOLVIDOS NO CÂNCER DE PELE DE MELANOMA ATRAVÉS DE MINERAÇÃO DE TEXTO Belo Horizonte Fevereiro de 2016 Diego Vinícius de Castro Pereira IDENTIFICAÇÃO E ANÁLISE DE REDE DE GENES ENVOLVIDOS NO CÂNCER DE PELE DE MELANOMA ATRAVÉS DE MINERAÇÃO DE TEXTO Dissertação apresentada ao Programa de pós- graduação da Faculdade Infórium de Belo horizonte, como requisito parcial a obtenção do título de mestre em Tecnologia da Informação Aplicada à Biologia Computacional. Orientador: Dr. Fabiano Sviatopolk-Mirsky Pais Coorientador: André Luiz Sena Guimaraes Belo Horizonte Fevereiro de 2016 2 Diego Vinícius de Castro Pereira. Identificação e Análise de Rede de Genes Envolvidos no Câncer de Pele de Melanoma Através de Mineração de Texto. Dissertação apresentada ao Programa de pós- graduação da Faculdade Infórium de Belo horizonte, como requisito parcial a obtenção do título de mestre em Tecnologia da Informação Aplicada à Biologia Computacional. Aprovada em ___/___/___ pela banca constituída dos seguintes professores: ______________________________________________________ Prof. Dr. Fabiano Sviatopolk-Mirsky Pais – Infórium _____________________________________________________ Prof. ______________________________________________________ Prof. Belo horizonte, fevereiro 2016. Faculdade Infórium de Belo Horizonte Rua dos Timbiras 1532 – 30.140-061 – Belo Horizonte, MG Telefone (31) 2103-2103 – www.mestradoti.com.br 3 Dedico este trabalho ao meu pai Francisco de Assis Cota Aguiar e à minha mãe Dalvemídia Pereira Aguiar, meus amores, que apesar das dificuldades soube transmitir toda sua sabedoria e apoio constante. 4 AGRADECIMENTOS A DEUS, que todos os dias de minha vida me deu forças para nunca desistir. A faculdade Infórium, por ter me dado à oportunidade de aprimorar meus conhecimentos. Aos meus colegas de mestrado, pelos bons momentos que passamos juntos. Ao meu orientador. Professor Dr. Fabiano Sviatopolk-Mirsky Pais e coorientador André Luiz Sena Guimarães, pelo apoio e amizade, além da dedicação, competência e especial atenção nas revisões e sugestões, fatores fundamentais para a conclusão deste trabalho. Aos professores que destinaram parte de seu precioso tempo para participarem desta pesquisa, em especial Marcos Flávio Silveira Vasconcelos D’angelo e Eloá Santos. A todos os professores do mestrado que de alguma forma contribuíram para a minha formação. Aos familiares e amigos que sempre me incentivaram e apoiaram nessa jornada. A minha namorada Joyce (Bisnaguinha), pelo carinho, apoio, paciência e massagens. Aos acadêmicos Tiago Caldeira e Raimundo pelo apoio no desenvolvimento da pesquisa. 5 Toda a sabedoria vem do Senhor Deus, ela sempre esteve com ele. Ela existe antes de todos os séculos. Quem pode contar os grãos de areia do mar, as gotas de chuva, os dias do tempo? Quem pode medir a altura do céu, a extensão da terra, a profundidade do abismo? Quem pode penetrar a sabedoria divina, anterior a tudo? A sabedoria foi criada antes de todas as coisas, a inteligência prudente existe antes dos séculos! O verbo de Deus nos céus é fonte de sabedoria, seus caminhos são os mandamentos eternos (ECLESIÁSTICO 1: 1-5). 6 RESUMO O câncer é definido como uma enfermidade caracterizada pelo crescimento descontrolado das células. É apontado como uma das principais causas de morte no mundo. Existem vários tipos de cânceres, sendo os mais frequentes na população masculina próstata, pulmão, cólon e reto. Entre as mulheres são mais comuns: mama, cólon, reto e pulmão. Contudo, o câncer de melanoma cutâneo é um tipo de câncer que vem apresentando um dos maiores índices de crescimento na última década. O melanoma inicia-se nos melanócitos, os quais são células que produzem a melanina e que garantem a proteção contra os danos causados pela radiação ultravioleta (UV). O desenvolvimento do melanoma é resultado de alterações no DNA. O estudo sobre o funcionamento de diversos genes vem sendo auxiliado pelas ferramentas de bioinformática. O objetivo deste trabalho foi identificar genes que podem estar envolvidos no desenvolvimento e/ou manutenção do câncer de pele melanoma e realizar uma comparação com os genes envolvidos na manutenção de uma pele saudável, através de pesquisa bibliográfica, bancos de dados genômicos e, sobretudo, com a utilização de ferramentas de bioinformática. Para a identificação dos genes envolvidos ou potencialmente envolvidos que foram analisados quanto a sua relação com o melanoma, utilizou-se como referência artigos científicos, livros, dissertações e teses da base de dados Pubmed. Após a identificação dos genes, as interações entre eles foram mapeadas, e um escore referente a essa interação, foi definida através do banco de dados STRING (Search Tool for the Retrieval of Interacting Genes/Proteins). Com base nesse escore, os genes foram agrupados usando o algoritmo de classificação K-means. Os genes do grupo que obteve o maior escore foram chamados genes líderes. Os outros grupos foram classificados por “B”, “C”, “D” e assim sucessivamente, de acordo com a força do escore. O estudo foi complementado por uma análise topológica dessa interação com os softwares Cytoscape, enquanto uma análise ontológica foi realizada com o software BinGO. A analise realizada permitiu sugerir genes com forte interação para o câncer de pele melanoma. Os genes líderes sugeridos foram o TP53, porém os genes pertencentes aos grupos B, C, e D (AKT1, JUN, STAT3 e MYC) também apresentaram escore relevante e obtiveram destaque no trabalho. Para a pele saudável, os genes líderes sugeridos foram o UBC, porém os genes dos grupos B, C, e D (TP53, JUN, AKT1, CREBBP, EP300 e SRC) também apresentaram o escore relevante. Uma comparação entre os genes identificados para câncer de pele melanoma e os genes da pele saudável, também foi realizada, sugerindo genes 7 que podem estar ativos, silenciados, ou apresentando variações em suas funções para este tipo de câncer. Palavras chave: bioinformática; câncer; melanoma; genes; pele; líder (res). 8 ABSTRACT Cancer is defined as a illness characterized by the uncontrolled growing of cells. It is appointed as the main cause of deaths in world. There are several types of cancers, being the most frequents in the male population: prostate, lung, colon and rectum. Among the women are more common: breast, colon, rectum and lung. However, cancer of cutaneous melanoma is a type of cancer which is showing one of the highest factors of growing on the last decade. Melanoma is started on melanocytes that are the cells that produce melanin and that staff the protection against the damages caused by the UV radiation. The development of melanoma is result of alterations on genes. The study of working of these genes has been helped by bioinformatic's tools. The purpose of this work was identify genes that can make part of development and maintenance of the skin cancer melanoma and make a comparison with the genes that make part of maintenance of healthy skin, through bibliographic search, genomic databases and mainly through the utilization of bioinformatic's tools. To identify the genes that potentially make part of the development and maintenance of the skin cancer and that had an analysis on their relations with the melanoma were utilized as reference: scientific articles, books, compositions and theses of Pubmed database. After the genes identification, their interactions were mapped, and a score (which was named WNL - Weighted Number of Links) relative to this interaction, was defined through STRING database (Search Tool for the Retrieval of Interacting Genes/Proteins). Based on this score, genes were grouped through the K-means classification algorithm. Genes of the group with the highest WNL were named leader genes. The others groups were classified as "B", "C", "D" etc. according to WNL. The study was completed with an topologic analysis of this interaction with the software Cytoscape, while an ontological analysis was made with the software BinGO. The analysis allowed suggest genes with a strong interaction with the skin cancer melanoma. The suggested leader genes were TP53's, but genes that belong to groups B, C, and D (AKT1, JUN, STAT3 and MYC) have also shown relevant WNL and got emphasis in this work. Suggested leader genes on healthy skin were UBC, but the genes of groups B, C and D (TP53, JUN, AKT1, CREBBP, EP300 e SRC) have also shown relevant WNL. A comparison between genes identified on skin cancer melanoma and genes of healthy skin was also made, suggesting genes that can be actives, silent, or showing variations on their functions to this type of cancer. Keywords: bioinformatic, cancer, melanoma, genes, skin, leader (s). 9 LISTA DE ILUSTRAÇÕES LISTA DE ILUSTRAÇÕES FIGURA 1 - Estrutura da Pele Humana...................................................................21 FIGURA 2 - Subtipos de melanomas......................................................................28 FIGURA 3 – Sistema ABCD(E) para identificação de melanomas.......................31 FIGURA 4 – Resultados dos tipos de associações em uma análise na base de dados STRING..........................................................................................................35 FIGURA 5 - Organização da Pesquisa....................................................................44 FIGURA 6 – Mapa de interação dos genes potencialmente envolvidos no câncer de pele melanoma........................................................................................46 FIGURA
Load more

Recommended publications
  • Transcriptome-Wide Profiling of the Neonatal Monocyte Response to E
    Transcriptome-wide profiling of the neonatal monocyte response to E. coli and S. epidermidis Emma de Jong, B.Sc. (Hons) This thesis is presented for the degree of Doctor of Philosophy School of Veterinary & Life Sciences 2015 Declaration I declare that this thesis is my own account of my research, and contains as its main content work that has not previously been submitted for a degree at any other tertiary education institution. .................................... (Emma de Jong) i ii Abstract Preterm infants are extremely vulnerable to life-threatening invasive infections (particularly with Staphylococcus epidermidis and Escherichia coli) however our understanding of their innate immune defences is limited. Furthermore, prenatal exposure to histologic chorioamnionitis (HCA) complicates 40–70% of preterm births and is known to modulate the risk for sepsis, yet the impact of HCA on the development of innate immunity is largely unknown. We hypothesised that inadequate monocyte activation by neonatal pathogens results in impaired innate immune responses thereby increasing preterm infants’ susceptibility to invasive infection, and that prenatal exposure to HCA overrides these impairments. Cell sorting and bacterial stimulation methodologies were developed and optimised specifically for working with human infant cord blood samples. RNA-sequencing was performed on purified cord blood monocytes from very preterm (≤31 weeks gestational age (GA)) and term infants (37–40 weeks GA) following challenge with live S. epidermidis or E. coli to identify gene/pathway differences specific to the preterm infant. Protein levels of inflammatory cytokines and chemokines were measured in paired monocyte culture supernatants. Preterm infants displayed a quantitative monocyte deficiency compared to term infants, manifesting as reduced frequencies of classical monocytes with significantly reduced CD14 expression.
    [Show full text]
  • Termination of RNA Polymerase II Transcription by the 5’-3’ Exonuclease Xrn2
    TERMINATION OF RNA POLYMERASE II TRANSCRIPTION BY THE 5’-3’ EXONUCLEASE XRN2 by MICHAEL ANDRES CORTAZAR OSORIO B.S., Universidad del Valle – Colombia, 2011 A thesis submitted to the Faculty of the Graduate School of the University of Colorado in partial fulfillment of the requirements for the degree of Doctor of Philosophy Molecular Biology Program 2018 This thesis for the Doctor of Philosophy degree by Michael Andrés Cortázar Osorio has been approved for the Molecular Biology Program by Mair Churchill, Chair Richard Davis Jay Hesselberth Thomas Blumenthal James Goodrich David Bentley, Advisor Date: Aug 17, 2018 ii Cortázar Osorio, Michael Andrés (Ph.D., Molecular Biology) Termination of RNA polymerase II transcription by the 5’-3’ exonuclease Xrn2 Thesis directed by Professor David L. Bentley ABSTRACT Termination of transcription occurs when RNA polymerase (pol) II dissociates from the DNA template and releases a newly-made mRNA molecule. Interestingly, an active debate fueled by conflicting reports over the last three decades is still open on which of the two main models of termination of RNA polymerase II transcription does in fact operate at 3’ ends of genes. The torpedo model indicates that the 5’-3’ exonuclease Xrn2 targets the nascent transcript for degradation after cleavage at the polyA site and chases pol II for termination. In contrast, the allosteric model asserts that transcription through the polyA signal induces a conformational change of the elongation complex and converts it into a termination-competent complex. In this thesis, I propose a unified allosteric-torpedo mechanism. Consistent with a polyA site-dependent conformational change of the elongation complex, I found that pol II transitions at the polyA site into a mode of slow transcription elongation that is accompanied by loss of Spt5 phosphorylation in the elongation complex.
    [Show full text]
  • Exploration of the Relationships Between Tumor Mutation Burden with Immune Infiltrates in Clear Cell Renal Cell Carcinoma
    648 Original Article Page 1 of 16 Exploration of the relationships between tumor mutation burden with immune infiltrates in clear cell renal cell carcinoma Chuanjie Zhang1#, Zongtai Li2#, Feng Qi3#, Xin Hu4, Jun Luo5 1Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; 2Department of Medical Oncology, Gaozhou People’s Hospital, Gaozhou 525200, China; 3Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China; 4First Clinical Medical College of Nanjing Medical University, Nanjing 210029, China; 5Department of Urology, Shanghai Fourth People’s Hospital affiliated to Tongji University School of Medicine, Shanghai 200081, China Contributions: (I) Conception and design: J Luo, C Zhang; (II) Administrative support: C Zhang; (III) Provision of study materials or patients: Z Li, F Qi; (IV) Collection and assembly of data: X Hu; (V) Data analysis and interpretation: J Luo, C Zhang; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors. #These authors contributed equally to this article. Correspondence to: Jun Luo. Department of Urology, Shanghai Fourth People’s Hospital affiliated to Tongji University School of Medicine, No. 1878 North Sichuan Road, Hongkou District, Shanghai 200081, China. Email: [email protected]. Background: Whether tumor mutation burden (TMB) correlated with improved survival outcomes or promotion of immunotherapies remained controversy in various malignancies. We aimed to investigate the prognosis of TMB and the potential association with immune infiltrates in clear cell renal cell carcinoma (ccRCC). Methods: We downloaded the somatic mutation data of 336 ccRCC patients from the Cancer Genome Atlas (TCGA) database, and analyzed the mutation profiles with “maftools” package.
    [Show full text]
  • Genome-Wide Meta-Analysis Identifies Six Novel Loci Associated With
    Molecular Psychiatry (2015) 20, 647–656 © 2015 Macmillan Publishers Limited All rights reserved 1359-4184/15 www.nature.com/mp ORIGINAL ARTICLE Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption The Coffee and Caffeine Genetics Consortium, MC Cornelis1,2, EM Byrne3,117, T Esko4,5,6,7,117, MA Nalls8,117, A Ganna9, N Paynter10, KL Monda11, N Amin12, K Fischer4, F Renstrom13, JS Ngwa14, V Huikari15, A Cavadino16, IM Nolte17, A Teumer18,KYu19, P Marques-Vidal20, R Rawal21, A Manichaikul22, MK Wojczynski23, JM Vink24, JH Zhao25, G Burlutsky26, J Lahti27,28, V Mikkilä29,30, RN Lemaitre31, J Eriksson32, SK Musani33, T Tanaka34, F Geller35, J Luan25, J Hui36,37,38,39, R Mägi4, M Dimitriou40, ME Garcia41, W-K Ho42, MJ Wright43, LM Rose10, PKE Magnusson9, NL Pedersen9, D Couper44, BA Oostra45, A Hofman12, MA Ikram12,46,47, HW Tiemeier12,48, AG Uitterlinden12,49, FJA van Rooij12, I Barroso50,51, I Johansson52, L Xue14, M Kaakinen15,53,54, L Milani4, C Power16, H Snieder17, RP Stolk17, SE Baumeister55, R Biffar56,FGu19, F Bastardot57, Z Kutalik58,59,60, DR Jacobs Jr61, NG Forouhi25, E Mihailov4, L Lind62, C Lindgren63, K Michaëlsson64, A Morris63, M Jensen2, K-T Khaw42, RN Luben42, JJ Wang26, S Männistö65, M-M Perälä65, M Kähönen66, T Lehtimäki67, J Viikari68, D Mozaffarian1,2,69,70, K Mukamal71, BM Psaty31,72,73,74, A Döring75, AC Heath76, GW Montgomery43, N Dahmen77, T Carithers78, KL Tucker79, L Ferrucci34, HA Boyd35, M Melbye35, JL Treur24, D Mellström32, JJ Hottenga24, I Prokopenko63,80, A Tönjes81,82,
    [Show full text]
  • Content Based Search in Gene Expression Databases and a Meta-Analysis of Host Responses to Infection
    Content Based Search in Gene Expression Databases and a Meta-analysis of Host Responses to Infection A Thesis Submitted to the Faculty of Drexel University by Francis X. Bell in partial fulfillment of the requirements for the degree of Doctor of Philosophy November 2015 c Copyright 2015 Francis X. Bell. All Rights Reserved. ii Acknowledgments I would like to acknowledge and thank my advisor, Dr. Ahmet Sacan. Without his advice, support, and patience I would not have been able to accomplish all that I have. I would also like to thank my committee members and the Biomed Faculty that have guided me. I would like to give a special thanks for the members of the bioinformatics lab, in particular the members of the Sacan lab: Rehman Qureshi, Daisy Heng Yang, April Chunyu Zhao, and Yiqian Zhou. Thank you for creating a pleasant and friendly environment in the lab. I give the members of my family my sincerest gratitude for all that they have done for me. I cannot begin to repay my parents for their sacrifices. I am eternally grateful for everything they have done. The support of my sisters and their encouragement gave me the strength to persevere to the end. iii Table of Contents LIST OF TABLES.......................................................................... vii LIST OF FIGURES ........................................................................ xiv ABSTRACT ................................................................................ xvii 1. A BRIEF INTRODUCTION TO GENE EXPRESSION............................. 1 1.1 Central Dogma of Molecular Biology........................................... 1 1.1.1 Basic Transfers .......................................................... 1 1.1.2 Uncommon Transfers ................................................... 3 1.2 Gene Expression ................................................................. 4 1.2.1 Estimating Gene Expression ............................................ 4 1.2.2 DNA Microarrays ......................................................
    [Show full text]
  • Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands That Promote Axonal Growth
    Research Article: New Research Development Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth Jeremy S. Toma,1 Konstantina Karamboulas,1,ª Matthew J. Carr,1,2,ª Adelaida Kolaj,1,3 Scott A. Yuzwa,1 Neemat Mahmud,1,3 Mekayla A. Storer,1 David R. Kaplan,1,2,4 and Freda D. Miller1,2,3,4 https://doi.org/10.1523/ENEURO.0066-20.2020 1Program in Neurosciences and Mental Health, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada, 2Institute of Medical Sciences University of Toronto, Toronto, Ontario M5G 1A8, Canada, 3Department of Physiology, University of Toronto, Toronto, Ontario M5G 1A8, Canada, and 4Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada Abstract Peripheral nerves provide a supportive growth environment for developing and regenerating axons and are es- sential for maintenance and repair of many non-neural tissues. This capacity has largely been ascribed to paracrine factors secreted by nerve-resident Schwann cells. Here, we used single-cell transcriptional profiling to identify ligands made by different injured rodent nerve cell types and have combined this with cell-surface mass spectrometry to computationally model potential paracrine interactions with peripheral neurons. These analyses show that peripheral nerves make many ligands predicted to act on peripheral and CNS neurons, in- cluding known and previously uncharacterized ligands. While Schwann cells are an important ligand source within injured nerves, more than half of the predicted ligands are made by nerve-resident mesenchymal cells, including the endoneurial cells most closely associated with peripheral axons. At least three of these mesen- chymal ligands, ANGPT1, CCL11, and VEGFC, promote growth when locally applied on sympathetic axons.
    [Show full text]
  • Mapping and Identification of Candidate Genes and Variants for Adiposity Traits in Outbred Rats Gregory R
    Original Article Obesity EPIDEMIOLOGY/GENETICS Genetic Fine-Mapping and Identification of Candidate Genes and Variants for Adiposity Traits in Outbred Rats Gregory R. Keele1, Jeremy W. Prokop2, Hong He3, Katie Holl3, John Littrell3, Aaron Deal4, Sanja Francic5, Leilei Cui5, Daniel M. Gatti6, Karl W. Broman7, Michael Tschannen3, Shirng-Wern Tsaih3, Maie Zagloul1, Yunjung Kim1, Brittany Baur3, Joseph Fox3, Melanie Robinson2, Shawn Levy2, Michael J. Flister3, Richard Mott5, William Valdar 1*, and Leah C. Solberg Woods 4* Objective: Obesity is a major risk factor for multiple diseases and is in part heritable, yet the majority of caus- ative genetic variants that drive excessive adiposity remain unknown. Here, outbred heterogeneous stock (HS) rats were used in controlled environmental conditions to fine-map novel genetic modifiers of adiposity. Methods: Body weight and visceral fat pad weights were measured in male HS rats that were also geno- typed genome-wide. Quantitative trait loci (QTL) were identified by genome-wide association of imputed single-nucleotide polymorphism (SNP) genotypes using a linear mixed effect model that accounts for unequal relatedness between the HS rats. Candidate genes were assessed by protein modeling and mediation analysis of expression for coding and noncoding variants, respectively. Results: HS rats exhibited large variation in adiposity traits, which were highly heritable and correlated with metabolic health. Fine-mapping of fat pad weight and body weight revealed three QTL and prioritized five can- didate genes. Fat pad weight was associated with missense SNPs in Adcy3 and Prlhr and altered expression of Krtcap3 and Slc30a3,whereasGrid2 was identified as a candidate within the body weight locus.
    [Show full text]
  • 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
    [Show full text]
  • ATRAID, a Genetic Factor That Regulates the Action of Nitrogen-Containing Bisphosphonates on Bone
    bioRxiv preprint doi: https://doi.org/10.1101/338350; this version posted January 10, 2019. 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. Title: ATRAID, a genetic factor that regulates the action of nitrogen-containing bisphosphonates on bone Authors: Lauren E. Surface1, Jiwoong Park2, Sandeep Kumar2, Damon T. Burrow2, Cheng Lyu2, Jinmei Li2, Niki Song2, Zhou Yu1, Abbhirami Rajagopal3,#, Yangjin Bae3, Brendan H. Lee3, Steven Mumm4, Gabe Haller5, Charles C. Gu6, Jonathan C. Baker7, Mahshid Mohseni4, Melissa Sum8, Margaret Huskey4, Shenghui Duan4, Vinieth N. Bijanki9, Roberto Civitelli4, Michael J. Gardner10, Chris M. McAndrew5, William M. Ricci11, Christina A. Gurnett5, Kathryn Diemer4, Jan E. Carette12, Malini Varadarajan13,*, Thijn R. Brummelkamp13, Kivanc Birsoy14, David M. Sabatini15-17, Timothy R. Peterson2* Affiliations: 1 Department of Molecular and Cellular Biology, Department of Chemistry and Chemical Biology, Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. 2 Division of Bone & Mineral Diseases, Department of Internal Medicine, Department of Genetics, Institute for Public Health, Washington University School of Medicine, BJC Institute of Health, 425 S. Euclid Ave., St. Louis, MO 63110, USA. 3 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. # (present address) Harris County Public health, Houston, TX, 77027, USA. 4 Division of Bone & Mineral Diseases, Department of Internal Medicine, Washington University School of Medicine, BJC Institute of Health, 425 S.
    [Show full text]
  • ATRAID Regulates the Action of Nitrogen-Containing Bisphosphonates on Bone 2 3 Authors: Lauren E
    bioRxiv preprint doi: https://doi.org/10.1101/338350; this version posted April 10, 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. 1 Title: ATRAID regulates the action of nitrogen-containing bisphosphonates on bone 2 3 Authors: Lauren E. Surface1,&, Damon T. Burrow2, Jinmei Li2, Jiwoong Park2, Sandeep Kumar2, 4 Cheng Lyu2, Niki Song2, Zhou Yu1,^, Abbhirami Rajagopal3,#, Yangjin Bae3, Brendan H. Lee3, 5 Steven Mumm2,4, Charles C. Gu5, Jonathan C. Baker6, Mahshid Mohseni2, Melissa Sum7, 6 Margaret Huskey2, Shenghui Duan2, Vinieth N. Bijanki4, Roberto Civitelli2, Michael J. Gardner8, 7 Chris M. McAndrew9, William M. Ricci10, Christina A. Gurnett9,11, Kathryn Diemer2, Fei Wan12, 8 Christina L. Costantino13, Kristen M. Shannon14, Noopur Raje14, Thomas B. Dodson15,@, Daniel 9 A. Haber14,16, Jan E. Carette17, Malini Varadarajan18, Thijn R. Brummelkamp19-21, Kivanc 10 Birsoy22, David M. Sabatini16,23-25, Gabe Haller11,26, Timothy R. Peterson2,27,28* 11 12 Affiliations: 13 1 Department of Molecular and Cellular Biology, Department of Chemistry and Chemical 14 Biology, Faculty of Arts and Sciences Center for Systems Biology, Harvard University, 15 Cambridge, MA 02138, USA. 16 & (present address) Endocrine Unit, 55 Fruit St., Massachusetts General Hospital, Harvard 17 Medical School, Boston, MA, 02114, USA. 18 ^ (present address) Howard Hughes Medical Institute (HHMI) Janelia Research Campus, 19700 19 Helix Drive, Ashburn, Virginia 20147, USA. 20 2 Division of Bone & Mineral Diseases, Department of Medicine, Washington University School 21 of Medicine, BJC Institute of Health, 425 S.
    [Show full text]
  • PWD/Ph-Encoded Genetic Variants Modulate the Cellular Wnt/B-Catenin Response to Suppress Apcmin-Triggered Intestinal Tumor Formation Alexandra L
    Published OnlineFirst November 5, 2020; DOI: 10.1158/0008-5472.CAN-20-1480 CANCER RESEARCH | GENOME AND EPIGENOME PWD/Ph-Encoded Genetic Variants Modulate the Cellular Wnt/b-Catenin Response to Suppress ApcMin-Triggered Intestinal Tumor Formation Alexandra L. Farrall1,2, Matthias Lienhard1, Christina Grimm1,3, Heiner Kuhl1,4, Susanna H.M. Sluka1, Marta Caparros1, Jiri Forejt5, Bernd Timmermann1, Ralf Herwig1, Bernhard G. Herrmann1,6, and Markus Morkel7 ABSTRACT ◥ Genetic predisposition affects the penetrance of tumor-initiating suggesting that PWD variants restrict adenoma initiation by mutations, such as APC mutations that stabilize b-catenin and controlling stem cell homeostasis. Gene expression of modifier cause intestinal tumors in mice and humans. However, the mechan- candidates and DNA methylation on chromosome 5 were isms involved in genetically predisposed penetrance are not well predominantly cis controlled and largely reflected parental understood. Here, we analyzed tumor multiplicity and gene expres- patterns, providing a genetic basis for inheritance of tumor þ sion in tumor-prone ApcMin/ mice on highly variant C57BL/6J susceptibility. Human SNP variants of several modifier candi- (B6) and PWD/Ph (PWD) genetic backgrounds. (B6 Â PWD) F1 dates were depleted in colorectal cancer genomes, suggesting APCMin offspring mice were largely free of intestinal adenoma, and that similar mechanisms may also affect the penetrance of several chromosome substitution (consomic) strains carrying single cancer driver mutations in humans. Overall, our analysis high- PWD chromosomes on the B6 genetic background displayed lights the strong impact that multiple genetic variants acting in reduced adenoma numbers. Multiple dosage-dependent modifier networks can exert on tumor development.
    [Show full text]
  • Peripheral Nerve Single Cell Analysis Identifies Mesenchymal Ligands That Promote Axonal Growth
    Research Article: New Research | Development Peripheral Nerve Single Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth https://doi.org/10.1523/ENEURO.0066-20.2020 Cite as: eNeuro 2020; 10.1523/ENEURO.0066-20.2020 Received: 24 February 2020 Revised: 20 April 2020 Accepted: 23 April 2020 This Early Release article has been peer-reviewed and accepted, but has not been through the composition and copyediting processes. The final version may differ slightly in style or formatting and will contain links to any extended data. Alerts: Sign up at www.eneuro.org/alerts to receive customized email alerts when the fully formatted version of this article is published. Copyright © 2020 Toma et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license, which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed. 1 Peripheral Nerve Single Cell Analysis Identifies Mesenchymal Ligands that Promote 2 Axonal Growth 3 4 Jeremy S. Toma1, Konstantina Karamboulas1*, Matthew J. Carr 1,2*, Adelaida Kolaj1,3, Scott A. 5 Yuzwa1, Neemat Mahmud 1,3, Mekayla A. Storer1, David R. Kaplan1,2,4 and Freda D. Miller1-4 6 7 Program in Neurosciences and Mental Health1, Hospital for Sick Children, Toronto, Canada 8 M5G 1L7, Institute of Medical Sciences2, Departments of Physiology3 and Molecular Genetics4, 9 University of Toronto, Toronto, Canada M5G 1A8. 10 11 *These authors contributed equally. 12 13 Abbreviated Title: scRNA-seq identifies nerve ligands 14 Author Contributions: JST, DRK and FDM designed research; JST, MJC, AK, and NM 15 performed research; JST, KK, SAY, NM, MAS and FDM analyzed data; and JST, DRK and 16 FDM wrote the paper.
    [Show full text]