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Taylor MA, Kandyba E, Halliwill K, Delrosario R, Khoroshkin M, Goodarzi H, Quigley D, Li YR, Wu D, Bollam SR, Mirzoeva OK, Akhurst RJ, Balmain A. Stem-cell states converge in multistage cutaneous squamous cell carcinoma development. Science 2024; 384:eadi7453. [PMID: 38815020 DOI: 10.1126/science.adi7453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 04/05/2024] [Indexed: 06/01/2024]
Abstract
Stem cells play a critical role in cancer development by contributing to cell heterogeneity, lineage plasticity, and drug resistance. We created gene expression networks from hundreds of mouse tissue samples (both normal and tumor) and integrated these with lineage tracing and single-cell RNA-seq, to identify convergence of cell states in premalignant tumor cells expressing markers of lineage plasticity and drug resistance. Two of these cell states representing multilineage plasticity or proliferation were inversely correlated, suggesting a mutually exclusive relationship. Treatment of carcinomas in vivo with chemotherapy repressed the proliferative state and activated multilineage plasticity whereas inhibition of differentiation repressed plasticity and potentiated responses to cell cycle inhibitors. Manipulation of this cell state transition point may provide a source of potential combinatorial targets for cancer therapy.
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Affiliation(s)
- Mark A Taylor
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Clinical Research Centre, Medical University of Bialystok, Bialystok 15-089, Poland
| | - Eve Kandyba
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kyle Halliwill
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- AbbVie, South San Francisco, CA 94080, USA
| | - Reyno Delrosario
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Matvei Khoroshkin
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Hani Goodarzi
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94518, USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94518, USA
- Arc Institute, Palo Alto, CA 94304, USA
| | - David Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94518, USA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA 94518, USA
| | - Yun Rose Li
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Radiation Oncology, City of Hope National Medical Center, Duarte, CA 91010, USA
- Department of Cancer Genetics & Epigenetics, City of Hope National Medical Center, Duarte, CA 91010, USA
- Division of Quantitative Medicine & Systems Biology, Translational Genomics Research Institute, Phoenix, CA 85004, USA
| | - Di Wu
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Saumya R Bollam
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA 94518, USA
| | - Olga K Mirzoeva
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Rosemary J Akhurst
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94518, USA
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94518, USA
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2
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Murillo Carrasco AG, Furuya TK, Uno M, Citrangulo Tortelli T, Chammas R. deltaXpress (ΔXpress): a tool for mapping differentially correlated genes using single-cell qPCR data. BMC Bioinformatics 2023; 24:402. [PMID: 37884889 PMCID: PMC10605457 DOI: 10.1186/s12859-023-05541-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND High-throughput experiments provide deep insight into the molecular biology of different species, but more tools need to be developed to handle this type of data. At the transcriptomics level, quantitative Polymerase Chain Reaction technology (qPCR) can be affordably adapted to produce high-throughput results through a single-cell approach. In addition to comparative expression profiles between groups, single-cell approaches allow us to evaluate and propose new dependency relationships among markers. However, this alternative has not been explored before for large-scale qPCR-based experiments. RESULTS Herein, we present deltaXpress (ΔXpress), a web app for analyzing data from single-cell qPCR experiments using a combination of HTML and R programming languages in a friendly environment. This application uses cycle threshold (Ct) values and categorical information for each sample as input, allowing the best pair of housekeeping genes to be chosen to normalize the expression of target genes. ΔXpress emulates a bulk analysis by observing differentially expressed genes, but in addition, it allows the discovery of pairwise genes differentially correlated when comparing two experimental conditions. Researchers can download normalized data or use subsequent modules to map differentially correlated genes, perform conventional comparisons between experimental groups, obtain additional information about their genes (gene glossary), and generate ready-to-publication images (600 dots per inch). CONCLUSIONS ΔXpress web app is freely available to non-commercial users at https://alexismurillo.shinyapps.io/dXpress/ and can be used for different experiments in all technologies involving qPCR with at least one housekeeping region.
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Affiliation(s)
- Alexis Germán Murillo Carrasco
- Center for Translational Research in Oncology (LIM24), Instituto Do Cancer Do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), São Paulo, SP, CEP 01246-000, Brazil.
- Comprehensive Center for Precision Oncology, Universidade de Sao Paulo, São Paulo, Brazil.
| | - Tatiane Katsue Furuya
- Center for Translational Research in Oncology (LIM24), Instituto Do Cancer Do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), São Paulo, SP, CEP 01246-000, Brazil
- Comprehensive Center for Precision Oncology, Universidade de Sao Paulo, São Paulo, Brazil
| | - Miyuki Uno
- Center for Translational Research in Oncology (LIM24), Instituto Do Cancer Do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), São Paulo, SP, CEP 01246-000, Brazil
- Comprehensive Center for Precision Oncology, Universidade de Sao Paulo, São Paulo, Brazil
| | - Tharcisio Citrangulo Tortelli
- Center for Translational Research in Oncology (LIM24), Instituto Do Cancer Do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), São Paulo, SP, CEP 01246-000, Brazil
- Comprehensive Center for Precision Oncology, Universidade de Sao Paulo, São Paulo, Brazil
| | - Roger Chammas
- Center for Translational Research in Oncology (LIM24), Instituto Do Cancer Do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), São Paulo, SP, CEP 01246-000, Brazil.
- Comprehensive Center for Precision Oncology, Universidade de Sao Paulo, São Paulo, Brazil.
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3
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Taylor MA, Kandyba E, Halliwill K, Delrosario R, Koroshkin M, Goodarzi H, Quigley D, Li YR, Wu D, Bollam S, Mirzoeva O, Akhurst RJ, Balmain A. Gene networks reveal stem-cell state convergence during preneoplasia and progression to malignancy in multistage skin carcinogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539863. [PMID: 37215032 PMCID: PMC10197547 DOI: 10.1101/2023.05.08.539863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Adult mammalian stem cells play critical roles in normal tissue homeostasis, as well as in tumor development, by contributing to cell heterogeneity, plasticity, and development of drug resistance. The relationship between different types of normal and cancer stem cells is highly controversial and poorly understood. Here, we carried out gene expression network analysis of normal and tumor samples from genetically heterogeneous mice to create network metagenes for visualization of stem-cell networks, rather than individual stem-cell markers, at the single-cell level during multistage carcinogenesis. We combined this approach with lineage tracing and single-cell RNASeq of stem cells and their progeny, identifying a previously unrecognized hierarchy in which Lgr6+ stem cells from tumors generate progeny that express a range of other stem-cell markers including Sox2, Pitx1, Foxa1, Klf5, and Cd44. Our data identify a convergence of multiple stem-cell and tumor-suppressor pathways in benign tumor cells expressing markers of lineage plasticity and oxidative stress. This same single-cell population expresses network metagenes corresponding to markers of cancer drug resistance in human tumors of the skin, lung and prostate. Treatment of mouse squamous carcinomas in vivo with the chemotherapeutic cis-platin resulted in elevated expression of the genes that mark this cell population. Our data have allowed us to create a simplified model of multistage carcinogenesis that identifies distinct stem-cell states at different stages of tumor progression, thereby identifying networks involved in lineage plasticity, drug resistance, and immune surveillance, providing a rich source of potential targets for cancer therapy.
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Affiliation(s)
- Mark A. Taylor
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Eve Kandyba
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Kyle Halliwill
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Reyno Delrosario
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Matvei Koroshkin
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Hani Goodarzi
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - David Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Yun Rose Li
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Di Wu
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Saumya Bollam
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Olga Mirzoeva
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Rosemary J. Akhurst
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
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4
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Kobia FM, Preusse K, Dai Q, Weaver N, Hass MR, Chaturvedi P, Stein SJ, Pear WS, Yuan Z, Kovall RA, Kuang Y, Eafergen N, Sprinzak D, Gebelein B, Brunskill EW, Kopan R. Notch dimerization and gene dosage are important for normal heart development, intestinal stem cell maintenance, and splenic marginal zone B-cell homeostasis during mite infestation. PLoS Biol 2020; 18:e3000850. [PMID: 33017398 PMCID: PMC7561103 DOI: 10.1371/journal.pbio.3000850] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 10/15/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022] Open
Abstract
Cooperative DNA binding is a key feature of transcriptional regulation. Here we examined the role of cooperativity in Notch signaling by CRISPR-mediated engineering of mice in which neither Notch1 nor Notch2 can homo- or heterodimerize, essential for cooperative binding to sequence-paired sites (SPS) located near many Notch-regulated genes. Although most known Notch-dependent phenotypes were unaffected in Notch1/2 dimer-deficient mice, a subset of tissues proved highly sensitive to loss of cooperativity. These phenotypes include heart development, compromised viability in combination with low gene dose, and the gut, developing ulcerative colitis in response to 1% dextran sulfate sodium (DSS). The most striking phenotypes-gender imbalance and splenic marginal zone B-cell lymphoma-emerged in combination with gene dose reduction or when challenged by chronic fur mite infestation. This study highlights the role of the environment in malignancy and colitis and is consistent with Notch-dependent anti-parasite immune responses being compromised in Notch dimer-deficient animals.
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Affiliation(s)
- Francis M. Kobia
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Kristina Preusse
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Quanhui Dai
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Nicholas Weaver
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Matthew R. Hass
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Praneet Chaturvedi
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Sarah J. Stein
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Warren S. Pear
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Zhenyu Yuan
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Rhett A. Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Yi Kuang
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Natanel Eafergen
- School of Neurobiology, Biochemistry, and Biophysics, The George S. Wise Faculty of Life Sciences Tel Aviv University, Tel Aviv, Israel
| | - David Sprinzak
- School of Neurobiology, Biochemistry, and Biophysics, The George S. Wise Faculty of Life Sciences Tel Aviv University, Tel Aviv, Israel
| | - Brian Gebelein
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Eric W. Brunskill
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Raphael Kopan
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
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5
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Lorenzo-Martín LF, Fernández-Parejo N, Menacho-Márquez M, Rodríguez-Fdez S, Robles-Valero J, Zumalave S, Fabbiano S, Pascual G, García-Pedrero JM, Abad A, García-Macías MC, González N, Lorenzano-Menna P, Pavón MA, González-Sarmiento R, Segrelles C, Paramio JM, Tubío JMC, Rodrigo JP, Benitah SA, Cuadrado M, Bustelo XR. VAV2 signaling promotes regenerative proliferation in both cutaneous and head and neck squamous cell carcinoma. Nat Commun 2020; 11:4788. [PMID: 32963234 PMCID: PMC7508832 DOI: 10.1038/s41467-020-18524-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/27/2020] [Indexed: 12/30/2022] Open
Abstract
Regenerative proliferation capacity and poor differentiation are histological features usually linked to poor prognosis in head and neck squamous cell carcinoma (hnSCC). However, the pathways that regulate them remain ill-characterized. Here, we show that those traits can be triggered by the RHO GTPase activator VAV2 in keratinocytes present in the skin and oral mucosa. VAV2 is also required to maintain those traits in hnSCC patient-derived cells. This function, which is both catalysis- and RHO GTPase-dependent, is mediated by c-Myc- and YAP/TAZ-dependent transcriptomal programs associated with regenerative proliferation and cell undifferentiation, respectively. High levels of VAV2 transcripts and VAV2-regulated gene signatures are both associated with poor hnSCC patient prognosis. These results unveil a druggable pathway linked to the malignancy of specific SCC subtypes. The Rho signalling pathway is frequently activated in squamous carcinomas. Here, the authors find that the Rho GEF VAV2 is over expressed in both cutaneous and head and neck squamous cell carcinomas and that at the molecular level VAV2 promotes a pro-tumorigenic stem cell-like signalling programme.
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Affiliation(s)
- L Francisco Lorenzo-Martín
- Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007, Salamanca, Spain
| | - Natalia Fernández-Parejo
- Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007, Salamanca, Spain
| | - Mauricio Menacho-Márquez
- Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Inmunología Clínica y Experimental de Rosario (IDICER, CONICET-UNR). Facultad de Ciencias Médicas Universidad Nacional de Rosario (M.M.-M.) and CellPress editorial office (S.F.), S2000LRJ, Rosario, Argentina
| | - Sonia Rodríguez-Fdez
- Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007, Salamanca, Spain
| | - Javier Robles-Valero
- Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007, Salamanca, Spain
| | - Sonia Zumalave
- Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Salvatore Fabbiano
- Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Inmunología Clínica y Experimental de Rosario (IDICER, CONICET-UNR). Facultad de Ciencias Médicas Universidad Nacional de Rosario (M.M.-M.) and CellPress editorial office (S.F.), S2000LRJ, Rosario, Argentina
| | - Gloria Pascual
- Institute for Research in Biomedicine, 33011, Barcelona, Spain.,The Barcelona Institute of Science and Technology, Barcelona, 33011, Spain
| | - Juana M García-Pedrero
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007, Salamanca, Spain.,Hospital Universitario Central de Asturias, Oviedo University, 33011, Oviedo, Spain
| | - Antonio Abad
- Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007, Salamanca, Spain
| | - María C García-Macías
- Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007, Salamanca, Spain
| | - Nazareno González
- Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain
| | - Pablo Lorenzano-Menna
- Laboratory of Molecular Oncology and National University of Quilmes, Buenos Aires, B1876BXD, Argentina.,National Council of Scientific and Technical Research (CONICET), National University of Quilmes, Buenos Aires, B1876BXD, Argentina
| | - Miguel A Pavón
- Institut Català d'Oncologia, 08908, L'Hospitalet de Llobregat, Spain.,Centro Biomédica de Investigación en Red de Enfermedades Respiratorias (CIBERESP), 08908, L'Hospitalet de Llobregat, Spain
| | - Rogelio González-Sarmiento
- Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca, 37007, Salamanca, Spain
| | - Carmen Segrelles
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007, Salamanca, Spain.,Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, 28040, Madrid, Spain
| | - Jesús M Paramio
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007, Salamanca, Spain.,Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, 28040, Madrid, Spain
| | - José M C Tubío
- Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Juan P Rodrigo
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007, Salamanca, Spain.,Hospital Universitario Central de Asturias, Oviedo University, 33011, Oviedo, Spain
| | - Salvador A Benitah
- Institute for Research in Biomedicine, 33011, Barcelona, Spain.,The Barcelona Institute of Science and Technology, Barcelona, 33011, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), 33011, Barcelona, Spain
| | - Myriam Cuadrado
- Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007, Salamanca, Spain
| | - Xosé R Bustelo
- Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain. .,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007, Salamanca, Spain.
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6
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Lander JM, Supp DM, He H, Martin LJ, Chen X, Weirauch MT, Boyce ST, Kopan R. Analysis of chromatin accessibility in human epidermis identifies putative barrier dysfunction-sensing enhancers. PLoS One 2017; 12:e0184500. [PMID: 28953906 PMCID: PMC5617145 DOI: 10.1371/journal.pone.0184500] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 08/24/2017] [Indexed: 01/12/2023] Open
Abstract
To identify putative gene regulatory regions that respond to epidermal injury, we mapped chromatin dynamics in a stratified human epidermis during barrier maturation and disruption. Engineered skin substitutes (ESS) cultured at the air-liquid interface were used as a model of developing human epidermis with incomplete barrier formation. The epidermal barrier stabilized following engraftment onto immunocompromised mice, and was compromised again upon injury. Modified formaldehyde-assisted isolation of regulatory elements (FAIRE) was used to identify accessible genomic regions characteristic of monolayer keratinocytes, ESS in vitro, grafted ESS, and tape-stripped ESS graft. We mapped differentiation- and maturation-associated changes in transcription factor binding sites enriched at each stage and observed overrepresentation of AP-1 gene family motifs in barrier-deficient samples. Transcription of TSLP, an important effector of immunological memory in response to allergen exposure, was dramatically elevated in our barrier-deficient samples. We identified dynamic DNA elements that correlated with TSLP induction and may contain enhancers that regulate TSLP. Two dynamic regions were located near the TSLP promoter and overlapped with allergy-associated SNPs rs17551370 and rs2289877, strongly implicating these loci in the regulation of TSLP expression in allergic disease. Additional dynamic chromatin regions ~250kb upstream of the TSLP promoter were found to be in high linkage disequilibrium with allergic disease SNPs. Taken together, these results define dynamic chromatin accessibility changes during epidermal development and dysfunction.
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Affiliation(s)
- Julie M. Lander
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Dorothy M. Supp
- Research Department, Shriners Hospitals for Children, Cincinnati, Ohio, United States of America
- Department of Surgery, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Hua He
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Lisa J. Martin
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Matthew T. Weirauch
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Division of Biomedical Informatics, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Steven T. Boyce
- Research Department, Shriners Hospitals for Children, Cincinnati, Ohio, United States of America
- Department of Surgery, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Raphael Kopan
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
- * E-mail:
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7
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Zhao Y, Forst CV, Sayegh CE, Wang IM, Yang X, Zhang B. Molecular and genetic inflammation networks in major human diseases. MOLECULAR BIOSYSTEMS 2017; 12:2318-41. [PMID: 27303926 DOI: 10.1039/c6mb00240d] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
It has been well-recognized that inflammation alongside tissue repair and damage maintaining tissue homeostasis determines the initiation and progression of complex diseases. Albeit with the accomplishment of having captured the most critical inflammation-involved molecules, genetic susceptibilities, epigenetic factors, and environmental factors, our schemata on the role of inflammation in complex diseases remain largely patchy, in part due to the success of reductionism in terms of research methodology per se. Omics data alongside the advances in data integration technologies have enabled reconstruction of molecular and genetic inflammation networks which shed light on the underlying pathophysiology of complex diseases or clinical conditions. Given the proven beneficial role of anti-inflammation in coronary heart disease as well as other complex diseases and immunotherapy as a revolutionary transition in oncology, it becomes timely to review our current understanding of the molecular and genetic inflammation networks underlying major human diseases. In this review, we first briefly discuss the complexity of infectious diseases and then highlight recently uncovered molecular and genetic inflammation networks in other major human diseases including obesity, type II diabetes, coronary heart disease, late onset Alzheimer's disease, Parkinson's disease, and sporadic cancer. The commonality and specificity of these molecular networks are addressed in the context of genetics based on genome-wide association study (GWAS). The double-sword role of inflammation, such as how the aberrant type 1 and/or type 2 immunity leads to chronic and severe clinical conditions, remains open in terms of the inflammasome and the core inflammatome network features. Increasingly available large Omics and clinical data in tandem with systems biology approaches have offered an exciting yet challenging opportunity toward reconstruction of more comprehensive and dynamic molecular and genetic inflammation networks, which hold great promise in transiting network snapshots to video-style multi-scale interplays of disease mechanisms, in turn leading to effective clinical intervention.
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Affiliation(s)
- Yongzhong Zhao
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA. and Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA
| | - Christian V Forst
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA. and Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA
| | - Camil E Sayegh
- Vertex Pharmaceuticals (Canada) Incorporated, 275 Armand-Frappier, Laval, Quebec H7V 4A7, Canada
| | - I-Ming Wang
- Informatics and Analysis, Merck Research Laboratories, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA.
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90025, USA.
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA. and Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA
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Jin M, Gu S, Ye D, Li Y, Jing F, Li Q, Chen K. Association between genetic variants in the promoter region of a novel antisense long noncoding RNA RP11-392P7.6 and colorectal cancer risk. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:434-442. [PMID: 28612367 DOI: 10.1002/em.22100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 04/28/2017] [Indexed: 06/07/2023]
Abstract
There is a widespread occurrence of antisense transcripts' regulation on cancer-related genes in cancer biology. RP11-392P7.6 is antisense to the coding region of cancer-related gene GPRC5D, which has been found recently. The aim of this study was to investigate the associations of tagSNPs in the promoter region of RP11-392P7.6 with the risk of colorectal cancer. We conducted a two-stage case-control study, with a discovery set (320 cases and 319 controls) and a validation set (501 cases and 538 controls). Four tagSNPs (rs1531970, rs1642199, rs4763903, and rs10845671) were selected based on 1000 Genomes Project data and genotyped by using the Sequenom MassARRAY genotyping platform. In the discovery set, three tagSNPs (rs1642199, rs4763903, and rs10845671) were revealed promising associations with the risk of colorectal cancer, among which the rs10845671 variants were further replicated in the validation set (OR = 1.47, 95% CI = 1.10-1.20 in heterozygote codominant model; OR = 1.38, 95% CI = 1.04-1.83 in dominant model). When combined the two sets, the above positive associations remained unchanged. Rs10845671 was found to be associated with an increased risk of colorectal cancer (OR = 1.43, 95% CI = 1.14-1.81 in heterozygote codominant model; OR = 1.35, 95% CI = 1.08-1.69 in dominant model). These findings indicate that rs10845671 may contribute to the susceptibility to colorectal cancer and be a candidate biomarker for colorectal cancer risk prediction. Environ. Mol. Mutagen. 58:434-442, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Mingjuan Jin
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, Hangzhou, 310058, Zhejiang, China
| | - Simeng Gu
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, Hangzhou, 310058, Zhejiang, China
| | - Ding Ye
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, Hangzhou, 310058, Zhejiang, China
| | - Yingjun Li
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, Hangzhou, 310058, Zhejiang, China
| | - Fangyuan Jing
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, Hangzhou, 310058, Zhejiang, China
| | - Qilong Li
- Institute for Cancer Prevention of Jiashan County, Zhejiang, China
| | - Kun Chen
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, Hangzhou, 310058, Zhejiang, China
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10
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Halliwill KD, Quigley DA, Kang HC, Del Rosario R, Ginzinger D, Balmain A. Panx3 links body mass index and tumorigenesis in a genetically heterogeneous mouse model of carcinogen-induced cancer. Genome Med 2016; 8:83. [PMID: 27506198 PMCID: PMC4977876 DOI: 10.1186/s13073-016-0334-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 07/11/2016] [Indexed: 01/01/2023] Open
Abstract
Background Body mass index (BMI) has been implicated as a primary factor influencing cancer development. However, understanding the relationship between these two complex traits has been confounded by both environmental and genetic heterogeneity. Methods In order to gain insight into the genetic factors linking BMI and cancer, we performed chemical carcinogenesis on a genetically heterogeneous cohort of interspecific backcross mice ((Mus Spretus × FVB/N) F1 × FVB/N). Using this cohort, we performed quantitative trait loci (QTL) analysis to identify regions linked to BMI. We then performed an integrated analysis incorporating gene expression, sequence comparison between strains, and gene expression network analysis to identify candidate genes influencing both tumor development and BMI. Results Analysis of QTL linked to tumorigenesis and BMI identified several loci associated with both phenotypes. Exploring these loci in greater detail revealed a novel relationship between the Pannexin 3 gene (Panx3) and both BMI and tumorigenesis. Panx3 is positively associated with BMI and is strongly tied to a lipid metabolism gene expression network. Pre-treatment Panx3 gene expression levels in normal skin are associated with tumor susceptibility and inhibition of Panx function strongly influences inflammation. Conclusions These studies have identified several genetic loci that influence both BMI and carcinogenesis and implicate Panx3 as a candidate gene that links these phenotypes through its effects on inflammation and lipid metabolism. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0334-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kyle D Halliwill
- Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Hio Chung Kang
- Invitae Corporation, 458 Brannan St, San Francisco, CA, 94107, USA
| | - Reyno Del Rosario
- Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - David Ginzinger
- Thermo Fisher Scientific, 5791 Van Allen Way, Carlsbad, CA, 92008, USA
| | - Allan Balmain
- Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA, USA. .,Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
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Quigley DA, Kandyba E, Huang P, Halliwill KD, Sjölund J, Pelorosso F, Wong CE, Hirst GL, Wu D, Delrosario R, Kumar A, Balmain A. Gene Expression Architecture of Mouse Dorsal and Tail Skin Reveals Functional Differences in Inflammation and Cancer. Cell Rep 2016; 16:1153-1165. [PMID: 27425619 DOI: 10.1016/j.celrep.2016.06.061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/16/2016] [Accepted: 06/14/2016] [Indexed: 12/13/2022] Open
Abstract
Inherited germline polymorphisms can cause gene expression levels in normal tissues to differ substantially between individuals. We present an analysis of the genetic architecture of normal adult skin from 470 genetically unique mice, demonstrating the effect of germline variants, skin tissue location, and perturbation by exogenous inflammation or tumorigenesis on gene signaling pathways. Gene networks related to specific cell types and signaling pathways, including sonic hedgehog (Shh), Wnt, Lgr family stem cell markers, and keratins, differed at these tissue sites, suggesting mechanisms for the differential susceptibility of dorsal and tail skin to development of skin diseases and tumorigenesis. The Pten tumor suppressor gene network is rewired in premalignant tumors compared to normal tissue, but this response to perturbation is lost during malignant progression. We present a software package for expression quantitative trait loci (eQTL) network analysis and demonstrate how network analysis of whole tissues provides insights into interactions between cell compartments and signaling molecules.
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Affiliation(s)
- David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo 0310, Norway; K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo 0313, Norway; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Eve Kandyba
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Phillips Huang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome Building, Singapore 138672, Singapore
| | - Kyle D Halliwill
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jonas Sjölund
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 22381 Lund, Sweden
| | - Facundo Pelorosso
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Instituto de Farmacología, Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155, 9(th) Floor, Ciudad Autónoma de Buenos Aires 1121, Argentina
| | - Christine E Wong
- Institute of Surgical Pathology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Gillian L Hirst
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Di Wu
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Reyno Delrosario
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Atul Kumar
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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12
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Cotroneo CE, Dassano A, Colombo F, Pettinicchio A, Lecis D, Dugo M, De Cecco L, Dragani TA, Manenti G. Expression quantitative trait analysis reveals fine germline transcript regulation in mouse lung tumors. Cancer Lett 2016; 375:221-230. [PMID: 26966001 DOI: 10.1016/j.canlet.2016.02.054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 02/25/2016] [Accepted: 02/26/2016] [Indexed: 01/24/2023]
Abstract
Gene expression modulates cellular functions in both physiologic and pathologic conditions. Herein, we carried out a genetic linkage study on the transcriptome of lung tumors induced by urethane in an (A/J x C57BL/6)F4 intercross population, whose individual lung tumor multiplicity (Nlung) is linked to the genotype at the Pulmonary adenoma susceptibility 1 (Pas1) locus. We found that expression levels of 1179 and 1579 genes are modulated by an expression quantitative trait locus (eQTL) in cis and in trans, respectively (LOD score > 5). Of note, the genomic area surrounding and including the Pas1 locus regulated 14 genes in cis and 857 genes in trans. In lung tumors of the same (A/J x C57BL/6)F4 mice, we found 1124 genes whose transcript levels associated with Nlung (FDR < 0.001). The expression levels of about a third of these genes (n = 401) were regulated by the genotype at the Pas1 locus. Pathway analysis of the sets of genes associated with Nlung and regulated by Pas1 revealed a set of 14 recurrently represented genes that are components or targets of the Ras-Erk and Pi3k-Akt signaling pathways. Altogether our results illustrate the architecture of germline control of gene expression in mouse lung cancer: they highlight the importance of Pas1 as a tumor-modifier locus, attribute to it a novel role as a major regulator of transcription in lung tumor nodules and strengthen the candidacy of the Kras gene as the effector of this locus.
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Affiliation(s)
- Chiara E Cotroneo
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Alice Dassano
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Francesca Colombo
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Angela Pettinicchio
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Daniele Lecis
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Matteo Dugo
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Loris De Cecco
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Tommaso A Dragani
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy.
| | - Giacomo Manenti
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
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Barcellos-Hoff MH, Mao JH. HZE Radiation Non-Targeted Effects on the Microenvironment That Mediate Mammary Carcinogenesis. Front Oncol 2016; 6:57. [PMID: 27014632 PMCID: PMC4786544 DOI: 10.3389/fonc.2016.00057] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/28/2016] [Indexed: 01/06/2023] Open
Abstract
Clear mechanistic understanding of the biological processes elicited by radiation that increase cancer risk can be used to inform prediction of health consequences of medical uses, such as radiotherapy, or occupational exposures, such as those of astronauts during deep space travel. Here, we review the current concepts of carcinogenesis as a multicellular process during which transformed cells escape normal tissue controls, including the immune system, and establish a tumor microenvironment. We discuss the contribution of two broad classes of radiation effects that may increase cancer: radiation targeted effects that occur as a result of direct energy deposition, e.g., DNA damage, and non-targeted effects (NTE) that result from changes in cell signaling, e.g., genomic instability. It is unknown whether the potentially greater carcinogenic effect of high Z and energy (HZE) particle radiation is a function of the relative contribution or extent of NTE or due to unique NTE. We addressed this problem using a radiation/genetic mammary chimera mouse model of breast cancer. Our experiments suggest that NTE promote more aggressive cancers, as evidenced by increased growth rate, transcriptomic signatures, and metastasis, and that HZE particle NTE are more effective than reference γ-radiation. Emerging evidence suggest that HZE irradiation dampens antitumor immunity. These studies raise concern that HZE radiation exposure not only increases the likelihood of developing cancer but also could promote progression to more aggressive cancer with a greater risk of mortality.
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Affiliation(s)
| | - Jian-Hua Mao
- Lawrence Berkeley National Laboratory , Berkeley, CA , USA
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Moharil J, May P, Gaile DP, Blair RH. Belief propagation in genotype-phenotype networks. Stat Appl Genet Mol Biol 2016; 15:39-53. [PMID: 26910752 DOI: 10.1515/sagmb-2015-0058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Graphical models have proven to be a valuable tool for connecting genotypes and phenotypes. Structural learning of phenotype-genotype networks has received considerable attention in the post-genome era. In recent years, a dozen different methods have emerged for network inference, which leverage natural variation that arises in certain genetic populations. The structure of the network itself can be used to form hypotheses based on the inferred direct and indirect network relationships, but represents a premature endpoint to the graphical analyses. In this work, we extend this endpoint. We examine the unexplored problem of perturbing a given network structure, and quantifying the system-wide effects on the network in a node-wise manner. The perturbation is achieved through the setting of values of phenotype node(s), which may reflect an inhibition or activation, and propagating this information through the entire network. We leverage belief propagation methods in Conditional Gaussian Bayesian Networks (CG-BNs), in order to absorb and propagate phenotypic evidence through the network. We show that the modeling assumptions adopted for genotype-phenotype networks represent an important sub-class of CG-BNs, which possess properties that ensure exact inference in the propagation scheme. The system-wide effects of the perturbation are quantified in a node-wise manner through the comparison of perturbed and unperturbed marginal distributions using a symmetric Kullback-Leibler divergence. Applications to kidney and skin cancer expression quantitative trait loci (eQTL) data from different mus musculus populations are presented. System-wide effects in the network were predicted and visualized across a spectrum of evidence. Sub-pathways and regions of the network responded in concert, suggesting co-regulation and coordination throughout the network in response to phenotypic changes. We demonstrate how these predicted system-wide effects can be examined in connection with estimated class probabilities for covariates of interest, e.g. cancer status. Despite the uncertainty in the network structure, we demonstrate the system-wide predictions are stable across an ensemble of highly likely networks. A software package, geneNetBP, which implements our approach, was developed in the R programming language.
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McCreery MQ, Halliwill KD, Chin D, Delrosario R, Hirst G, Vuong P, Jen KY, Hewinson J, Adams DJ, Balmain A. Evolution of metastasis revealed by mutational landscapes of chemically induced skin cancers. Nat Med 2015; 21:1514-20. [PMID: 26523969 PMCID: PMC5094808 DOI: 10.1038/nm.3979] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/23/2015] [Indexed: 12/15/2022]
Abstract
Human tumors show a high level of genetic heterogeneity, but the processes that influence the timing and route of metastatic dissemination of the subclones are unknown. Here we have used whole-exome sequencing of 103 matched benign, malignant and metastatic skin tumors from genetically heterogeneous mice to demonstrate that most metastases disseminate synchronously from the primary tumor, supporting parallel rather than linear evolution as the predominant model of metastasis. Shared mutations between primary carcinomas and their matched metastases have the distinct A-to-T signature of the initiating carcinogen dimethylbenzanthracene, but non-shared mutations are primarily G-to-T, a signature associated with oxidative stress. The existence of carcinomas that either did or did not metastasize in the same host animal suggests that there are tumor-intrinsic factors that influence metastatic seeding. We also demonstrate the importance of germline polymorphisms in determining allele-specific mutations, and we identify somatic genetic alterations that are specifically related to initiation of carcinogenesis by Hras or Kras mutations. Mouse tumors that mimic the genetic heterogeneity of human cancers can aid our understanding of the clonal evolution of metastasis and provide a realistic model for the testing of novel therapies.
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Affiliation(s)
- Melissa Q McCreery
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, Cancer Research Institute, University of California, San Francisco, San Francisco, California, USA
| | - Kyle D Halliwill
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, Cancer Research Institute, University of California, San Francisco, San Francisco, California, USA
| | - Douglas Chin
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, Cancer Research Institute, University of California, San Francisco, San Francisco, California, USA
| | - Reyno Delrosario
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, Cancer Research Institute, University of California, San Francisco, San Francisco, California, USA
| | - Gillian Hirst
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, Cancer Research Institute, University of California, San Francisco, San Francisco, California, USA
| | - Peter Vuong
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, Cancer Research Institute, University of California, San Francisco, San Francisco, California, USA
| | - Kuang-Yu Jen
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, Cancer Research Institute, University of California, San Francisco, San Francisco, California, USA
| | - James Hewinson
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Allan Balmain
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, Cancer Research Institute, University of California, San Francisco, San Francisco, California, USA
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Statistical thermodynamics of transcription profiles in normal development and tumorigeneses in cohorts of patients. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 44:709-26. [PMID: 26290059 DOI: 10.1007/s00249-015-1069-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/26/2015] [Accepted: 07/30/2015] [Indexed: 10/23/2022]
Abstract
Experimental biology is providing the distribution of numerous different biological molecules inside cells and in body fluids of patients. Statistical methods of analysis have very successfully examined these rather large databases. We seek to use a thermodynamic analysis to provide a physical understanding and quantitative characterization of human cancers and other pathologies within a molecule-centered approach. The key technical development is the introduction of a Lagrangian. By imposing constraints the minimal value of the Lagrangian defines a thermodynamically stable state of the cellular system. The minimization also allows using experimental data measured at a number of different conditions to evaluate the steady-state distribution of biomolecules such as messenger RNAs. Thereby the number of effectively accessible quantum states of biomolecules is determined from the experimentally measured expression levels. With the increased resolution provided by the minimization of the Lagrangian one can differentiate between normal and diseased patients and further between disease subtypes. Each such refinement corresponds to imposing an additional constraint of biological origin. The constraints are the unbalanced ongoing biological processes in the system. MicroRNA expression level data for control and diseased lung cancer patients are analyzed as an example.
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Abstract
BACKGROUND Gene expression microarrays measure the levels of messenger ribonucleic acid (mRNA) in a sample using probe sequences that hybridize with transcribed regions. These probe sequences are designed using a reference genome for the relevant species. However, most model organisms and all humans have genomes that deviate from their reference. These variations, which include single nucleotide polymorphisms, insertions of additional nucleotides, and nucleotide deletions, can affect the microarray's performance. Genetic experiments comparing individuals bearing different population-associated single nucleotide polymorphisms that intersect microarray probes are therefore subject to systemic bias, as the reduction in binding efficiency due to a technical artifact is confounded with genetic differences between parental strains. This problem has been recognized for some time, and earlier methods of compensation have attempted to identify probes affected by genome variants using statistical models. These methods may require replicate microarray measurement of gene expression in the relevant tissue in inbred parental samples, which are not always available in model organisms and are never available in humans. RESULTS By using sequence information for the genomes of organisms under investigation, potentially problematic probes can now be identified a priori. However, there is no published software tool that makes it easy to eliminate these probes from an annotation. I present equalizer, a software package that uses genome variant data to modify annotation files for the commonly used Affymetrix IVT and Gene/Exon platforms. These files can be used by any microarray normalization method for subsequent analysis. I demonstrate how use of equalizer on experiments mapping germline influence on gene expression in a genetic cross between two divergent mouse species and in human samples significantly reduces probe hybridization-induced bias, reducing false positive and false negative findings. CONCLUSIONS The equalizer package reduces probe hybridization bias from experiments performed on the Affymetrix microarray platform, allowing accurate assessment of germline influence on gene expression.
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Affiliation(s)
- David Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, 94158, USA.
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Nassar D, Latil M, Boeckx B, Lambrechts D, Blanpain C. Genomic landscape of carcinogen-induced and genetically induced mouse skin squamous cell carcinoma. Nat Med 2015; 21:946-54. [PMID: 26168291 DOI: 10.1038/nm.3878] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 05/18/2015] [Indexed: 12/17/2022]
Abstract
Mouse models of cancers are routinely used to study cancer biology. However, it remains unclear whether carcinogenesis in mice is driven by the same spectrum of genomic alterations found in humans. Here we conducted a comprehensive genomic analysis of 9,10-dimethyl-1,2-benzanthracene (DMBA)-induced skin cancer, the most commonly used skin cancer model, which appears as benign papillomas that progress into squamous cell carcinomas (SCCs). We also studied genetically induced SCCs that expressed G12D mutant Kras (Kras G12D) but were deficient for p53. Using whole-exome sequencing, we uncovered a characteristic mutational signature of DMBA-induced SCCs. We found that the vast majority of DMBA-induced SCCs presented recurrent mutations in Hras, Kras or Rras2 and mutations in several additional putative oncogenes and tumor-suppressor genes. Similar genes were recurrently mutated in mouse and human SCCs that were from different organs or had been exposed to different carcinogens. Invasive SCCs, but not papillomas, presented substantial chromosomal aberrations, especially in DMBA-induced and genetically induced Trp53-mutated SCCs. Metastasis occurred through sequential spreading, with relatively few additional genetic events. This study provides a framework for future functional cancer genomic studies in mice.
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Affiliation(s)
- Dany Nassar
- Institut de recherche interdisciplinaire en biologie humaine et moléculaire (IRIBHM), Université libre de Buxelles (ULB), Brussels, Belgium
| | - Mathilde Latil
- Institut de recherche interdisciplinaire en biologie humaine et moléculaire (IRIBHM), Université libre de Buxelles (ULB), Brussels, Belgium
| | - Bram Boeckx
- 1] Vesalius Research Center, Vlaams Instituut voor Biotechnologie VIB, Leuven, Belgium. [2] Laboratory for Translational Genetics, Department of Oncology, Katholieke Universiteit Leuven (KUL), Leuven, Belgium
| | - Diether Lambrechts
- 1] Vesalius Research Center, Vlaams Instituut voor Biotechnologie VIB, Leuven, Belgium. [2] Laboratory for Translational Genetics, Department of Oncology, Katholieke Universiteit Leuven (KUL), Leuven, Belgium
| | - Cédric Blanpain
- 1] Institut de recherche interdisciplinaire en biologie humaine et moléculaire (IRIBHM), Université libre de Buxelles (ULB), Brussels, Belgium. [2] WELBIO, Brussels, Belgium
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Abstract
Sprouty proteins are evolutionarily conserved modulators of MAPK/ERK pathway. Through interacting with an increasing number of effectors, mediators, and regulators with ultimate influence on multiple targets within or beyond ERK, Sprouty orchestrates a complex, multilayered regulatory system and mediates a crosstalk among different signaling pathways for a coordinated cellular response. As such, Sprouty has been implicated in various developmental and physiological processes. Evidence shows that ERK is aberrantly activated in malignant conditions. Accordingly, Sprouty deregulation has been reported in different cancer types and shown to impact cancer development, progression, and metastasis. In this article, we have tried to provide an overview of the current knowledge about the Sprouty physiology and its regulatory functions in health, as well as an updated review of the Sprouty status in cancer. Putative implications of Sprouty in cancer biology, their clinical relevance, and their proposed applications are also revisited. As a developing story, however, role of Sprouty in cancer remains to be further elucidated.
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Affiliation(s)
- Samar Masoumi-Moghaddam
- UNSW Department of Surgery, University of New South Wales, St George Hospital, Kogarah, Sydney, NSW, 2217, Australia,
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20
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Chen QR, Hu Y, Yan C, Buetow K, Meerzaman D. Systematic genetic analysis identifies Cis-eQTL target genes associated with glioblastoma patient survival. PLoS One 2014; 9:e105393. [PMID: 25133526 PMCID: PMC4136869 DOI: 10.1371/journal.pone.0105393] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/19/2014] [Indexed: 01/23/2023] Open
Abstract
Prior expression quantitative trait locus (eQTL) studies have demonstrated heritable variation determining differences in gene expression. The majority of eQTL studies were based on cell lines and normal tissues. We performed cis-eQTL analysis using glioblastoma multiforme (GBM) data sets obtained from The Cancer Genome Atlas (TCGA) to systematically investigate germline variation's contribution to tumor gene expression levels. We identified 985 significant cis-eQTL associations (FDR<0.05) mapped to 978 SNP loci and 159 unique genes. Approximately 57% of these eQTLs have been previously linked to the gene expression in cell lines and normal tissues; 43% of these share cis associations known to be associated with functional annotations. About 25% of these cis-eQTL associations are also common to those identified in Breast Cancer from a recent study. Further investigation of the relationship between gene expression and patient clinical information identified 13 eQTL genes whose expression level significantly correlates with GBM patient survival (p<0.05). Most of these genes are also differentially expressed in tumor samples and organ-specific controls (p<0.05). Our results demonstrated a significant relationship of germline variation with gene expression levels in GBM. The identification of eQTLs-based expression associated survival might be important to the understanding of genetic contribution to GBM cancer prognosis.
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Affiliation(s)
- Qing-Rong Chen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Ying Hu
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chunhua Yan
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kenneth Buetow
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Daoud Meerzaman
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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21
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Xu J, Weng Z, Arumugam A, Tang X, Chaudhary SC, Li C, Christiano AM, Elmets CA, Bickers DR, Athar M. Hair follicle disruption facilitates pathogenesis to UVB-induced cutaneous inflammation and basal cell carcinoma development in Ptch(+/-) mice. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:1529-40. [PMID: 24631180 DOI: 10.1016/j.ajpath.2014.01.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Revised: 12/23/2013] [Accepted: 01/23/2014] [Indexed: 01/01/2023]
Abstract
Hairless mice carrying homozygous mutations in hairless gene manifest rudimentary hair follicles (HFs), epidermal cysts, hairless phenotype, and enhanced susceptibility to squamous cell carcinomas. However, their susceptibility to basal cell carcinomas (BCCs), a neoplasm considered originated from HF-localized stem cells, is unknown. To demonstrate the role of HFs in BCC development, we bred Ptch(+/-)/C57BL6 with SKH-1 hairless mice, followed by brother-sister cross to get F2 homozygous mutant (hairless) or wild-type (haired) mice. UVB-induced inflammation was less pronounced in shaved haired than in hairless mice. In hairless mice, inflammatory infiltrate was found around the rudimentary HFs and epidermal cysts. Expression of epidermal IL1f6, S100a8, vitamin D receptor, repetin, and major histocompatibility complex II, biomarkers depicting susceptibility to cutaneous inflammation, was also higher. In these animals, HF disruption altered susceptibility to UVB-induced BCCs. Tumor onset in hairless mice was 10 weeks earlier than in haired littermates. The incidence of BCCs was significantly higher in hairless than in haired animals; however, the magnitude of sonic hedgehog signaling did not differ significantly. Overall, 100% of hairless mice developed >12 tumors per mouse after 32 weeks of UVB therapy, whereas haired mice developed fewer than three tumors per mouse after 44 weeks of long-term UVB irradiation. Tumors in hairless mice were more aggressive than in haired littermates and manifested decreased E-cadherin and enhanced mesenchymal proteins. These data provide novel evidence that disruption of HFs in Ptch(+/-) mice enhances cutaneous susceptibility to inflammation and BCCs.
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Affiliation(s)
- Jianmin Xu
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Zhiping Weng
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Aadithya Arumugam
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Xiuwei Tang
- Department of Dermatology, Columbia University, New York, New York
| | - Sandeep C Chaudhary
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Changzhao Li
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Craig A Elmets
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - David R Bickers
- Department of Dermatology, Columbia University, New York, New York
| | - Mohammad Athar
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama.
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22
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Barcellos-Hoff MH, Adams C, Balmain A, Costes SV, Demaria S, Illa-Bochaca I, Mao JH, Ouyang H, Sebastiano C, Tang J. Systems biology perspectives on the carcinogenic potential of radiation. JOURNAL OF RADIATION RESEARCH 2014; 55. [PMCID: PMC3941546 DOI: 10.1093/jrr/rrt211] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
This review focuses on recent experimental and modeling studies that attempt to define the physiological context in which high linear energy transfer (LET) radiation increases epithelial cancer risk and the efficiency with which it does so. Radiation carcinogenesis is a two-compartment problem: ionizing radiation can alter genomic sequence as a result of damage due to targeted effects (TE) from the interaction of energy and DNA; it can also alter phenotype and multicellular interactions that contribute to cancer by poorly understood non-targeted effects (NTE). Rather than being secondary to DNA damage and mutations that can initiate cancer, radiation NTE create the critical context in which to promote cancer. Systems biology modeling using comprehensive experimental data that integrates different levels of biological organization and time-scales is a means of identifying the key processes underlying the carcinogenic potential of high-LET radiation. We hypothesize that inflammation is a key process, and thus cancer susceptibility will depend on specific genetic predisposition to the type and duration of this response. Systems genetics using novel mouse models can be used to identify such determinants of susceptibility to cancer in radiation sensitive tissues following high-LET radiation. Improved understanding of radiation carcinogenesis achieved by defining the relative contribution of NTE carcinogenic effects and identifying the genetic determinants of the high-LET cancer susceptibility will help reduce uncertainties in radiation risk assessment.
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Affiliation(s)
- Mary Helen Barcellos-Hoff
- Department of Radiation Oncology, New York University School of Medicine, 566 First Avenue, New York, NY 10016, USA
- Corresponding author. Department of Radiation Oncology, New York University School of Medicine, 450 East 29th Street, New York, NY 10016, USA. Tel: +1-212-263-3021;
| | - Cassandra Adams
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 Third Street, San Francisco, CA 94158, USA
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 Third Street, San Francisco, CA 94158, USA
| | - Sylvain V. Costes
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS977, Berkeley CA 94720, USA
| | - Sandra Demaria
- Department of Pathology, New York University School of Medicine, 566 First Avenue, New York, NY 10016, USA
| | - Irineu Illa-Bochaca
- Department of Radiation Oncology, New York University School of Medicine, 566 First Avenue, New York, NY 10016, USA
| | - Jian Hua Mao
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS977, Berkeley CA 94720, USA
| | - Haoxu Ouyang
- Department of Radiation Oncology, New York University School of Medicine, 566 First Avenue, New York, NY 10016, USA
| | - Christopher Sebastiano
- Department of Pathology, New York University School of Medicine, 566 First Avenue, New York, NY 10016, USA
| | - Jonathan Tang
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS977, Berkeley CA 94720, USA
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23
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Joeckel LT, Bird PI. Are all granzymes cytotoxic in vivo? Biol Chem 2014; 395:181-202. [DOI: 10.1515/hsz-2013-0238] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 08/30/2013] [Indexed: 01/01/2023]
Abstract
Abstract
Granzymes are serine proteases mainly found in cytotoxic lymphocytes. The most-studied member of this group is granzyme B, which is a potent cytotoxin that has set the paradigm that all granzymes are cyototoxic. In the last 5 years, this paradigm has become controversial. On one hand, there is a plethora of sometimes contradictory publications showing mainly caspase-independent cytotoxic effects of granzyme A and the so-called orphan granzymes in vitro. On the other hand, there are increasing numbers of reports of granzymes failing to induce cell death in vitro unless very high (potentially supra-physiological) concentrations are used. Furthermore, experiments with granzyme A or granzyme M knock-out mice reveal little or no deficit in their cytotoxic lymphocytes’ killing ability ex vivo, but indicate impairment in the inflammatory response. These findings of non-cytotoxic effects of granzymes challenge dogma, and thus require alternative or additional explanations to be developed of the role of granzymes in defeating pathogens. Here we review evidence for granzyme cytotoxicity, give an overview of their non-cytotoxic functions, and suggest technical improvements for future investigations.
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24
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Li B, Tsoi LC, Swindell WR, Gudjonsson JE, Tejasvi T, Johnston A, Ding J, Stuart PE, Xing X, Kochkodan JJ, Voorhees JJ, Kang HM, Nair RP, Abecasis GR, Elder JT. Transcriptome analysis of psoriasis in a large case-control sample: RNA-seq provides insights into disease mechanisms. J Invest Dermatol 2014; 134:1828-1838. [PMID: 24441097 PMCID: PMC4057954 DOI: 10.1038/jid.2014.28] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/27/2013] [Accepted: 12/09/2013] [Indexed: 02/08/2023]
Abstract
To increase our understanding of psoriasis, we utilized RNA-seq to assay the transcriptomes of lesional psoriatic and normal skin. We sequenced polyadenylated RNA-derived cDNAs from 92 psoriatic and 82 normal punch biopsies, generating an average of ~38 million single-end 80-bp reads per sample. Comparison of 42 samples examined by both RNA-seq and microarray revealed marked differences in sensitivity, with transcripts identified only by RNA-seq having much lower expression than those also identified by microarray. RNA-seq identified many more differentially expressed transcripts enriched in immune system processes. Weighted gene co-expression network analysis (WGCNA) revealed multiple modules of coordinately expressed epidermal differentiation genes, overlapping significantly with genes regulated by the long non-coding RNA TINCR, its target gene, staufen-1 (STAU1), the p63 target gene ZNF750, and its target KLF4. Other coordinately expressed modules were enriched for lymphoid and/or myeloid signature transcripts and genes induced by IL-17 in keratinocytes. Dermally-expressed genes were significantly down-regulated in psoriatic biopsies, most likely due to expansion of the epidermal compartment. These results demonstrate the power of WGCNA to elucidate gene regulatory circuits in psoriasis, and emphasize the influence of tissue architecture in both differential expression and co-expression analysis.
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Affiliation(s)
- Bingshan Li
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA; Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Lam C Tsoi
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - William R Swindell
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Hospital, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew Johnston
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jun Ding
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA; Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Xianying Xing
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - James J Kochkodan
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - John J Voorhees
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Hyun M Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Rajan P Nair
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Goncalo R Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Hospital, University of Michigan, Ann Arbor, Michigan, USA.
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25
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Quigley DA, Fiorito E, Nord S, Van Loo P, Alnæs GG, Fleischer T, Tost J, Moen Vollan HK, Tramm T, Overgaard J, Bukholm IR, Hurtado A, Balmain A, Børresen-Dale AL, Kristensen V. The 5p12 breast cancer susceptibility locus affects MRPS30 expression in estrogen-receptor positive tumors. Mol Oncol 2013; 8:273-84. [PMID: 24388359 DOI: 10.1016/j.molonc.2013.11.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 11/19/2013] [Accepted: 11/21/2013] [Indexed: 11/17/2022] Open
Abstract
Genome-wide association studies have identified numerous loci linked to breast cancer susceptibility, but the mechanism by which variations at these loci influence susceptibility is usually unknown. Some variants are only associated with particular clinical subtypes of breast cancer. Understanding how and why these variants influence subtype-specific cancer risk contributes to our understanding of cancer etiology. We conducted a genome-wide expression Quantitative Trait Locus (eQTL) study in a discovery set of 287 breast tumors and 97 normal mammary tissue samples and a replication set of 235 breast tumors. We found that the risk-associated allele of rs7716600 in the 5p12 estrogen receptor-positive (ER-positive) susceptibility locus was associated with elevated expression of the nearby gene MRPS30 exclusively in ER-positive tumors. We replicated this finding in 235 independent tumors. Further, we showed the rs7716600 risk genotype was associated with decreased MRPS30 promoter methylation exclusively in ER-positive breast tumors. In vitro studies in MCF-7 cells carrying the protective genotype showed that estrogen stimulation decreased MRPS30 promoter chromatin availability and mRNA levels. In contrast, in 600MPE cells carrying the risk genotype, estrogen increased MRPS30 expression and did not affect promoter availability. Our data suggest the 5p12 risk allele affects MRPS30 expression in estrogen-responsive tumor cells after tumor initiation by a mechanism affecting chromatin availability. These studies emphasize that the genetic architecture of breast cancer is context-specific, and integrated analysis of gene expression and chromatin remodeling in normal and tumor tissues will be required to explain the mechanisms of risk alleles.
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Affiliation(s)
- David A Quigley
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, USA.
| | - Elisa Fiorito
- Breast Cancer Research Group, Nordic EMBL Partnership, Centre for Molecular Medicine Norway, (NCMM), University of Oslo, Norway.
| | - Silje Nord
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton UK; Department of Human Genetics, VIB and KU Leuven, Leuven, Belgium.
| | - Grethe Grenaker Alnæs
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Thomas Fleischer
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Jorg Tost
- Laboratory for Functional Genomics, Fondation Jean Dausset, Centre Etude Polymorphism Humain, (CEPH), Paris, France; Laboratory of Epigenetics, Centre National de Génotypage, Commissariat à l'énergie Atomique et, aux énergies Alternatives (CEA)-Institut de Génomique, Evry, France.
| | - Hans Kristian Moen Vollan
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Trine Tramm
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark.
| | - Jens Overgaard
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark.
| | - Ida R Bukholm
- Department of Breast-Endocrine Surgery, Akershus University Hospital, Oslo, Norway; Department of Oncology, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Oslo, Norway.
| | - Antoni Hurtado
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Breast Cancer Research Group, Nordic EMBL Partnership, Centre for Molecular Medicine Norway, (NCMM), University of Oslo, Norway.
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, USA.
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Medical Division, Akershus University Hospital, Lørenskog, Norway.
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26
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Rewiring of human lung cell lineage and mitotic networks in lung adenocarcinomas. Nat Commun 2013; 4:1701. [PMID: 23591868 PMCID: PMC4450149 DOI: 10.1038/ncomms2660] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 02/26/2013] [Indexed: 12/21/2022] Open
Abstract
Analysis of gene expression patterns in normal tissues and their perturbations in tumors can help to identify the functional roles of oncogenes or tumor suppressors and identify potential new therapeutic targets. Here, gene expression correlation networks were derived from 92 normal human lung samples and patient-matched adenocarcinomas. The networks from normal lung show that NKX2-1 is linked to the alveolar type 2 lineage, and identify PEBP4 as a novel marker expressed in alveolar type 2 cells. Differential correlation analysis shows that the NKX2-1 network in tumors includes pathways associated with glutamate metabolism, and identifies Vaccinia-related kinase (VRK1) as a potential drug target in a tumor-specific mitotic network. We show that VRK1 inhibition cooperates with inhibition of PARP signaling to inhibit growth of lung tumor cells. Targeting of genes that are recruited into tumor mitotic networks may provide a wider therapeutic window than that seen by inhibition of known mitotic genes.
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27
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Genome-wide association study in breast cancer survivors reveals SNPs associated with gene expression of genes belonging to MHC class I and II. Genomics 2013; 102:278-87. [DOI: 10.1016/j.ygeno.2013.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/30/2013] [Accepted: 07/12/2013] [Indexed: 11/18/2022]
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28
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Ha NH, Hunter KW. Using a systems biology approach to understand and study the mechanisms of metastasis. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 6:107-14. [PMID: 23873855 DOI: 10.1002/wsbm.1237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/11/2013] [Accepted: 06/21/2013] [Indexed: 11/07/2022]
Abstract
Metastasis remains the main cause for cancer-related deaths due to the lack of effective therapy. The clonal selection model has long been thought to be the primary mechanism of metastatic progression but many different mechanisms have been hypothesized for the progression from tumorigenesis to the successful dissemination and expansion of tumor cells at the secondary site. MicroRNAs, germline polymorphisms in combination with the tumor microenvironment are few of the different pathways to explain the metastatic cascade. Technological advances for high-throughput screening of cells such as expression profiling, next generation sequencing, as well as global network analyses have advanced the studies of these mechanisms. Combined with new insights into the various mechanisms of metastasis a systems biology approach has also been shown to be useful in identifying metastasis-specific gene signatures as well as predicting disease outcome. Furthermore, the results of these studies have been relevant for identifying biomarkers for metastatic disease.
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Affiliation(s)
- Ngoc-Han Ha
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, USA
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29
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A network perspective on unraveling the role of TRP channels in biology and disease. Pflugers Arch 2013; 466:173-82. [PMID: 23677537 DOI: 10.1007/s00424-013-1292-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/22/2013] [Accepted: 05/03/2013] [Indexed: 02/08/2023]
Abstract
Transient receptor potential (TRP) channels are a large family of non-selective cation channels that mediate numerous physiological and pathophysiological processes; however, still largely unknown are the underlying molecular mechanisms. With data generated on an unprecedented scale, network-based approaches have been revolutionizing the way in which we understand biology and disease, discover disease genes, and develop therapeutic strategies. These circumstances have created opportunities to encounter TRP channel research to data-intensive science. In this review, we provide an introduction of network-based approaches in biomedical science, describe the current state of TRP channel network biology, and discuss the future direction of TRP channel research. Network perspective will facilitate the discovery of latent roles and underlying mechanisms of TRP channels in biology and disease.
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30
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Cohen N, Kravchenko-Balasha N, Klein S, Levitzki A. Heterogeneity of gene expression in murine squamous cell carcinoma development-the same tumor by different means. PLoS One 2013; 8:e57748. [PMID: 23526950 PMCID: PMC3601100 DOI: 10.1371/journal.pone.0057748] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 01/25/2013] [Indexed: 02/04/2023] Open
Abstract
Transformation is a complex process, involving many changes in the cell. In this work, we investigated the transcriptional changes that arose during the development of squamous cell carcinoma (SCC) in mice. Using microarray analysis, we looked at gene expression during different stages in cancer progression in 31 mice. By analyzing tumor progression in each mouse separately, we were able to define the global changes that were common to all 31 mice, as well as significant changes that occurred in fewer individuals. We found that different genes can contribute to the tumorigenic process in different mice, and that there are many ways to acquire the malignant properties defined by Hanahan and Weinberg as "hallmarks of cancer". Eventually, however, all these changes lead to a very similar cancerous phenotype. The finding that gene expression is strongly heterogeneous in tumors that were induced by a standardized protocol in closely related mice underscores the need for molecular characterization of human tumors and personalized therapy.
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Affiliation(s)
- Noam Cohen
- Unit of Cellular Signaling, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nataly Kravchenko-Balasha
- Unit of Cellular Signaling, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shoshana Klein
- Unit of Cellular Signaling, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alexander Levitzki
- Unit of Cellular Signaling, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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31
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Wong CE, Yu JS, Quigley DA, To MD, Jen KY, Huang PY, Del Rosario R, Balmain A. Inflammation and Hras signaling control epithelial-mesenchymal transition during skin tumor progression. Genes Dev 2013; 27:670-82. [PMID: 23512660 PMCID: PMC3613613 DOI: 10.1101/gad.210427.112] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 02/22/2013] [Indexed: 12/19/2022]
Abstract
Epithelial-mesenchymal transition (EMT) is thought to be an important, possibly essential, component of the process of tumor dissemination and metastasis. About 20%-30% of Hras mutant mouse skin carcinomas induced by chemical initiation/promotion protocols have undergone EMT. Reduced exposure to TPA-induced chronic inflammation causes a dramatic reduction in classical papillomas and squamous cell carcinomas (SCCs), but the mice still develop highly invasive carcinomas with EMT properties, reduced levels of Hras and Egfr signaling, and frequent Ink4/Arf deletions. Deletion of Hras from the mouse germline also leads to a strong reduction in squamous tumor development, but tumors now acquire activating Kras mutations and exhibit more aggressive metastatic properties. We propose that invasive carcinomas can arise by different genetic and biological routes dependent on exposure to chronic inflammation and possibly from different target cell populations within the skin. Our data have implications for the use of inhibitors of inflammation or of Ras/Egfr pathway signaling for prevention or treatment of invasive cancers.
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Affiliation(s)
- Christine E. Wong
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California 94158, USA
| | - Jennifer S. Yu
- Department of Radiation Oncology
- Department of Stem Cell Biology and Regenerative Medicine, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - David A. Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California 94158, USA
| | - Minh D. To
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California 94158, USA
| | - Kuang-Yu Jen
- Department of Pathology, University of California at San Francisco, San Francisco, California 94143, USA
| | - Phillips Y. Huang
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California 94158, USA
| | - Reyno Del Rosario
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California 94158, USA
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California 94158, USA
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32
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Blair RH, Trichler DL, Gaille DP. Mathematical and statistical modeling in cancer systems biology. Front Physiol 2012; 3:227. [PMID: 22754537 PMCID: PMC3385354 DOI: 10.3389/fphys.2012.00227] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 06/05/2012] [Indexed: 11/13/2022] Open
Abstract
Cancer is a major health problem with high mortality rates. In the post-genome era, investigators have access to massive amounts of rapidly accumulating high-throughput data in publicly available databases, some of which are exclusively devoted to housing Cancer data. However, data interpretation efforts have not kept pace with data collection, and gained knowledge is not necessarily translating into better diagnoses and treatments. A fundamental problem is to integrate and interpret data to further our understanding in Cancer Systems Biology. Viewing cancer as a network provides insights into the complex mechanisms underlying the disease. Mathematical and statistical models provide an avenue for cancer network modeling. In this article, we review two widely used modeling paradigms: deterministic metabolic models and statistical graphical models. The strength of these approaches lies in their flexibility and predictive power. Once a model has been validated, it can be used to make predictions and generate hypotheses. We describe a number of diverse applications to Cancer Biology, including, the system-wide effects of drug-treatments, disease prognosis, tumor classification, forecasting treatment outcomes, and survival predictions.
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Affiliation(s)
- Rachael Hageman Blair
- Department of Biostatistics, State University of New York at BuffaloBuffalo, NY, USA
| | - David L. Trichler
- Department of Biostatistics, State University of New York at BuffaloBuffalo, NY, USA
- Department of Biostatistics, University of TorontoToronto, ON, Canada
| | - Daniel P. Gaille
- Department of Biostatistics, State University of New York at BuffaloBuffalo, NY, USA
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Abstract
Computers are organized into hardware and software. Using a theoretical approach to identify patterns in gene expression in a variety of species, organs, and cell types, we found that biological systems similarly are comprised of a relatively unchanging hardware-like gene pattern. Orthogonal patterns of software-like transcripts vary greatly, even among tumors of the same type from different individuals. Two distinguishable classes could be identified within the hardware-like component: those transcripts that are highly expressed and stable and an adaptable subset with lower expression that respond to external stimuli. Importantly, we demonstrate that this structure is conserved across organisms. Deletions of transcripts from the highly stable core are predicted to result in cell mortality. The approach provides a conceptual thermodynamic-like framework for the analysis of gene-expression levels and networks and their variations in diseased cells.
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To MD, Quigley DA, Mao JH, Del Rosario R, Hsu J, Hodgson G, Jacks T, Balmain A. Progressive genomic instability in the FVB/Kras(LA2) mouse model of lung cancer. Mol Cancer Res 2011; 9:1339-45. [PMID: 21807965 DOI: 10.1158/1541-7786.mcr-11-0219] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Alterations in DNA copy number contribute to the development and progression of cancers and are common in epithelial tumors. We have used array Comparative Genomic Hybridization (aCGH) to visualize DNA copy number alterations across the genomes of lung tumors in the Kras(LA2) model of lung cancer. Copy number gain involving the Kras locus, as focal amplification or whole chromosome gain, is the most common alteration in these tumors and with a prevalence that increased significantly with increasing tumor size. Furthermore, Kras amplification was the only major genomic event among the smallest lung tumors, suggesting that this alteration occurs early during the development of mutant Kras-driven lung cancers. Recurring gains and deletions of other chromosomes occur progressively more frequently among larger tumors. These results are in contrast to a previous aCGH analysis of lung tumors from Kras(LA2) mice on a mixed genetic background, in which relatively few DNA copy number alterations were observed regardless of tumor size. Our model features the Kras(LA2) allele on the inbred FVB/N mouse strain, and in this genetic background, there is a highly statistically significant increase in level of genomic instability with increasing tumor size. These data suggest that recurring DNA copy alterations are important for tumor progression in the Kras(LA2) model of lung cancer and that the requirement for these alterations may be dependent on the genetic background of the mouse strain.
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Affiliation(s)
- Minh D To
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
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Teasing apart cancer's influences. Nature 2011. [DOI: 10.1038/470143e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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