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Quan L, Demant P. Clustering of colon, lung, and other cancer susceptibility genes with protein tyrosine phosphatases and protein kinases in multiple short genomic regions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566108. [PMID: 37986945 PMCID: PMC10659278 DOI: 10.1101/2023.11.07.566108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Interactions of large gene families are poorly understood. We found that human, mouse, and rat colon and lung cancer susceptibility genes, presently considered as separate gene families, were frequently pairwise linked. The orthologous mouse map positions of 142 of 159 early discovered colon and lung cancer susceptibility genes formed 41 genomic clusters conserved >70 million years. These linked gene pairs concordantly affected both tumors and their majority was linked with two other gene families - protein tyrosine phosphatases and cancer driver protein kinases. 25% of both protein tyrosine phosphatases and protein kinases mapped <1 cM from a colon or lung cancer susceptibility gene, and 50% in <3 cM. Similar linkage was detected with most other human susceptibility genes that controlled 29 different cancer types. This concentration of tumor susceptibility genes with protein tyrosine phosphatases and driver protein kinases in multiple relatively short genomic regions suggests their possible functional diversity.
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Borrego A, Jensen JR, Cabrera WHK, Massa S, Ribeiro OG, Starobinas N, De Franco M, Eto SF, Manenti G, Dragani TA, Ibañez OM. Mapping of novel loci involved in lung and colon tumor susceptibility by the use of genetically selected mouse strains. Genes Immun 2021; 23:23-32. [PMID: 34966170 PMCID: PMC8866122 DOI: 10.1038/s41435-021-00159-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/29/2021] [Accepted: 12/13/2021] [Indexed: 11/29/2022]
Abstract
Two non-inbred mouse lines, phenotypically selected for maximal (AIRmin) and minimal (AIRmax) acute inflammatory response, show differential susceptibility/resistance to the development of several chemically-induced tumor types. An intercross pedigree of these mice was generated and treated with the chemical carcinogen dimethylhydrazine, which induces lung and intestinal tumors. Genome wide high-density genotyping with the Restriction Site-Associated DNA genotyping (2B-RAD) technique was used to map genetic loci modulating individual genetic susceptibility to both lung and intestinal cancer. Our results evidence new common quantitative trait loci (QTL) for those phenotypes and provide an improved understanding of the relationship between genomic variation and individual genetic predisposition to tumorigenesis in different organs.
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Affiliation(s)
- Andrea Borrego
- Laboratory of Immunogenetics, Instituto Butantan, São Paulo, Brazil
| | | | | | - Solange Massa
- Laboratory of Immunogenetics, Instituto Butantan, São Paulo, Brazil
| | | | - Nancy Starobinas
- Laboratory of Immunogenetics, Instituto Butantan, São Paulo, Brazil
| | | | - Silas Fernandes Eto
- Laboratory of Development and Innovation, Instituto Butantan, São Paulo, Brazil
| | - Giacomo Manenti
- Genetic Epidemiology and Pharmacogenomics Unit Fondazione IRCCS, Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Tommaso Antonio Dragani
- Genetic Epidemiology and Pharmacogenomics Unit Fondazione IRCCS, Istituto Nazionale dei Tumori di Milano, Milan, Italy.
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Mansoori F, Rahgozar M, Kavousi K. FoPA: identifying perturbed signaling pathways in clinical conditions using formal methods. BMC Bioinformatics 2019; 20:92. [PMID: 30808299 PMCID: PMC6390332 DOI: 10.1186/s12859-019-2635-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 01/17/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Accurate identification of perturbed signaling pathways based on differentially expressed genes between sample groups is one of the key factors in the understanding of diseases and druggable targets. Most pathway analysis methods prioritize impacted signaling pathways by incorporating pathway topology using simple graph-based models. Despite their relative success, these models are limited in describing all types of dependencies and interactions that exist in biological pathways. RESULTS In this work, we propose a new approach based on the formal modeling of signaling pathways. Signaling pathways are formally modeled, and then model checking tools are applied to find the likelihood of perturbation for each pathway in a given condition. By adopting formal methods, various complex interactions among biological parts are modeled, which can contribute to reducing the false-positive rate of the proposed approach. We have developed a tool named Formal model checking based pathway analysis (FoPA) based on this approach. FoPA is compared with three well-known pathway analysis methods: PADOG, CePa, and SPIA on the benchmark of 36 GEO datasets from various diseases by applying the target pathway technique. This validation technique eliminates the need for possibly biased human assessments of results. In the cases that, there is no apriori knowledge of all relevant pathways, simulated false inputs (permuted class labels and decoy pathways) are chosen as a set of negative controls to test the false positive rate of the methods. Finally, to further evaluate the efficiency of FoPA, it is applied to a list of autism-related genes. CONCLUSIONS The results obtained by the target pathway technique demonstrate that FoPA is able to prioritize target pathways as well as PADOG but better than CePa and SPIA. Also, the false-positive rate of finding significant pathways using FoPA is lower than other compared methods. Also, FoPA can detect more consistent relevant pathways than other methods. The results of FoPA on autism-related genes highlight the role of "Renin-angiotensin system" pathway. This pathway has been supposed to have a pivotal role in some neurodegenerative diseases, while little attention has been paid to its impact on autism development so far.
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Affiliation(s)
- Fatemeh Mansoori
- Database Research Group, Control and Intelligent Processing Center of Excellence, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
| | - Maseud Rahgozar
- Database Research Group, Control and Intelligent Processing Center of Excellence, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran.
| | - Kaveh Kavousi
- Complex Biological Systems and Bioinformatics Lab (CBB), Bioinformatics department, University of Tehran, Tehran, Iran.
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Izadi F. Differential Connectivity in Colorectal Cancer Gene Expression Network. IRANIAN BIOMEDICAL JOURNAL 2019; 23. [PMID: 29843204 PMCID: PMC6305824 DOI: 10.29252/.23.1.34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the challenging types of cancers; thus, exploring effective biomarkers related to colorectal could lead to significant progresses toward the treatment of this disease. METHODS In the present study, CRC gene expression datasets have been reanalyzed. Mutual differentially expressed genes across 294 normal mucosa and adjacent tumoral samples were then utilized in order to build two independent transcriptional regulatory networks. By analyzing the networks topologically, genes with differential global connectivity related to cancer state were determined for which the potential transcriptional regulators including transcription factors were identified. RESULTS The majority of differentially connected genes (DCGs) were up-regulated in colorectal transcriptome experiments. Moreover, a number of these genes have been experimentally validated as cancer or CRC-associated genes. The DCGs, including GART, TGFB1, ITGA2, SLC16A5, SOX9, and MMP7, were investigated across 12 cancer types. Functional enrichment analysis followed by detailed data mining exhibited that these candidate genes could be related to CRC by mediating in metastatic cascade in addition to shared pathways with 12 cancer types by triggering the inflammatory events. DISCUSSION Our study uncovered correlated alterations in gene expression related to CRC susceptibility and progression that the potent candidate biomarkers could provide a link to disease.
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Affiliation(s)
- Fereshteh Izadi
- Sari Agricultural Sciences and Natural Resources University (SANRU), Farah Abad Road, Mazandaran 4818168984, Iran,Corresponding Author: Fereshteh Izadi Sari Agricultural Sciences and Natural Resources University (SANRU), Farah Abad Road, Mazandaran 4818168984, Iran; Mobile: (+98-918) 6291302; E-mail:
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Collin R, Balmer L, Morahan G, Lesage S. Common Heritable Immunological Variations Revealed in Genetically Diverse Inbred Mouse Strains of the Collaborative Cross. THE JOURNAL OF IMMUNOLOGY 2018; 202:777-786. [DOI: 10.4049/jimmunol.1801247] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/16/2018] [Indexed: 12/28/2022]
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Hung RJ, Fehringer G, Casey G, Gruber SB, Peters U, Goode EL, Sellers TA, Haiman CA, Hunter DJ, Kraft P, Amos CI, Freedman ML, Wilson MD. Cross-Cancer Analysis Reveals Novel Pleiotropic Associations-Response. Cancer Res 2017; 77:6045-6046. [PMID: 29066515 PMCID: PMC8083975 DOI: 10.1158/0008-5472.can-17-1584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/31/2017] [Accepted: 09/06/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Gordon Fehringer
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Stephen B Gruber
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Ulrike Peters
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | | | | | - David J Hunter
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Peter Kraft
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | | | | | - Michael D Wilson
- Hospital of Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
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Quan L, Hutson A, Demant P. Cross-Cancer Analysis Reveals Novel Pleiotropic Associations-Letter. Cancer Res 2017; 77:6042-6044. [PMID: 29066516 DOI: 10.1158/0008-5472.can-16-3262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/23/2017] [Accepted: 09/06/2017] [Indexed: 11/16/2022]
Affiliation(s)
- Lei Quan
- Tianjin Key Laboratory of Exercise Physiology and Sport Medicine, School of Health and Exercise Sciences, Tianjin University of Sport, Tianjin, China
| | - Alan Hutson
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York
| | - Peter Demant
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York.
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Izadi F, Zamanian-Azodi M, Mansouri V, Khodadoostan M, Naderi N. Exploring conserved mRNA-miRNA interactions in colon and lung cancers. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2017; 10:184-193. [PMID: 29118934 PMCID: PMC5660268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/18/2017] [Indexed: 12/04/2022]
Abstract
AIM The main goal of this analysis was prioritization of co-expressed genes and miRNAs that are thought to have important influences in the pathogenesis of colon and lung cancers. BACKGROUND MicroRNAs (miRNAs) as small and endogenous noncoding RNAs which regulate gene expression by repressing mRNA translation or decreasing stability of mRNAs; they have proven pivotal roles in different types of cancers. Accumulating evidence indicates the role of miRNAs in a wide range of biological processes from oncogenesis and tumor suppressors to contribution to tumor progression. Colon and lung cancers are frequently encountered challenging types of cancers; therefore, exploring trade-off among underlying biological units such as miRNA with mRNAs will probably lead to identification of promising biomarkers involved in these malignancies. METHODS Colon cancer and lung cancer expression data were downloaded from Firehose and TCGA databases and varied genes extracted by DCGL software were subjected to build two gene regulatory networks by parmigene R package. Afterwards, a network-driven integrative analysis was performed to explore prognosticates genes, miRNAs and underlying pathways. RESULTS A total of 192 differentially expressed miRNAs and their target genes within gene regulatory networks were derived by ARACNE algorithm. BTF3, TP53, MYC, CALR, NEM2, miR-29b-3p and miR-145 were identified as bottleneck nodes and enriched via biological gene ontology (GO) terms and pathways chiefly in biosynthesis and signaling pathways by further screening. CONCLUSION Our study uncovered correlated alterations in gene expression that may relate with colon and lung cancers and highlighted the potent common biomarker candidates for the two diseases.
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Affiliation(s)
- Fereshteh Izadi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mona Zamanian-Azodi
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Mansouri
- Physiotherapy Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahsa Khodadoostan
- Department of Gastroenterology and Hepatology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Nosratollah Naderi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Gerber MM, Hampel H, Zhou XP, Schulz NP, Suhy A, Deveci M, Çatalyürek ÜV, Ewart Toland A. Allele-specific imbalance mapping at human orthologs of mouse susceptibility to colon cancer (Scc) loci. Int J Cancer 2015; 137:2323-31. [PMID: 25973956 DOI: 10.1002/ijc.29599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 04/27/2015] [Accepted: 04/30/2015] [Indexed: 12/14/2022]
Abstract
Colorectal cancer (CRC) can be classified into different types. Chromosomal instable (CIN) colon cancers are thought to be the most common type of colon cancer. The risk of developing a CIN-related CRC is due in part to inherited risk factors. Genome-wide association studies have yielded over 40 single nucleotide polymorphisms (SNPs) associated with CRC risk, but these only account for a subset of risk alleles. Some of this missing heritability may be due to gene-gene interactions. We developed a strategy to identify interacting candidate genes/loci for CRC risk that utilizes both linkage and RNA-seq data from mouse models in combination with allele-specific imbalance (ASI) studies in human tumors. We applied our strategy to three previously identified CRC susceptibility loci in the mouse that show evidence of genetic interaction: Scc4, Scc5 and Scc13. 525 SNPs from genes showing differential expression in the mouse and/or a previous role in cancer from the literature were evaluated for allele-specific imbalance in 194 paired human normal/tumor DNAs from CIN-related CRCs. One hundred three SNPs showing suggestive evidence of ASI (31 variants with uncorrected p values < 0.05) were genotyped in a validation set of 296 paired DNAs. Two variants in SNX10 (SCC13) showed significant evidence of allelic selection after multiple comparisons testing. Future studies will evaluate the role of these variants in combination with interacting genetic partners in colon cancer risk in mouse and humans.
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Affiliation(s)
- Madelyn M Gerber
- Biomedical Sciences Graduate Program, The Ohio State University College of Medicine, Columbus, OH
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State Wexner Medical Center, Columbus, OH.,The OSU Comprehensive Cancer Center, Columbus, OH
| | - Xiao-Ping Zhou
- The OSU Comprehensive Cancer Center, Columbus, OH.,Department of Pathology, The Ohio State Wexner Medical Center, Columbus, OH
| | - Nathan P Schulz
- Department of Psychiatry, University of Illinois Health System, Chicago, IL.,Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine, The Ohio State University, Columbus, OH
| | - Adam Suhy
- Biomedical Sciences Graduate Program, The Ohio State University College of Medicine, Columbus, OH
| | - Mehmet Deveci
- Biomedical Informatics, Computer Science and Engineering, The Ohio State University, Columbus, OH
| | - Ümit V Çatalyürek
- Biomedical Informatics, Electrical and Computer Engineering, the Ohio State University, Columbus, OH
| | - Amanda Ewart Toland
- Division of Human Genetics, Department of Internal Medicine, The Ohio State Wexner Medical Center, Columbus, OH.,The OSU Comprehensive Cancer Center, Columbus, OH.,Department of Molecular Virology, Immunology and Medical Genetics, the Ohio State University, Columbus, OH
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A strategy to identify dominant point mutant modifiers of a quantitative trait. G3-GENES GENOMES GENETICS 2014; 4:1113-21. [PMID: 24747760 PMCID: PMC4065254 DOI: 10.1534/g3.114.010595] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A central goal in the analysis of complex traits is to identify genes that modify a phenotype. Modifiers of a cancer phenotype may act either intrinsically or extrinsically on the salient cell lineage. Germline point mutagenesis by ethylnitrosourea can provide alleles for a gene of interest that include loss-, gain-, or alteration-of-function. Unlike strain polymorphisms, point mutations with heterozygous quantitative phenotypes are detectable in both essential and nonessential genes and are unlinked from other variants that might confound their identification and analysis. This report analyzes strategies seeking quantitative mutational modifiers of ApcMin in the mouse. To identify a quantitative modifier of a phenotype of interest, a cluster of test progeny is needed. The cluster size can be increased as necessary for statistical significance if the founder is a male whose sperm is cryopreserved. A second critical element in this identification is a mapping panel free of polymorphic modifiers of the phenotype, to enable low-resolution mapping followed by targeted resequencing to identify the causative mutation. Here, we describe the development of a panel of six “isogenic mapping partner lines” for C57BL/6J, carrying single-nucleotide markers introduced by mutagenesis. One such derivative, B6.SNVg, shown to be phenotypically neutral in combination with ApcMin, is an appropriate mapping partner to locate induced mutant modifiers of the ApcMin phenotype. The evolved strategy can complement four current major initiatives in the genetic analysis of complex systems: the Genome-wide Association Study; the Collaborative Cross; the Knockout Mouse Project; and The Cancer Genome Atlas.
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B-9-3, a novel β-carboline derivative exhibits anti-cancer activity via induction of apoptosis and inhibition of cell migration in vitro. Eur J Pharmacol 2013; 724:219-30. [PMID: 24380828 DOI: 10.1016/j.ejphar.2013.12.038] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 12/05/2013] [Accepted: 12/13/2013] [Indexed: 11/24/2022]
Abstract
Peganum harmala L is an important medicinal plant that has been used from ancient time due to its alkaloids rich of ß-carbolines. Harmane is a naturally occurring ß-carboline extracted from Peganum harmala L, that exhibits a wide range of biological, psychopharmacological, and toxicological actions. The synthesis of novel derivatives with high anti-cancer activity and less side effects is necessary. In the present study, B-9-3-a semi-synthetic compound that is formed of two harmane molecules bound by a butyl group-showed a strong anti-cancer activity against a human lung cancer cell line, a human breast cancer cell line, and a human colorectal carcinoma cell line. B-9-3 anti-proliferative effect followed a similar pattern in the three cell lines. This pattern includes a dose-dependent induction of apoptosis, or necroptosis as confirmed by Hoechst staining, flow cytometry and western blot analyses, and the inhibition of cancer cells migration that was shown to be dependent on the drug׳s concentration as well. Moreover, B-9-3 inhibited tube formation in human umbilical vascular endothelial cell line (HUVEC), which indicates an anti-angiogenesis activity in vitro. In summary, B-9-3, a semi-synthetic derivative of ß-carboline, has an anti-proliferative effect against tumor cells via induction of apoptosis and inhibition of cell migration.
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Chaudhuri A, Wilson NS, Yang B, Paler Martinez A, Liu J, Zhu C, Bricker N, Couto S, Modrusan Z, French D, Cupp J, Ashkenazi A. Host genetic background impacts modulation of the TLR4 pathway by RON in tissue-associated macrophages. Immunol Cell Biol 2013; 91:451-60. [PMID: 23817579 PMCID: PMC3736205 DOI: 10.1038/icb.2013.27] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 05/04/2013] [Accepted: 05/20/2013] [Indexed: 12/27/2022]
Abstract
Toll-like receptors (TLRs) enable metazoans to mount effective innate immune responses to microbial and viral pathogens, as well as to endogenous host-derived ligands. It is understood that genetic background of the host can influence TLR responsiveness, altering susceptibility to pathogen infection, autoimmunity and cancer. Macrophage stimulatory protein (MSP), which activates the receptor tyrosine kinase recepteur d'origine nantais (RON), promotes key macrophage functions such as motility and phagocytic activity. MSP also acts via RON to modulate signaling by TLR4, which recognizes a range of pathogen or endogenous host-derived molecules. Here, we show that RON exerts divergent control over TLR4 activity in macrophages from different mouse genetic backgrounds. RON potently modulated the TLR4 response in macrophages from M2-prone FVB mice, as compared with M1-skewed C57Bl6 mice. Moreover, global expression analysis revealed that RON suppresses the TLR4-dependent type-I interferon gene signature only in FVB macrophages. This leads to attenuated production of the potent inflammatory mediator, tumor necrosis factor-α. Eliminating RON kinase activity markedly decreased carcinogen-mediated tumorigenesis in M2/Th2-biased FVB mice. We propose that host genetic background influences RON function, thereby contributing to the variability in TLR4 responsiveness in rodents and, potentially, in humans. These findings provide novel insight into the complex interplay between genetic context and immune function.
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Affiliation(s)
- Amitabha Chaudhuri
- Department of Molecular Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Nicholas S Wilson
- Department of Molecular Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Becky Yang
- Department of Molecular Oncology, Genentech Inc., South San Francisco, CA, USA
| | | | - Jinfeng Liu
- Department of Bioinformatics, Genentech Inc., South San Francisco, CA, USA
| | - Catherine Zhu
- Department of Molecular Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Nicole Bricker
- Department of Molecular Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Suzana Couto
- Departments of Pathology and Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - Zora Modrusan
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA, USA
| | - Dorothy French
- Departments of Pathology and Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - James Cupp
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA, USA
| | - Avi Ashkenazi
- Department of Molecular Oncology, Genentech Inc., South San Francisco, CA, USA
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Quan L, Dittmar A, Zhou Y, Hutson A, Stassen APM, Demant P. Susceptibility loci affecting ERBB2/neu-induced mammary tumorigenesis in mice. Genes Chromosomes Cancer 2012; 51:631-43. [PMID: 22419448 DOI: 10.1002/gcc.21949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 01/19/2012] [Accepted: 01/25/2012] [Indexed: 02/05/2023] Open
Abstract
Twenty percent of breast cancers exhibit amplification or overexpression of ERBB2/neu and a poor prognosis. As the susceptibility genes controlling ERBB2 tumorgenesis are unknown, in a genetic mapping project we crossed transgenic mice expressing the neu oncogene under control of MMTV promoter with recombinant congenic (RC) strains, which provided a high mapping power. RC strains differed considerably in tumor latency (P = 0.0002), suggesting a strong genetic control of tumor development. Linkage analysis in neu-transgene carrying F2 hybrids between the most susceptible and most resistant RC strain revealed three mammary tumor susceptibility (Mts) loci with main effects, Mts1 (chr. 4), Mts2 (chr. 10), Mts3 (chr. 19), and two interacting loci Mts4 (chr.6) and Mts5 (chr. 8), significantly affecting mammary tumor latency. Suggestive significance levels indicated control of tumor numbers by Mts1 alone and in interaction with Mts5, and by two additional interacting loci on chromosomes 1 and 8. These loci combined explain to a large extent the tumor latency and number in individual F2 mouse. We also identified a suggestive locus on chromosome 17 controls metastasis to the lung. The loci Mts1, Mts1b, and Mts3 are located in the Naad4-4,5 and Naad19-2 LOH-regions of neu-induced mammary tumors, corresponding to the frequent human breast cancer LOH-regions 1p34/1p36, and 10q25, respectively. These results expand the knowledge of ERBB2 tumorigenesis and point to a combined control of specific tumor phenotypes by germ-line polymorphisms and somatic alterations.
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Affiliation(s)
- Lei Quan
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
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Physical confirmation and mapping of overlapping rat mammary carcinoma susceptibility QTLs, Mcs2 and Mcs6. PLoS One 2011; 6:e19891. [PMID: 21625632 PMCID: PMC3097214 DOI: 10.1371/journal.pone.0019891] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 04/14/2011] [Indexed: 12/03/2022] Open
Abstract
Only a portion of the estimated heritability of breast cancer susceptibility has been explained by individual loci. Comparative genetic approaches that first use an experimental organism to map susceptibility QTLs are unbiased methods to identify human orthologs to target in human population-based genetic association studies. Here, overlapping rat mammary carcinoma susceptibility (Mcs) predicted QTLs, Mcs6 and Mcs2, were physically confirmed and mapped to identify the human orthologous region. To physically confirm Mcs6 and Mcs2, congenic lines were established using the Wistar-Furth (WF) rat strain, which is susceptible to developing mammary carcinomas, as the recipient (genetic background) and either Wistar-Kyoto (WKy, Mcs6) or Copenhagen (COP, Mcs2), which are resistant, as donor strains. By comparing Mcs phenotypes of WF.WKy congenic lines with distinct segments of WKy chromosome 7 we physically confirmed and mapped Mcs6 to ∼33 Mb between markers D7Rat171 and gUwm64-3. The predicted Mcs2 QTL was also physically confirmed using segments of COP chromosome 7 introgressed into a susceptible WF background. The Mcs6 and Mcs2 overlapping genomic regions contain multiple annotated genes, but none have a clear or well established link to breast cancer susceptibility. Igf1 and Socs2 are two of multiple potential candidate genes in Mcs6. The human genomic region orthologous to rat Mcs6 is on chromosome 12 from base positions 71,270,266 to 105,502,699. This region has not shown a genome-wide significant association to breast cancer risk in pun studies of breast cancer susceptibility.
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