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He L, Zhong C, Chang H, Inman JL, Celniker SE, Ioakeim-Ioannidou M, Liu KX, Haas-Kogan D, MacDonald SM, Threadgill DW, Kogan SC, Mao JH, Snijders AM. Genetic architecture of the acute and persistent immune cell response after radiation exposure. CELL GENOMICS 2023; 3:100422. [PMID: 38020972 PMCID: PMC10667298 DOI: 10.1016/j.xgen.2023.100422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/19/2023] [Accepted: 09/12/2023] [Indexed: 12/01/2023]
Abstract
Hematologic toxicity is a common side effect of multimodal cancer therapy. Nearly all animal studies investigating the causes of radiotherapy-induced hematologic toxicity use inbred strains with limited genetic diversity and do not reflect the diverse responses observed in humans. We used the population-based Collaborative Cross (CC) mouse resource to investigate the genetic architecture of the acute and persistent immune response after radiation exposure by measuring 22 immune parameters in 1,720 CC mice representing 35 strains. We determined relative acute and persistent radiation resistance scores at the individual strain level considering contributions from all immune parameters. Genome-wide association analysis identified quantitative trait loci associated with baseline and radiation responses. A cross-species radiation resistance score predicted recurrence-free survival in medulloblastoma patients. We present a community resource of immune parameters and genome-wide association analyses before and after radiation exposure for future investigations of the contributions of host genetics on radiosensitivity.
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Affiliation(s)
- Li He
- Department of Hematology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei 430079, China
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chenhan Zhong
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Medical Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jamie L. Inman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Susan E. Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California Berkeley, Berkeley, CA 94720, USA
| | | | - Kevin X. Liu
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daphne Haas-Kogan
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shannon M. MacDonald
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - David W. Threadgill
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX 77843, USA
- Departments of Nutrition and Cell Biology and Genetics, Texas A&M University, College Station, TX 77843, USA
| | - Scott C. Kogan
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California Berkeley, Berkeley, CA 94720, USA
| | - Antoine M. Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California Berkeley, Berkeley, CA 94720, USA
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2
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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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3
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Bult CJ, Krupke DM, Begley DA, Richardson JE, Neuhauser SB, Sundberg JP, Eppig JT. Mouse Tumor Biology (MTB): a database of mouse models for human cancer. Nucleic Acids Res 2014; 43:D818-24. [PMID: 25332399 PMCID: PMC4384039 DOI: 10.1093/nar/gku987] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The Mouse Tumor Biology (MTB; http://tumor.informatics.jax.org) database is a unique online compendium of mouse models for human cancer. MTB provides online access to expertly curated information on diverse mouse models for human cancer and interfaces for searching and visualizing data associated with these models. The information in MTB is designed to facilitate the selection of strains for cancer research and is a platform for mining data on tumor development and patterns of metastases. MTB curators acquire data through manual curation of peer-reviewed scientific literature and from direct submissions by researchers. Data in MTB are also obtained from other bioinformatics resources including PathBase, the Gene Expression Omnibus and ArrayExpress. Recent enhancements to MTB improve the association between mouse models and human genes commonly mutated in a variety of cancers as identified in large-scale cancer genomics studies, provide new interfaces for exploring regions of the mouse genome associated with cancer phenotypes and incorporate data and information related to Patient-Derived Xenograft models of human cancers.
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Affiliation(s)
- Carol J Bult
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA
| | - Debra M Krupke
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA
| | - Dale A Begley
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA
| | | | | | - John P Sundberg
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA
| | - Janan T Eppig
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA
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4
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van der Weyden L, Adams DJ. Cancer of mice and men: old twists and new tails. J Pathol 2013; 230:4-16. [PMID: 23436574 DOI: 10.1002/path.4184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 01/28/2013] [Accepted: 02/16/2013] [Indexed: 12/18/2022]
Abstract
In this review we set out to celebrate the contribution that mouse models of human cancer have made to our understanding of the fundamental mechanisms driving tumourigenesis. We take the opportunity to look forward to how the mouse will be used to model cancer and the tools and technologies that will be applied, and indulge in looking back at the key advances the mouse has made possible.
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Lorimore SA, Rastogi S, Mukherjee D, Coates PJ, Wright EG. The influence of p53 functions on radiation-induced inflammatory bystander-type signaling in murine bone marrow. Radiat Res 2013; 179:406-15. [PMID: 23578188 DOI: 10.1667/rr3158.2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Radiation-induced bystander and abscopal effects, in which DNA damage is produced by inter-cellular communication, indicate mechanisms of generating damage in addition to those observed in directly irradiated cells. In this article, we show that the bone marrow of irradiated p53(+/+) mice, but not p53(-/-) mice, produces the inflammatory pro-apoptotic cytokines FasL and TNF-α able to induce p53-independent apoptosis in vitro in nonirradiated p53(-/-) bone marrow cells. Using a congenic sex-mismatch bone marrow transplantation protocol to generate chimeric mice, p53(-/-) hemopoietic cells functioning in a p53(+/+) bone marrow stromal microenvironment exhibited greater cell killing after irradiation than p53(-/-) hemopoietic cells in a p53(-/-) microenvironment. Cytogenetic analysis demonstrated fewer damaged p53(-/-) cells in a p53(+/+) microenvironment than p53(-/-) cells in a p53(-/-) microenvironment. Using the two different model systems, the findings implicate inflammatory tissue processes induced as a consequence of p53-dependent cellular responses to the initial radiation damage, producing cytokines that subsequently induce ongoing p53-independent apoptosis. As inactivation of the p53 tumor suppressor pathway is a common event in malignant cells developing in a stromal microenvironment that has normal p53 function, the signaling processes identified in the current investigations have potential implications for disease pathogenesis and therapy.
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Affiliation(s)
- Sally A Lorimore
- University of Dundee, Centre for Oncology and Molecular Medicine, Division of Medical Science, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom
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Using genome-wide expression profiling to define gene networks relevant to the study of complex traits: from RNA integrity to network topology. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2012. [PMID: 23195313 DOI: 10.1016/b978-0-12-398323-7.00005-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Postgenomic studies of the function of genes and their role in disease have now become an area of intense study since efforts to define the raw sequence material of the genome have largely been completed. The use of whole-genome approaches such as microarray expression profiling and, more recently, RNA-sequence analysis of transcript abundance has allowed an unprecedented look at the workings of the genome. However, the accurate derivation of such high-throughput data and their analysis in terms of biological function has been critical to truly leveraging the postgenomic revolution. This chapter will describe an approach that focuses on the use of gene networks to both organize and interpret genomic expression data. Such networks, derived from statistical analysis of large genomic datasets and the application of multiple bioinformatics data resources, potentially allow the identification of key control elements for networks associated with human disease, and thus may lead to derivation of novel therapeutic approaches. However, as discussed in this chapter, the leveraging of such networks cannot occur without a thorough understanding of the technical and statistical factors influencing the derivation of genomic expression data. Thus, while the catch phrase may be "it's the network … stupid," the understanding of factors extending from RNA isolation to genomic profiling technique, multivariate statistics, and bioinformatics are all critical to defining fully useful gene networks for study of complex biology.
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Lorimore SA, Mukherjee D, Robinson JI, Chrystal JA, Wright EG. Long-lived inflammatory signaling in irradiated bone marrow is genome dependent. Cancer Res 2011; 71:6485-91. [PMID: 21903768 DOI: 10.1158/0008-5472.can-11-1926] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ionizing radiation is carcinogenic, but genotype is a key determinant of susceptibility. Mutational DNA damage is generally attributed to cause disease, but irradiation also affects multicellular interactions as a result of poorly understood bystander effects that may influence carcinogenic susceptibility. In this study, we show that the bone marrow of irradiated mice will retain the ability to kill hemopoietic clonogenic stem cells and to induce chromosomal instability for up to 3 months after irradiation. Chromosomal instability was induced in bone marrow cells derived from CBA/Ca mice, a strain that is susceptible to radiation-induced acute myeloid leukemia (r-AML), but not in C57BL6 mice that are resistant to r-AML. Similarly, clonogenic cell lethality was exhibited in C57BL/6 mice but not CBA/Ca mice. Mechanistic investigations revealed that these genotype-dependent effects involved cytokine-mediated signaling and were mediated by a cyclooxygenase-2-dependent mechanism. Thus, our results suggested that inflammatory processes were responsible for mediating and sustaining the durable effects of ionizing radiation observed on bone marrow cells. Because most exposures to ionizing radiation are directed to only part of the body, our findings imply that genotype-directed tissue responses may be important determinants of understanding the specific consequence of radiation exposure in different individuals.
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Affiliation(s)
- Sally A Lorimore
- University of Dundee Medical School, Centre for Oncology and Molecular Medicine, Scotland, United Kingdom
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Integrating mechanistic and polymorphism data to characterize human genetic susceptibility for environmental chemical risk assessment in the 21st century. Toxicol Appl Pharmacol 2011; 271:395-404. [PMID: 21291902 DOI: 10.1016/j.taap.2011.01.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 12/28/2010] [Accepted: 01/24/2011] [Indexed: 12/27/2022]
Abstract
Response to environmental chemicals can vary widely among individuals and between population groups. In human health risk assessment, data on susceptibility can be utilized by deriving risk levels based on a study of a susceptible population and/or an uncertainty factor may be applied to account for the lack of information about susceptibility. Defining genetic susceptibility in response to environmental chemicals across human populations is an area of interest in the NAS' new paradigm of toxicity pathway-based risk assessment. Data from high-throughput/high content (HT/HC), including -omics (e.g., genomics, transcriptomics, proteomics, metabolomics) technologies, have been integral to the identification and characterization of drug target and disease loci, and have been successfully utilized to inform the mechanism of action for numerous environmental chemicals. Large-scale population genotyping studies may help to characterize levels of variability across human populations at identified target loci implicated in response to environmental chemicals. By combining mechanistic data for a given environmental chemical with next generation sequencing data that provides human population variation information, one can begin to characterize differential susceptibility due to genetic variability to environmental chemicals within and across genetically heterogeneous human populations. The integration of such data sources will be informative to human health risk assessment.
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Mori N. Two loci controlling susceptibility to radiation-induced lymphomagenesis on mouse chromosome 4: cdkn2a, a candidate for one locus, and a novel locus distinct from cdkn2a. Radiat Res 2010; 173:158-64. [PMID: 20095847 DOI: 10.1667/rr1855.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BALB/c mice are sensitive to radiation-induced lymphomagenesis, while STS mice are resistant. Using 219 [(BALB/c x STS)F(1) x BALB/c] (N2C) and 197 [(BALB/c x STS)F(1) x STS] (N2S) animals, we performed a genome-wide search for loci controlling susceptibility to lymphomagenesis induced by radiation. Association of markers with the survival of animals was analyzed by the log rank test. For N2C mice, a significant correlation was detected, with four markers on the proximal to mid portion of chromosome 4: D4Mit302 and D4Mit255, P = 0.0075; D4Mit17, P = 0.034; and D4Mit86, P = 0.048. On the other hand, no significant linkage was detected in N2S mice. We analyzed BALB/c mice congenic for the STS allele in different regions of chromosome 4 and identified a locus with a conspicuous effect on survival located within a 7-Mb region between D4Mit302 and D4Mit144, where BALB/c mice harbor hypomorphic variant alleles of the tumor suppressor gene Cdkn2a, which encodes the cyclin-dependent kinase inhibitor protein p16INK4a. Using pooled F(2) intercrosses between the BALB/c and congenic lines carrying the STS allele near D4Mit17, but not in the range from D4Mit302 to D4Mit144, we assigned the second locus to an 11.4-Mb region in the vicinity of D4Mit17. Although Cdkn2a is a likely candidate for the locus controlling susceptibility to lymphomagenesis on chromosome 4, a novel tumor susceptibility gene different from Cdkn2a exists near the primary locus.
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Affiliation(s)
- Nobuko Mori
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai-shi, Osaka 599-8570, Japan.
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Dewal N, Freedman ML, LaFramboise T, Pe'er I. Power to detect selective allelic amplification in genome-wide scans of tumor data. ACTA ACUST UNITED AC 2009; 26:518-28. [PMID: 20031965 DOI: 10.1093/bioinformatics/btp694] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
MOTIVATION Somatic amplification of particular genomic regions and selection of cellular lineages with such amplifications drives tumor development. However, pinpointing genes under such selection has been difficult due to the large span of these regions. Our recently-developed method, the amplification distortion test (ADT), identifies specific nucleotide alleles and haplotypes that confer better survival for tumor cells when somatically amplified. In this work, we focus on evaluating ADT's power to detect such causal variants across a variety of tumor dataset scenarios. RESULTS Towards this end, we generated multiple parameter-based, synthetic datasets-derived from real data-that contain somatic copy number aberrations (CNAs) of various lengths and frequencies over germline single nucleotide polymorphisms (SNPs) genome-wide. Gold-standard causal sub-regions were assigned within these CNAs, followed by an assessment of ADT's ability to detect these sub-regions. Results indicate that ADT possesses high sensitivity and specificity in large sample sizes across most parameter cases, including those that more closely reflect existing SNP and CNA cancer data.
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Affiliation(s)
- Ninad Dewal
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA.
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Santos J, González-Sánchez L, Matabuena-deYzaguirre M, Villa-Morales M, Cozar P, López-Nieva P, Fernández-Navarro P, Fresno M, Díaz-Muñoz MD, Guenet JL, Montagutelli X, Fernández-Piqueras J. A Role for Stroma-Derived Annexin A1 as Mediator in the Control of Genetic Susceptibility to T-Cell Lymphoblastic Malignancies through Prostaglandin E2 Secretion. Cancer Res 2009; 69:2577-87. [DOI: 10.1158/0008-5472.can-08-1821] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
Genetically modified animals represent a resource of immense potential for cancer research. Classically, genetic modifications in mice were obtained through selected breeding experiments or treatments with powerful carcinogens capable of inducing random mutagenesis. A new era began in the early 1980s when genetic modifications by inserting foreign DNA genes into the cells of an animal allowed for the development of transgenic mice. Since that moment, genetic modifications have been able to be made in a predetermined way. Gene targeting emerged later as a method of in vivo mutagenesis whereby the sequence of a predetermined gene is selectively modified within an intact cell. In this review we focus on how genetically modified mice can be created to study tumour development, and how these models have contributed to an understanding of the genetic alterations involved in human cancer. We also discuss the strengths and weaknesses of the different mouse models for identifying cancer genes, and understanding the consequences of their alterations in order to obtain the maximum benefit for cancer patients.
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Abstract
The laboratory mouse has long been an important tool in the study of the biology and genetics of human cancer. With the advent of genetic engineering techniques, DNA microarray analyses, tissue arrays and other large-scale, high-throughput data generating methods, the amount of data available for mouse models of cancer is growing exponentially. Tools to integrate, locate and visualize these data are crucial to aid researchers in their investigations. The Mouse Tumor Biology database (http://tumor.informatics.jax.org) seeks to address that need.
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Affiliation(s)
- Debra M Krupke
- Jackson Laboratory, Mouse Tumour Biology Database, 600 Main Street, Bar Harbor, Maine 04609, USA.
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Zhu M, Zhao S. Candidate gene identification approach: progress and challenges. Int J Biol Sci 2007; 3:420-7. [PMID: 17998950 PMCID: PMC2043166 DOI: 10.7150/ijbs.3.420] [Citation(s) in RCA: 182] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2007] [Accepted: 10/24/2007] [Indexed: 11/05/2022] Open
Abstract
Although it has been widely applied in identification of genes responsible for biomedically, economically, or even evolutionarily important complex and quantitative traits, traditional candidate gene approach is largely limited by its reliance on the priori knowledge about the physiological, biochemical or functional aspects of possible candidates. Such limitation results in a fatal information bottleneck, which has apparently become an obstacle for further applications of traditional candidate gene approach on many occasions. While the identification of candidate genes involved in genetic traits of specific interest remains a challenge, significant progress in this subject has been achieved in the last few years. Several strategies have been developed, or being developed, to break the barrier of information bottleneck. Recently, being a new developing method of candidate gene approach, digital candidate gene approach (DigiCGA) has emerged and been primarily applied to identify potential candidate genes in some studies. This review summarizes the progress, application software, online tools, and challenges related to this approach.
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Affiliation(s)
- Mengjin Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding, Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
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Abstract
OBJECTIVE To summarize the scientific principles underlying cancer prevention. DATA SOURCES Articles, text books, personal communications, and experience. CONCLUSION The scientific basis of cancer prevention is complex and involves experimental and epidemiologic approaches and clinical trials. IMPLICATIONS FOR NURSING PRACTICE As more information becomes available regarding proven and potential cancer-prevention strategies, oncology nurses are regularly called upon to guide patients and others in making choices regarding preventative options. It is important for oncology nurses to stay abreast of this growing body of knowledge.
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Affiliation(s)
- Frank L Meyskens
- Department of Medicine and Biological Chemistry, Chao Family Comprehensive Cancer Center, University of California, Irvine, CA 92868, USA.
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Rzeszowska-Wolny J, Polanska J, Pietrowska M, Palyvoda O, Jaworska J, Butkiewicz D, Hancock R. Influence of polymorphisms in DNA repair genes XPD, XRCC1 and MGMT on DNA damage induced by gamma radiation and its repair in lymphocytes in vitro. Radiat Res 2005; 164:132-40. [PMID: 16038584 DOI: 10.1667/rr3400] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DNA single-strand breaks (SSBs) were quantified by single-cell gel electrophoresis and micronucleated and apoptotic cells were quantified by microscopic assays in peripheral blood lymphocytes after irradiation on ice with 2 Gy of 60Co gamma radiation, and their association with polymorphisms of genes that encode proteins of different DNA repair pathways and influence cancer risk (XPD codon 312Asp --> Asn and 751Lys --> Gln, XRCC1 399Arg --> Gln, and MGMT 84Leu --> Phe) was studied. In unirradiated lymphocytes, SSBs were significantly more frequent in individuals older than the median age (52 years) (P = 0.015; n = 81), and the frequency of apoptotic or micronucleated cells was higher in individuals with alleles coding for Asn at XPD 312 or Gln at 751 (P = 0.030 or 0.023 ANOVA, respectively; n = 54). The only polymorphism associated with the background SSB level was MGMT 84Phe (P = 0.04, ANOVA; n = 66). After irradiation, SSB levels and repair parameters did not differ significantly with age or smoking habit. The SSB level varied more than twofold and the repair rate and level of unrepaired SSBs more than 10-fold between individuals. The presence of variant alleles coding for Asn at XPD 312 was associated with more radiation-induced SSBs (P = 0.014) and fewer unrepaired SSBs (P = 0.008), and the phenotype (> median induced SSBs/< median unrepaired SSBs) was seen in the majority of XPD 312Asn/Asn homozygotes; the odds ratio for variant homozygotes to show this phenotype was 5.2 (95% confidence interval 1.4-19.9). The hypothesis is discussed that XPD could participate in repair of ionizing radiation-induced DNA damage. While it cannot be excluded that the effects observed are due to cosegregating polymorphisms or that the responses of lymphocytes are not typical of other cell types, the results suggest that polymorphism of DNA repair genes, particularly XPD, is one factor implicated in the variability of responses to ionizing radiation between different individuals.
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Affiliation(s)
- Joanna Rzeszowska-Wolny
- Department of Experimental and Clinical Radiobiology, Center of Oncology, Maria Sklodowska-Curie Memorial Institute, Gliwice, Poland
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