Development of transcriptome-based biomarkers from melanoma in hybrid fish

杂交鱼黑色素瘤转录组生物标志物的开发

基本信息

批准号：
7845359
负责人：
Ziping Zhang
金额：
$ 13.08万
依托单位：
TEXAS STATE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2010
资助国家：
美国
起止时间：
2010-04-01 至 2011-08-16
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7845359
关键词：
Adult Affect Aftercare Alleles American Animal Model Animals Award Backcrossings Biochemical Biochemistry Bioinformatics Biological Markers Blast Cell CDKN2A gene Candidate Disease Gene Cell Cycle Cell Cycle Regulation Cells Chemicals Chin Chromosomes Clinical Cloning Code Collection Communities Complementary DNA Complex DNA Damage DNA Repair DNA Sequence Data Databases Deltastab Development Diagnosis Dideoxy Chain Termination DNA Sequencing Digestion Disease Dorsal Embryo Etiology Exhibits Experimental Models Expressed Sequence Tags Female Fishes Functional RNA Future Gene Duplication Gene Expression Gene Expression Profile Genes Genetic Genetic Crosses Genetic Markers Genetic Predisposition to Disease Genome Genomics German population Goals Growth Factor Receptors Human Hybrids In Situ Hybridization Incidence Individual Inherited International Investigation Laboratories Lead Length Light Literature Longitudinal Studies Malignant Neoplasms Maps Measurement Mediating Methods Methylnitrosourea MicroRNAs Mind Modeling Molecular Molecular Target Myron National Center for Research Resources Neural Crest Neurilemmoma Normal tissue morphology Oncogenes Ontology Organ Organism Other Genetics Partner in relationship Pathway interactions Patients Pattern Pharmaceutical Preparations Pharmacogenomics Phenotype Pigments Platyfish Probability Process Proteins RNA RNA Ligase (ATP)RNA Sequences Reading Receptor Cell Regulation Regulator Genes Research Retinoblastoma Role Route Running SAGE Library Sampling Scientist Skin Skin Cancer Source Spottings Staging Students Sunlight System Technology Testing Time Tissues Titanium Transcend Transcript Translating Tumor Suppression Tumor Suppressor Genes UVB induced Ultraviolet B Radiation United States United States National Institutes of Health Work Xiphophorus base cancer genetics cancer type carcinogenesis cohort comparative data mining functional genomics gene function genetic association graduate student insight male man melanocyte melanoma next generation novel nuclease outcome forecast prognostic prognostic indicator public health relevance segregation tool tumor tumorigenesis

项目摘要

DESCRIPTION (provided by applicant): Melanoma is a serious form of skin cancer which is rising in the United States. Our studies plus others demonstrated that interspecies Xiphophorus hybrids exhibit spontaneous and environmentally induced tumors of several types, including melanoma and other cancers. Biochemical and histological similarities between Xiphophorus and human melanoma have been revealed making these hybrids an attractive model for melanoma research. We will test the hypothesis that each of these different melanoma models share a common set of modulated genetic factors (due to the interspecies cross) that predispose interspecies hybrid individuals to induced melanoma development. These genetic factors and pathways they represent may be identified by study of melanoma paradigms in these Xiphophorus hybrid models and may be translated to melanoma study in other organisms, including humans. We have employed traditional cloning as well as next generation 454 titanium (454-Ti) analyses to examine the Xiphophorus transcriptome. We have identified 10,679 unique EST sequences encoding proteins from seven different organs of adult male and female X. maculatus Jp 163 A. We propose to investigate two inter-species crosses Xiphophorus that produce animals representing a spontaneous melanoma model and an induced model whereby melanoma forms only after treatment with MNU or UVB light. In aim 1, RNA from melanoma and normal tissues will be isolated then used to synthesis normalized full-length cDNAs. 454-Ti will be employed to develop deep transcript sequence coverage of these samples. ESTs obtained from the 454-Ti from melanoma and control tissues will be added to our EST database and used to data mine those genes showing specific expression in the melanoma. In aim 2, each of the RNAs collected in aim 1 will be used to construct SAGE libraries. 454-Ti will be used for deep transcriptome sequence coverage of these SAGE libraries to develop transcript profiles of each sample. SAGE tags will be mapped to the ESTs obtained in aim 1 to identify genes that are specifically expressed in melanoma and those subsets of genes that appear to be expressed in each distinct melanoma model (spontaneous, UVB-induced, and MNU-induced). For aim 3, real time PCR and in situ hybridization will be used to validate and confirm our results. Results from these studies will further illuminate the range of genetic factors that may lead to genetic predisposition to induced melanoma. PUBLIC HEALTH RELEVANCE: Melanoma is a serious form of skin cancer. This proposal focuses on understanding the various genetic routes to melanoma, among varied Xiphophorus interspecies hybrid models will further illuminate the range of genetic factors that may be shared in humans that may lead to genetic predisposition to induced melanoma. Robust melanoma biomarker candidates can be identified in this investigation.

描述（由申请人提供）：黑色素瘤是一种严重的皮肤癌，在美国呈上升趋势。我们的研究和其他研究表明，种间剑鱼杂交体表现出多种类型的自发和环境诱发的肿瘤，包括黑色素瘤和其他癌症。剑尾鱼和人类黑色素瘤之间的生物化学和组织学相似性已被揭示，使这些杂交品种成为黑色素瘤研究的有吸引力的模型。我们将测试以下假设：这些不同的黑色素瘤模型中的每一个都共享一组共同的调节遗传因素（由于种间杂交），这些因素使种间杂交个体易于诱发黑色素瘤的发展。它们所代表的这些遗传因素和途径可以通过对这些剑尾鱼杂交模型中的黑色素瘤范式的研究来鉴定，并且可以转化为包括人类在内的其他生物体中的黑色素瘤研究。我们采用传统克隆以及下一代 454 钛 (454-Ti) 分析来检查剑尾鱼转录组。我们已经鉴定了 10,679 个独特的 EST 序列，编码来自成年雄性和雌性 X. maculatus Jp 163 A 七个不同器官的蛋白质。我们建议研究两个种间杂交剑尾鱼，它们产生代表自发黑色素瘤模型和黑色素瘤形成的诱导模型的动物仅在使用 MNU 或 UVB 光处理后。在目标 1 中，将从黑色素瘤和正常组织中分离 RNA，然后用于合成标准化全长 cDNA。 454-Ti 将用于开发这些样本的深度转录序列覆盖。从黑色素瘤和对照组织的 454-Ti 中获得的 EST 将添加到我们的 EST 数据库中，并用于数据挖掘那些在黑色素瘤中显示特定表达的基因。在目标 2 中，目标 1 中收集的每个 RNA 将用于构建 SAGE 文库。 454-Ti 将用于这些 SAGE 文库的深度转录组序列覆盖，以开发每个样本的转录谱。 SAGE 标签将映射到目标 1 中获得的 EST，以识别在黑色素瘤中特异性表达的基因以及似乎在每个不同黑色素瘤模型（自发性、UVB 诱导性和 MNU 诱导性）中表达的基因子集。对于目标 3，将使用实时 PCR 和原位杂交来验证和确认我们的结果。这些研究的结果将进一步阐明可能导致诱发黑色素瘤的遗传倾向的遗传因素的范围。公众健康相关性：黑色素瘤是一种严重的皮肤癌。该提案的重点是了解黑色素瘤的各种遗传途径，在不同的剑尾鱼种间杂交模型中，将进一步阐明人类可能共有的一系列遗传因素，这些因素可能导致诱发黑色素瘤的遗传倾向。在这项研究中可以鉴定出稳健的黑色素瘤候选生物标志物。