High Throughput Method to Assess SNP Functionality in Prostate Cancer

高通量方法评估前列腺癌中的 SNP 功能

• 批准号: 8222682
• 负责人: Mary Szatkowski Ozers
• 金额: $ 15万
• 依托单位: PROTEOVISTA, LLC
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-21 至 2013-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8222682
• 关键词: 8q24; Adverse effects; Affect; Affinity; Binding; Binding Proteins; Binding Sites; Biological Assay; Cancer Etiology; Cells; Clinic; Colorectal Cancer; Custom; DNA; DNA Binding; DNA Microarray Chip; DNA Sequence; Data; Devices; Diagnosis; Diagnostic Neoplasm Staging; Disease; Disease model; Drug Delivery Systems; Fluorescence; Gene Expression Regulation; Genes; Genetic; Genetic Variation; Genome; Genomics; Goals; Hand; Human Genome; Incidence; Incubated; Industry; Junk DNA; Laboratories; Malignant Neoplasms; Malignant neoplasm of ovary; Malignant neoplasm of prostate; Marketing; Measures; Medical; Medicine; Methods; Pathway interactions; Patients; Phase; Positioning Attribute; Prevalence; Protein Microchips; Proteins; Risk; Risk Assessment; S-nitro-N-acetylpenicillamine; Services; Single Nucleotide Polymorphism; Site; Sorting - Cell Movement; Source; Specificity; TCF Transcription Factor; Technology; Therapeutic; Translating; United States; Variant; cancer cell; cancer diagnosis; cancer type; chromatin immunoprecipitation; commercialization; cost; design; disorder risk; ds-DNA; improved; malignant breast neoplasm; men; patient population; preference; prototype; research study; therapeutic target; transcription factor; tumor molecular fingerprint

DESCRIPTION (provided by applicant): A critical unmet need in implementing personalized medicine is the ability to sort through the millions of single nucleotide polymorphisms (SNPs) present in the human genome and to pinpoint which of these DNA variations are causative in disease. A key under-studied function of SNPs is their ability to generate or disrupt genomic binding sites for transcription factors involved in cancer. Toward this goal, we are inventing the SNP-SNAP (Specificity and Affinity for Proteins) microarray as a prototype high throughput device to evaluate SNP function. The SNP-SNAP arrays will be used to display a quarter-million prostate cancer- related SNPs as double-stranded DNA molecules and to assay transcription factors (i.e., drug targets) for their binding to these SNP DNA sequences. The resulting data will be correlated with prostate cancer incidence. The million-plus data points from the SNP-SNAP arrays will be analyzed using SNP-Sequence Specificity Landscapes, creating a prostate cancer "molecular signature" that relates transcription factor binding, SNP preferences, and chromosomal position of the nearest genes. Our findings will also relate prostate cancer-associated SNP function with cancer stage and aggressiveness. Understanding SNP function will have a major impact on personalized medicine, by providing individualized disease risk assessment, identifying new personalized therapeutic targets, and predicting efficacy and potential off- target side effects of common therapeutics. The goals of this Phase I project are to: 1. Design and synthesize a customized SNP-SNAP DNA microarray to tile across a quarter-million SNPs that are associated with prostate cancer. 2. Examine the DNA binding specificity and affinity of 5 prostate cancer-related transcription factors, as purified proteins and from cell lysates, on the SNP-SNAP array and annotate the human genome with the transcription factor binding differences due to SNPs. Verify results with chromatin immunoprecipitation in prostate cancer cells. 3. Obtain SNP data from patients with prostate cancer and determine if there is a statistically significant association of functional SNPs, which yielded differential binding of prostate cancer specific transcription factors on the SNP-SNAP array, with prostate cancer incidence. This technology can assay millions of SNPs and multiple transcription factors simultaneously, thus representing one of the first methods to evaluate SNP functionality in a high throughput manner. Our SNP- SNAP technology, by virtue of the array custom design and ability to examine millions of DNA permutations, is also broadly applicable to any cancer type and disease model. PUBLIC HEALTH RELEVANCE: A critical unmet need in implementing personalized medicine is the ability to sort through the millions of single nucleotide polymorphisms (SNPs) present in the human genome and to pinpoint which of these DNA variations are causative in disease. A key under-studied function of SNPs is their ability to generate or disrupt genomic binding sites for transcription factors which regulate genes involved in cancer. Toward this goal, we are inventing the SNP-SNAP (Specificity and Affinity for Proteins) microarray as a prototype high throughput device to evaluate SNP function by displaying a quarter-million prostate cancer-related SNPs as double-stranded DNA molecules, assaying transcription factors (i.e. drug targets) for their binding to these SNP DNA sequences, and correlating these findings with prostate cancer incidence.

描述(由申请人提供)：在实施个性化医学方面，一个尚未得到满足的关键需求是能够对人类基因组中存在的数百万个单核苷酸多态(SNPs)进行分类，并精确定位这些DNA变异中的哪些是导致疾病的原因。SNPs一个未被研究的关键功能是它们产生或破坏与癌症相关的转录因子的基因组结合位点的能力。为了实现这一目标，我们正在发明SNP-SNAP(蛋白质的特异性和亲和力)微阵列，作为评估SNP功能的高通量设备的原型。SNP-SNAP阵列将被用于展示25万个与前列腺癌相关的SNPs作为双链DNA分子，并用于检测转录因子(即药物靶标)与这些SNP DNA序列的结合。由此得出的数据将与前列腺癌发病率相关联。来自SNP-SNAP阵列的100多万个数据点将使用SNP序列特异性景观进行分析，创建与转录因子结合、SNP偏好和最近基因的染色体位置有关的前列腺癌“分子签名”。我们的发现还将与前列腺癌相关的SNP功能与癌症分期和侵袭性相关。通过提供个性化的疾病风险评估，确定新的个性化治疗靶点，以及预测常见疗法的疗效和潜在的非靶点副作用，了解SNP的功能将对个性化医学产生重大影响。这个第一阶段项目的目标是：1.设计和合成定制的SNP-SNAP DNA微阵列，以覆盖25万个与前列腺癌相关的SNP。2.在SNP-SNAP阵列上检测5种前列腺癌相关转录因子作为纯化蛋白和细胞裂解物的DNA结合特异性和亲和力，并用SNPs引起的转录因子结合差异来注释人类基因组。用染色质免疫沉淀法在前列腺癌细胞中验证结果。3.获得前列腺癌患者的SNP数据，并确定功能性SNP是否与前列腺癌发病率有统计学意义的关联，SNP-SNAP阵列上的SNP-SNAP阵列上产生前列腺癌特异性转录因子的差异结合。这项技术可以同时检测数百万个SNP和多个转录因子，从而成为高通量评估SNP功能的最早方法之一。我们的SNP-SNAP技术，凭借阵列定制设计和检测数百万DNA排列的能力，也广泛适用于任何癌症类型和疾病模型。 公共卫生相关性：在实施个性化医疗方面，一个尚未得到满足的关键需求是有能力对人类基因组中存在的数百万个单核苷酸多态(SNPs)进行分类，并查明这些DNA变异中的哪些是导致疾病的原因。SNPs一个关键的未被研究的功能是它们产生或破坏转录因子的基因组结合位点的能力，转录因子调控与癌症相关的基因。为此，我们正在发明SNP-SNAP(蛋白质的特异性和亲和力)微阵列作为一个原型高通量设备来评估SNP功能，方法是将25万个与前列腺癌相关的SNPs显示为双链DNA分子，检测转录因子(即药物靶标)与这些SNP DNA序列的结合，并将这些发现与前列腺癌发病率相关联。