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）：实施个性化医疗的一个关键的未满足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性 (SNP) 进行分类，并查明这些 DNA 变异中哪些是导致疾病的。 SNP 的一个尚未被研究的关键功能是它们生成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，我们发明了 SNP-SNAP（蛋白质特异性和亲和力）微阵列作为原型高通量设备来评估 SNP 功能。 SNP-SNAP 阵列将用于将 25 万个前列腺癌相关 SNP 显示为双链 DNA 分子，并分析转录因子（即药物靶标）与这些 SNP DNA 序列的结合。所得数据将与前列腺癌发病率相关。来自 SNP-SNAP 阵列的数百万个数据点将使用 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相关的前列腺癌“分子特征”。我们的研究结果还将前列腺癌相关的 SNP 功能与癌症分期和侵袭性联系起来。了解 SNP 功能将对个性化医疗产生重大影响，提供个体化疾病风险评估、识别新的个性化治疗靶点以及预测常见疗法的疗效和潜在的脱靶副作用。该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，以覆盖与前列腺癌相关的 25 万个 SNP。 2. 在 SNP-SNAP 阵列上检查 5 种前列腺癌相关转录因子（纯化蛋白和细胞裂解物）的 DNA 结合特异性和亲和力，并用 SNP 导致的转录因子结合差异注释人类基因组。使用前列腺癌细胞中的染色质免疫沉淀验证结果。 3.从前列腺癌患者获取SNP数据，并确定功能性SNP（其在SNP-SNAP阵列上产生前列腺癌特异性转录因子的差异结合）与前列腺癌发病率是否存在统计上显着的关联。该技术可以同时检测数百万个 SNP 和多个转录因子，因此代表了以高通量方式评估 SNP 功能的首批方法之一。我们的 SNP-SNAP 技术凭借阵列定制设计和检查数百万 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：实施个性化医疗的一个关键的未满足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性 (SNP) 进行分类，并查明这些 DNA 变异中哪些是导致疾病的。 SNP 的一个尚未被研究的关键功能是它们生成或破坏转录因子基因组结合位点的能力，这些转录因子调节与癌症相关的基因。为了实现这一目标，我们正在发明 SNP-SNAP（蛋白质特异性和亲和力）微阵列作为原型高通量设备，通过将 25 万个前列腺癌相关 SNP 显示为双链 DNA 分子来评估 SNP 功能，分析转录因子（即药物靶点）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。