Accelerating target identification and validation in leukemia: Integrating siRNA-

描述（由申请人提供）：本申请涉及广泛的挑战领域（08）基因组学和特定的挑战主题，08-CA-106：开发与癌症相关的基因发现的验证方法。用激酶抑制剂特异性靶向致癌信号传导通路，极大地改善了患有各种癌症诊断的患者的临床结果，最显著的是患有慢性髓性白血病的患者。为了将这种靶向治疗方法扩展到所有形式的癌症，必须首先确定致病基因。为此，我们和其他人已经应用了各种技术来检测基因组水平上的致癌畸变，包括癌细胞中的基因重测序或基因表达谱。我们还开发了一种基于RNAi的筛选方法，可以快速识别直接从白血病患者获得的原发癌细胞中的靶基因。然而，以零碎的方式应用这些分析导致了大量未经验证的目标。区分没有疾病相关性的假阳性和表现出复杂和难以捉摸的肿瘤发生机制的真正的癌基因是困难的。我们的基于RNAi的功能筛选与最近可用的下一代测序和基于外显子的表达阵列技术的整合代表了技术的完美补充-siRNA敏感基因的知识将指导测序和阵列分析，而高通量序列和基因表达谱将加快功能靶标验证的过程。我们建议，整合技术功能分析，下一代测序和基因表达阵列将显着加快目标识别和验证的步伐。 公共卫生相关性：加速临床癌症治疗发展的有效范例必须采用一种综合方法，其中基于功能测定的靶点鉴定与基于基因组和基因表达的验证技术相结合。通过将白血病患者样本的功能性siRNA分析与下一代测序和基因表达阵列相结合，我们假设我们将显著加快靶标鉴定和验证的步伐。

DESCRIPTION (provided by applicant): This application addresses broad Challenge Area (08) Genomics and specific Challenge Topic, 08-CA-106: Development of methods for the validation of gene discoveries as they relate to cancer. Specific targeting of oncogenic signaling pathways with kinase inhibitors has vastly improved clinical outcomes for patients with a variety of cancer diagnoses, most notably patients with chronic myeloid leukemia. To expand this targeted-therapy approach to all forms of cancer, disease-causing genes must first be identified. Towards that end, we and others have applied a variety of techniques to detect oncogenic aberrations at the genomic level, including gene resequencing or gene expression profiling in cancer cells. We have also developed an RNAi-based screen to rapidly identify target genes in primary cancer cells obtained directly from leukemia patients. However, application of these analyses in piecemeal fashion has resulted in large numbers of unvalidated targets. Distinguishing between false-positives that have no disease-relevance and bona fide oncogenes that exhibit complex and elusive mechanisms of oncogenesis has been difficult. Integration of our RNAi-based functional screen with recently available techniques of Next Generation sequencing and exonbased expression arrays represents a perfect complement of technologies-knowledge of siRNA-sensitive genes will guide sequencing and array analysis, while high-throughput sequence and gene expression profiles will expedite the process of functional target validation. We propose that integration of techniques-functional profiling, Next Generation sequencing, and gene expression arrays-will significantly accelerate the pace of target identification and validation. PUBLIC HEALTH RELEVANCE: An effective paradigm for accelerating development of clinical cancer therapeutics must entail an integrated approach in which functional assay-based target identification is supported with genomic and gene expression-based validation techniques. By integrating functional siRNA profiling of leukemia patient samples with Next Generation sequencing and gene expression arrays, we hypothesize that we will significantly accelerate the pace of target identification and validation.