Project 1: Race-related RNA splicing in non-small cell lung cancer: functional interrogation and therapeutic targeting

项目 1：非小细胞肺癌中的种族相关 RNA 剪接：功能询问和治疗靶向

• 批准号: 10263343
• 负责人: Jennifer Ann Freedman
• 金额: $ 27.49万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-14 至 2023-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10263343
• 关键词: Address; African; African American; Age; Alternative Splicing; Area; Biological; Biological Markers; Biological Specimen Banks; Biology; Bronchi; CRISPR/Cas technology; Cancer Etiology; Cancer Patient; Cellular biology; Cessation of life; Characteristics; Clinical; Data; Development; Developmental Therapeutics Program; Diagnosis; Drug Targeting; Ethnic Origin; European; Event; Exhibits; Gene Expression; Genes; Genetic Transcription; Genotype; Institution; Intervention; Intervention Studies; Lead; Libraries; Lung; Lung Adenocarcinoma; Malignant Neoplasms; Malignant neoplasm of lung; Methodology; Modeling; Molecular; Non-Small-Cell Lung Carcinoma; North Carolina; Oligonucleotides; Oncogenic; Oncology; Organoids; Pathology; Pathway interactions; Patient-Focused Outcomes; Patients; Pharmaceutical Preparations; Positioning Attribute; Pre-Clinical Model; RNA Splicing; Race; Reagent; Reporting; Research; Resistance; Resources; Scientist; Signal Pathway; Smoking Status; Spliced Genes; Squamous Cell Lung Carcinoma; Subgroup; Technology; The Cancer Genome Atlas; Therapeutic; Therapeutic Agents; Tissues; Transfection; Tumor Suppressor Genes; United States; Universities; Variant; Work; actionable mutation; base; biological heterogeneity; black patient; cancer health disparity; clinical heterogeneity; clinically relevant; cohort; differential expression; driver mutation; drug use screening; exon skipping; high-throughput drug screening; improved; in vivo; interest; lung cancer cell; new therapeutic target; novel; patient subsets; precision oncology; response; targeted treatment; therapeutic target; tool; transcriptome; transcriptome sequencing

ABSTRACT – Project 1 Lung and bronchus cancer is the leading cause of cancer-related deaths in the United States and in our institution’s state of North Carolina, with blacks having the highest number of deaths and being diagnosed three years younger on average than whites. Biological drivers of non-small cell lung cancer (NSCLC) in black patients remain underexplored, with only a small number of studies on race-related differences in actionable mutations and aggregate gene expression. As a result, these efforts have likely missed other important drivers of race- related NSCLC biological and clinical heterogeneity. The proposed work addresses the urgent need to functionally characterize and therapeutically target novel race-related RNA splicing targets in NSCLC. We are the first team to identify alternative RNA splicing differences in NSCLC between patients of African and European ancestry. Specifically, in lung squamous cell carcinomas (LUSCs), the number of race-related differentially spliced genes (DSGs) (4,830) far exceeded the number of genes exhibiting race-related differential aggregate gene expression (DEGs) (267) in the same tissues. Among the DSGs, 17% are reported to be oncogenes, tumor suppressor genes and/or drivers and 355 RNA splicing events within DSGs are associated with LUSC survival. Among the DEGs, 6% are reported to be cancer-related and 18 are associated with LUSC survival. A number of the DSGs and DEGs involve therapeutically targetable signaling pathways. Furthermore, we have mined The Cancer Genome Atlas (TCGA) and have identified DSGs and DEGs in additional LUSCs or lung adenocarcinomas (LUADs). The objectives of the proposed work are to extend this novel area of inquiry with significance for precision oncology in NSCLC disparities by 1) examining DSGs and DEGs in an expanded cohort of clinically relevant NSCLC subgroups of patients annotated for survival and smoking status, 2) functionally characterizing prioritized race-related alternative RNA splicing events, and 3) drugging prioritized race-related alternative RNA splicing events for therapeutic application. To reach these objectives, we propose to conduct three aims. Aim 1: To assess the expression of RNA splice variants and genes encoding trans-acting splicing factors across clinically relevant NSCLC subgroups in patients of African and European ancestry. Aim 2: To interrogate the functional significance of prioritized race-related RNA splice variants for the biology of NSCLC. Aim 3: A) To develop novel splice-switching oligonucleotide (SSO) morpholino drugs to modulate RNA splicing events critical to race-related NSCLC for therapeutic application and B) To identify available targeted therapeutic agents that inhibit race-related NSCLC based on dysregulated RNA splicing pathway(s). The rationale for and impact of this study is that it will 1) increase understanding of the molecular mechanisms underlying lung cancer disparities, 2) provide an abundance of novel RNA splicing-related targets for development of new biomarkers and therapeutic agents for NSCLC in patients of African ancestry, 3) when combined with TCGA data, this study will more than double the number of molecularly characterized NSCLC biospecimens from patients of African ancestry, and generate additional preclinical models, making such data and models available to the nationwide cohort of scientists conducting research on lung cancer and lung cancer disparities, and 4) position lead novel RNA splicing-targeted drugs for NSCLC in patients of African ancestry for in vivo studies. Ultimately, such precision oncology interventions and further studies enabled by the molecularly characterized cohort of biospecimens and models will have the potential to mitigate NSCLC disparities.

摘要 - 项目1 肺癌和支气管癌是美国与我们的主要原因 机构的北卡罗来纳州，黑人死亡人数最多，被诊断出三个 平均比白人年轻。黑人患者的非小细胞肺癌（NSCLC）的生物驱动因素 保持不足，只有少量关于种族相关突变中与种族相关的差异的研究 和聚集基因表达。结果，这些努力可能错过了种族的其他重要驱动力 - 相关的NSCLC生物学和临床异质性。拟议的工作解决了迫切需要 在功能上表征和热靶向NSCLC中的新型种族相关RNA剪接靶标。我们是 第一支识别非洲患者和非洲患者NSCLC中替代RNA剪接差异的团队 欧洲血统。具体而言，在肺鳞状细胞癌（LUSC）中，与种族相关的数量 差异剪接的基因（DSG）（4,830）远远超过了表现出种族相关差异的基因数量 同一组织中的聚集基因表达（DEGS）（267）。在DSG中，据报道17％ DSG中的癌基因，肿瘤抑制基因和/或驱动因素以及355个RNA剪接事件与 LUSC生存。在DEG中，据报道6％与癌症相关，18个与LUSC有关 生存。许多DSG和DEG涉及热目标信号通路。此外， 我们已经挖掘了癌症基因组图集（TCGA），并在其他LUSC或 肺腺癌（LUADS）。拟议工作的目标是扩展这个新颖的询问领域 在NSCLC分布中精确肿瘤学的显着性，通过1）检查扩展的DSG和DEG 注释的生存和吸烟状况的患者的临床相关NSCLC亚组的队列，2） 在功能上表征优先级与种族相关的替代RNA剪接事件，3）优先吸毒 用于治疗应用的与种族有关的替代RNA剪接事件。为了达到这些目标，我们提出了 执行三个目标。目标1：评估编码反式作用的RNA剪接变体和基因的表达 非洲和欧洲血统患者的临床相关NSCLC亚组的剪接因子。目的 2：询问优先种族相关的RNA剪接变体的功能意义 NSCLC。目的3：a）开发新型的剪接开关开关寡核苷酸（SSO）吗啡药物来调节RNA 对种族相关的NSCLC至关重要的剪接事件，用于治疗应用，b）确定可用的目标 基于失调的RNA剪接途径抑制种族相关的NSCLC的治疗剂。这 这项研究的基本原理和影响是1）增加对分子机制的理解 潜在的肺癌分布，2）提供大量的新型RNA剪接相关靶标的 在非洲血统患者中为NSCLC开发新的生物标志物和治疗剂，3） 结合TCGA数据，这项研究将是分子表征NSCLC的数量的两倍以上 来自非洲血统患者的生物测量，并产生其他临床前模型，制作此类数据 以及针对有关肺癌和肺癌研究的全国科学家队列的模型 差异和4）在非洲血统患者的NSCLC中铅NSCLC的新型RNA剪接靶向药物的位置 体内研究。最终，这种精确的肿瘤学干预措施和进一步的研究由分子启用 表征的生物测量和模型队列将有可能减轻NSCLC分布。