Investigating tRNA biology as a prognostic and oncogenic feature in pancreatic adenocarcinoma

研究 tRNA 生物学作为胰腺腺癌的预后和致癌特征

• 批准号: 10749469
• 负责人: Ryan Kawalerski
• 金额: $ 5.27万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-01 至 2026-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10749469
• 关键词: Academic Medical Centers; Affect; Amino Acids; Anticodon; Archives; Basic Science; Biochemical; Biological; Biological Markers; Biology; Cancer Biology; Cell Line; Cell Proliferation; Cell Survival; Cell physiology; Cells; Cellular biology; ChIP-seq; Chemicals; Chemoresistance; Classification; Clinical; Clinical Sciences; Codon Nucleotides; Colorectal Neoplasms; Complement; Couples; Cox Proportional Hazards Models; Cysteine; Data; Data Set; Dependence; Development; Diagnosis; Disease; Disease Management; Disease Progression; Doctor of Philosophy; Epithelium; Exhibits; Fostering; Gene Targeting; Genes; Genetic Transcription; Half-Life; High-Throughput Nucleotide Sequencing; Histologic; Histology; Human; In Situ Hybridization; In Vitro; Investigation; Knock-out; Label; Lead; Link; Literature; Logistics; Lung; Maintenance; Malignant - descriptor; Malignant Neoplasms; Malignant neoplasm of pancreas; Mediating; Mediator; Medical; Messenger RNA; Metabolic; Metastatic Neoplasm to the Lung; Methods; Modality; Modeling; Modification; Molecular Disease; Nature; Neoplasm Metastasis; Normal Cell; Normal tissue morphology; Nucleotides; Nutrient availability; Oncogenic; Outcome; Pancreatic Adenocarcinoma; Pancreatic Ductal Adenocarcinoma; Pathogenesis; Patients; Phenotype; Physicians; Pilot Projects; Production; Prognosis; Proteins; RNA; RNA Polymerase III; Regulation; Regulator Genes; Reporting; Research; Research Personnel; Ribosomes; Role; Sampling; Scientist; Severity of illness; Site; Solid; Structure; Survival Rate; Survivors; Training; Transcript; Transfer RNA; Transfer RNA Aminoacylation; Translations; Tumor stage; Untranslated RNA; Validation; Work; amino acid metabolism; biobank; career development; cell type; chemoradiation; clinical decision-making; clinical practice; cohort; deprivation; disorder subtype; experimental study; innovation; mRNA Decay; mRNA Stability; molecular marker; molecular subtypes; neoplastic cell; novel; novel marker; pancreatic ductal adenocarcinoma model; patient prognosis; pharmacologic; pressure; prognostic; programs; screening; skills; tissue culture; transcriptome; transcriptomics; tumor; tumorigenic

PROJECT SUMMARY Pancreatic ductal adenocarcinoma (PDAC) is uniquely difficult to treat due to late diagnosis and limited medical management options for a majority of patients. This is despite a wealth of watershed studies on disease driver mechanisms over the past decade, highlighting a need for alternative approaches to studying this disease. It is now clear that PDACs present along a bimodal continuum of transcriptomic subtypes that exhibit distinct prognoses, and additional work on advanced PDAC models has uncovered that these tumors, though highly chemoresistant, are sensitive to external amino acid supply through metabolic dysregulation. Transcripts that define known PDAC molecular subtypes present unique codon biases, suggesting that PDACs are subject to biologically deterministic codon-level selective pressures. Work from our lab and others has shown that the abundance of properly aminoacylated transfer RNAs (tRNAs), highly structured and chemically modified non- coding RNAs, is highly deterministic of mRNA half-life. This mechanism acts through codon-anticodon recognition and ribosome elongation rate, and alterations of functional tRNA abundance can dictate cellular functions via concomitant regulation of mRNA stability. Furthermore, a wealth of literature evidence in diverse cell types across species demonstrates that tRNA regulation can be disease-specific. Thus, tRNAs may likely serve a key regulatory role in PDAC subtype expression and amino acid sensitivity, given their function in bridging codon-amino acid pairings during protein production. As proof of concept, I have strong preliminary evidence that tRNA expression can be highly predictive of disease stage in a limited cohort of primary colorectal tumor samples. Furthermore, a pilot study of PDACs revealed widespread tRNA dysregulation, with increased use of cysteine-decoding transcripts, matching existing literature that PDACs are specifically sensitive to deprivation of this amino acid. In this proposal, I seek to interrogate linked roles of tRNAs as regulators of mRNA and nutrient availability phenotypes in PDAC. My central hypothesis is that PDACs specifically regulate tRNA expression to confer cell survival and proliferation advantages and that tRNA profiling can reveal novel biomarkers for use in clinical decision-making. I will address this hypothesis through the following aims: Aim 1: Characterize tRNA expression and modifications in primary patient PDACs; Aim 2: Investigate PDAC tRNA regulation as a driver of tumor cell survival. These aims will be achieved through a combination of biochemical and high-throughput sequencing approaches using archived patient samples and established in vitro cell lines. Beyond biological interrogation, this proposal involves novel technical development in the experimental and analytical application of tRNA sequencing for large patient sample cohorts. This project would be the first to analyze tRNA gene-specific regulation in cancer, and will be significant in that it may reveal novel targetable mechanisms of PDAC maintenance and a potent set of disease-associated clinical features that are likely to inform fundamental cancer biology.

项目摘要 胰腺导管腺癌（PDAC）由于晚期诊断和医疗有限而难以治疗 大多数患者的管理选择。尽管有大量有关疾病驱动器的流域研究 在过去的十年中，机制强调了对研究这种疾病的替代方法的需求。这是 现在清楚地表明，PDAC沿着双峰连续体的转录组亚型的连续体显示出不同 预后和对高级PDAC模型的其他工作发现这些肿瘤虽然很高 化学抗性，对外部氨基酸供应通过代谢失调敏感。成绩单 定义已知的PDAC分子亚型具有独特的密码子偏见，表明PDAC受到 生物学确定性的密码子级选择性压力。我们实验室和其他人的工作表明 适当的氨基化转移RNA（TRNA），高度结构化和化学改性的非氨基化转移RNA（TRNA） 编码RNA是mRNA半衰期的高度决定性的。该机制通过密码子 - 抗原作用 识别和核糖体的伸长率以及功能性tRNA丰度的改变可以决定细胞 通过同时调节mRNA稳定性的功能。此外，多种文献证据 跨物种的细胞类型表明，tRNA调控可能是特异性的。因此，trnas可能 鉴于它们的功能 蛋白质生产过程中桥接密码子氨基酸配对。 作为概念证明，我有强有力的初步证据表明tRNA表达可以高度预测疾病 阶段有限的主要结直肠肿瘤样品。此外，PDAC的试点研究显示 广泛的tRNA失调，随着半胱氨酸描述成绩单的使用增加，与现有文献相匹配 PDAC对这种氨基酸的剥夺特别敏感。在此提案中，我试图讯问 将TRNA作为mRNA的调节剂和PDAC中养分可用性表型的作用。我的中心假设 PDAC是特异性调节tRNA表达以赋予细胞存活和增殖优势的，并且 tRNA分析可以揭示用于临床决策的新型生物标志物。我将解决这个假设 通过以下目的：目标1：表征tRNA表达和原代患者PDAC中的修饰； AIM 2：研究PDAC tRNA调节是肿瘤细胞存活的驱动因素。这些目标将通过 使用存档的患者样本和 建立的体外细胞系。除了生物学询问之外，该建议还涉及新的技术发展 在大型患者样本队列的tRNA测序的实验和分析应用中。这个项目 将是第一个分析癌症中tRNA基因特异性调节的人，并且很重要，因为它可能揭示 PDAC维护的新型目标机制和一套有效的疾病相关临床特征 可能会为基本癌症生物学提供信息。