Novel ultra-short cell free DNA biomarkers for early detection of non-small cell lung cancer.

项目摘要/摘要 肺癌仍然是美国和全世界与癌症相关的死亡的主要原因。非小蜂窝 肺癌(NSCLC)约占所有肺癌的85%。早期发现不确定因素 胸部低剂量计算机断层扫描(LDCT)筛查肺结节(IPN) 与胸部X光检查相比，治疗可以将死亡率降低20%。然而，较高的假阳性率 发现AS&>95%会限制其应用。未得到满足的临床早期诊断需求是缺乏非侵入性的 一种可应用于CT检测到的肺结节患者的测试，并可靠地区分 恶性或良性结节。液体活检侧重于肿瘤相关基因的特征 无细胞循环的肿瘤DNA的改变可以非侵入性地描绘实体肿瘤的分子图景。 然而，ctDNA的生物浓度低、体细胞突变频率低、混杂 克隆性造血相关变异体对早期肺癌的影响限制了ctDNA检测的敏感性 液体活组织检查。如果可以包括更多的无细胞DNA生物标记物，以允许 开发更灵敏的分子诊断方法用于肺癌的早期评估。 我们已经发现了一个独特的超短单链无细胞DNA(USCF/ctDNA)群体，具有 正常人和非小细胞肺癌患者血浆中的DNA大小为40-70nT。我们的初步数据显示，碎片组特征， 包括uscfDNA分子的功能元件图谱、片段模式和末端基序，可以 区分非小细胞肺癌患者和健康捐赠者。此R21应用程序旨在探索和测试我们的假设 UscfDNA分子的片段组学特征可作为鉴别非小细胞肺癌患者的新生物标志物 来自患有IPN的非癌症受试者，并允许更敏感的液体活检分子诊断早期 NSCLC检测。假设检验有两个具体目标。目标1是开发一种预测模型 应用uscfDNA-seq法进行非小细胞肺癌液体活检的uscfDNA片段分析。目标2是预验证 UscfDNA-Seq试验在非小细胞肺癌早期检测中的应用翻译和预验证、确定目标 UscfDNA用于非小细胞肺癌的早期检测可以开辟新的天地，将先前的发现扩展到有影响力的 新方向及临床应用。

PROJECT SUMMARY/ABSTRACT Lung cancer remains the leading cause of cancer-related deaths in the U.S. and worldwide. Non–small cell lung cancer (NSCLC) accounts for approximately 85% of all lung cancers. Early detection of indeterminate pulmonary nodules (IPNs) with chest low dose computed tomography (LDCT) screening followed by effective treatments can reduce mortality by 20% relative to chest radiography. However, the high false positive rate finding as >95% limits the application. The unmet clinical need for early diagnosis is the lack of a noninvasive test that can be applied to individuals with CT-detected lung nodules and reliably discriminates between malignant or benign nodules. Liquid biopsy focused on the characterization of tumor-associated genetic alterations in cell free circulating tumor DNA can non-invasively profile the molecular landscape of solid tumors. However, the low biological concentrations of ctDNA, low frequency of somatic mutations and the confounding impact of clonal hematopoiesis-related variants in early-stage lung cancer limit the sensitivity of ctDNA-based liquid biopsy assays. It would be essential if additional cell free DNA biomarkers could be included to allow the development of more sensitive molecular diagnostics approaches for the early assessment of lung cancer. We have discovered a distinct population of ultra-short single-stranded cell-free DNA (uscf/ctDNA) with a size of 40-70nt in healthy and NSCLC plasma. Our preliminary data showed that the fragmentomic features, including functional element profile, fragmentation patterns and end motifs of uscfDNA molecules, can distinguish NSCLC patients from healthy donors. This R21 application is to explore and test our hypothesis that the fragmentomic features of uscfDNA molecules can serve as novel biomarkers to differentiate NSCLC patients from non-cancer subjects with IPNs and allow more sensitive liquid biopsy molecular diagnostics for early NSCLC detection. Two specific aims are in place for hypothesis testing. Aim 1 is to develop a predictive model using uscfDNA-seq assay on uscfDNA fragmentomic analysis for liquid biopsy of NSCLC. Aim 2 is to pre-validate uscfDNA-Seq test for the early detection of NSCLC. Together, the translational and pre-validation, targeting uscfDNA for early detection of NSCLC can break new ground and extend previous discoveries towards impactful new directions and clinical applications.