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

项目概要/摘要 肺癌仍然是美国和世界范围内癌症相关死亡的主要原因。非小细胞 肺癌（NSCLC）约占所有肺癌的85%。早期发现不确定 肺结节（IPN）与胸部低剂量计算机断层扫描（LDCT）筛查，随后有效 相对于胸部X线摄影，治疗可以将死亡率降低20%。然而，高假阳性率 发现>95%限制了应用。早期诊断的未满足的临床需求是缺乏无创的 测试，可应用于个人与CT检测肺结节，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表征 无细胞循环肿瘤DNA的改变可以非侵入性地描绘实体瘤的分子景观。 然而，ctDNA的低生物浓度、低频率的体细胞突变和混杂因素， 克隆性造血相关变异在早期肺癌中的影响限制了基于ctDNA的 液体活检测定。如果可以包括额外的无细胞DNA生物标志物以允许在细胞内进行生物标记，这将是至关重要的。 发展更敏感的分子诊断方法，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， 在健康和NSCLC血浆中大小为40- 70 nt。我们的初步数据显示， 包括uscfDNA分子的功能元件概况、片段化模式和末端基序，可以 区分NSCLC患者和健康供体。这个R21应用程序是为了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NSCLC患者的新生物标志物 从非癌症受试者与IPN，并允许更敏感的液体活检分子诊断的早期 NSCLC检测。假设检验有两个具体目标。目标1：建立预测模型 使用uscfDNA-seq检测对NSCLC液体活检的uscfDNA片段组学分析。目标2是预先验证 uscfDNA-Seq检测用于NSCLC的早期检测。同时，翻译和预验证， 用于NSCLC早期检测的uscfDNA可以开辟新天地，并将先前的发现扩展到有影响力的 新的方向和临床应用。

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.