Developing a CLIA compliant LDT for detecting plasma piR-Ls/pfeRNAs to distinguish benign and malignant lung nodules

项目摘要： 肺癌是美国癌症相关死亡的主要原因，在很大程度上，因为诊断往往 在癌症发展到最晚期后才进行。目前的诊断技术 用于检测早期非小细胞肺癌（NSCLC）的方法要么是侵入性的，要么准确性差。我们 最近报道，piR-Ls和pfeRNA在蛋白质功能中起着重要作用， 在肺癌的肿瘤发生和分化中起关键作用。我们开发了一种新技术 准确且稳健地测量血浆中的piR-Ls和pfeRNA。我们还鉴定了2个piR-L和6个 pfeRNA作为有前途的非侵入性生物标志物，使用下一代sncRNA深度测序119 生物样本，包括（i）来自健康对照的血浆，（ii）具有匹配的、相应的 组织学证实的NSCLC组织以及来自分期患者的组织学正常的邻近肺组织 I/II NSCLC（iii）来自具有活检证实的良性和恶性肺结节的患者的血浆。此外，委员会认为， 我们在352个临床血浆样本中验证了这些生物标志物，包括77个健康对照，44个 良性病变及恶性肺结节231例。此外，我们制定了预测规则， 用于我们检测早期非小细胞肺癌的检测。仅使用血浆，我们能够：（1）区分患者 无肺结节者的敏感性和特异性分别为98.5%和98.7%，是临床诊断肺结核的重要依据。 在世界上偏远、贫困、吸烟者流行率高但无法获得 CT扫描）;（2）区分恶性与良性肺结节的患者，敏感性和 特异性分别为96.5%和72.7%（对于招募吸烟者的经济发达国家很重要 CT肺癌筛查项目）。这些数据有力地表明，我们的2个piR-Ls和6个pfeRNA的组 是用于检测早期肺癌的非侵入性推定生物标志物。我们的多学科协作 该团队由一名物理科学家，基础研究人员，一名CLIA认证实验室的物理科学家组成， 统计学家和商业开发人员。该团队将开发符合CLIA的LDT，用于验证我们的核酸- 现有的酸基检测试剂盒已在460多份临床标本中进行了有效检测。的技术 我们将用于我们的测试，目前FDA批准用于临床实验室，和设备， 而且我们的所有检测试剂都已用于体外诊断测试。我们的合作团队旨在 开发一种分子诊断检测方法，可以整合到未来的临床试验中，用于早期检测 NSCLC，并最终改善这种疾病的惨淡生存率。

Project Summary: Lung cancer is the leading cause of cancer-related death in the U.S., in large part, because the diagnosis tends to be made after the cancer has progressed to its most advanced stages. However, current diagnostic techniques for detecting early-stage non-small cell lung cancer (NSCLC) are either invasive or have poor accuracy. We recently reported that piRNA-like sncRNAs (piR-Ls) and protein function effector sncRNAs (pfeRNAs) play critical roles in the tumorigenesis and differentiation of lung cancer. We have developed a novel technology for accurately and robustly measuring piR-Ls and pfeRNAs in plasma. We also have identified 2 piR-Ls and 6 pfeRNAs as promising non-invasive biomarkers using next generation sncRNAs deep sequencing of 119 biospecimens, including (i) plasma from healthy controls (ii) patient plasma with the matched, corresponding histologically proven NSCLC tissue as well as histologically normal adjacent lung tissue from patients with Stage I/II NSCLC (iii) plasma from patients with both biopsy proven benign and malignant lung nodules. Furthermore, we validated these biomarkers in 352 clinical plasma specimens, including 77 healthy controls, 44 patients with benign disease as well as 231 patients with malignant lung nodules. Moreover, we formulated prediction rules for our assay in detecting early-stage NSCLC. Using only plasma, we were able to: (1) differentiate patients with and without lung nodules, with a sensitivity and specificity of 98.5% and 98.7%, respectively (an important clinical assay needed in remote, impoverished areas of the world with a high prevalence of smokers but no access to CT scanning); (2) differentiate patients who had malignant versus benign lung nodules, with a sensitivity and specificity of 96.5% and 72.7%, respectively (important for economically advanced countries enrolling smokers to CT lung cancer screening programs). These data strongly suggest that our panel of 2 piR-Ls and 6 pfeRNAs are non-invasive putative biomarkers for detecting early-stage lung cancers. Our multi-disciplinary collaborative team consists of a physician-scientist, basic researchers, a physician-scientist in the CLIA-certified laboratory, statisticians, and a commercial developer. This team will develop a CLIA compliant LDT for validating our nucleic- acid-based existing assay which now has been tested as valid in over 460 clinical specimens. The technologies that we will utilize for our testing are currently FDA-cleared for use in clinical laboratories, and the equipment as well as all reagents for our assays already are used in in-vitro-diagnostic testing. Our collaborative team aims to develop a molecular diagnostic assay that can be integrated into future clinical trials for the early detection of NSCLC, and ultimately, improve the dismal survival rates of that disease.