A Cost-Effective and Non-Invasive pfeRNA-Based Test Differentiates Benign and Suspicious Pulmonary Nodules from Malignant Ones

Wei Liu, Yuyan Wang, Hongchan Huang, Nadege Fackche, Kristen Rodgers, Beverly Lee, Wasay Nizam, Hamza Khan, Zhihao Lu, Xiangqian Kong, Yanfei Li, Naixin Liang, Xin Zhao, Xin Jin, Haibo Liu, Charles Conover Talbot, Peng Huang, James R. Eshleman, Qi Lai, Yi ZhangMalcolm V. Brock, Yuping Mei

Research output: Contribution to journalArticlepeer-review

Abstract

The ability to differentiate between benign, suspicious, and malignant pulmonary nodules is imperative for definitive intervention in patients with early stage lung cancers. Here, we report that plasma protein functional effector sncRNAs (pfeRNAs) serve as non-invasive biomarkers for determining both the existence and the nature of pulmonary nodules in a three-stage study that included the healthy group, patients with benign pulmonary nodules, patients with suspicious nodules, and patients with malignant nodules. Following the standards required for a clinical laboratory improvement amendments (CLIA)-compliant laboratory-developed test (LDT), we identified a pfeRNA classifier containing 8 pfeRNAs in 108 biospecimens from 60 patients by sncRNA deep sequencing, deduced prediction rules using a separate training cohort of 198 plasma specimens, and then applied the prediction rules to another 230 plasma specimens in an independent validation cohort. The pfeRNA classifier could (1) differentiate patients with or without pulmonary nodules with an average sensitivity and specificity of 96.2% and 97.35% and (2) differentiate malignant versus benign pulmonary nodules with an average sensitivity and specificity of 77.1% and 74.25%. Our biomarkers are cost-effective, non-invasive, sensitive, and specific, and the qPCR-based method provides the possibility for automatic testing of robotic applications.

Original languageEnglish (US)
Article number80
JournalNon-coding RNA
Volume7
Issue number4
DOIs
StatePublished - Dec 2021

Keywords

  • CLIA
  • LDT
  • NSCLC
  • Non-invasive biomarker
  • PfeRNA
  • Pulmonary nodules

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Biochemistry

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