Subtyping Lung Cancer Using DNA Methylation in Liquid Biopsies

Abstract

Background: Lung cancer (LCa) is the most frequently diagnosed and lethal cancer worldwide. Histopathological subtyping, which has important therapeutic and prognostic implications, requires material collection through invasive procedures, which might be insufficient to enable definitive diagnosis. Aberrant DNA methylation is an early event in carcinogenesis, detectable in circulating cell-free DNA (ccfDNA). Herein, we aimed to assess methylation of selected genes in ccfDNA from LCa patients and determine its accuracy for tumor subtyping. Methods: Methylation levels of APC, HOXA9, RARβ2, and RASSF1A were assessed in three independent study groups (study group #1: 152 tissue samples; study group #2: 129 plasma samples; study group #3: 28 benign lesions of lung) using quantitative methylation-specific PCR. Associations between gene promoter methylation levels and LCa subtypes were evaluated using non-parametric tests. Receiver operating characteristic (ROC) curve analysis was performed. Results: In study group #2, HOXA9 and RASSF1A displayed higher methylation levels in small-cell lung cancer (SCLC) than in non-small-cell lung cancer (NSCLC). HOXA9 displayed high sensitivity (63.8%), whereas RASSF1A disclosed high specificity (96.2%) for SCLC detection in ccfDNA. Furthermore, HOXA9 methylation levels showed to be higher in squamous cell carcinoma in comparison with adenocarcinoma in study group #1. Conclusions: Methylation level assessments in ccfDNA may provide a minimally invasive procedure for LCa subtyping, complementing standard diagnostic procedures.

Epigenetic Research in Stem Cell Bioengineering—Anti-Cancer Therapy, Regenerative and Reconstructive Medicine in Human Clinical Trials

“…Methylation levels in adenomatous polyposis coli (APC), homeobox gene A9 (HOXA9), retinoic acid receptor beta 2 (RARβ2), and Ras association domain-containing protein 1 (RASSF1A) were assessed as a novel non-invasive method for lung cancer subtyping. Higher methylation patterns of HOXA9 and RASSF1A were detected in small-cell lung cancer rather than non-small-cell lung cancer [97]. Quantitative panel assessment of two-gene promoter methylation patterns (singleplex-miR-34b/c, miR-193b and multiplex-APC, GSTP1, RARβ2, respectively), in tissue biopsies and urine of prostate cancer patients demonstrated higher methylation levels of both panels compared to controls [98].…”

Hypermethylation of tumor necrosis factor decoy receptor gene in non‑small lung cancer

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Detection of Circulating Tumor-specific DNA Methylation Markers in the Blood of Patients with Pituitary Tumors

“…The copyright holder for this preprint this version posted May 30, 2020. ; https://doi.org/10.1101/2020.05.29.20116202 doi: medRxiv preprint helpful to distinguish PT from other rare primary or secondary sellar tumors whose diagnosis by morphologic and immunohistochemical approaches may be challenging, unavailable and/or inconclusive (e.g. craniopharyngioma variants, lymphoma, metastasis etc) 5,34,45,46 .…”