KMT2C promoter methylation in plasma‐circulating tumor DNA is a prognostic biomarker in non‐small cell lung cancer

Abstract

MLL3 histone methyltransferase, encoded by the KMT2C gene, is a tumor suppressor that has an essential role in cell type-specific gene expression. We evaluated the prognostic significance of KMT2C promoter methylation as a circulating epigenetic biomarker in plasma cell-free DNA (cfDNA) in non-small cell lung cancer (NSCLC). We examined the methylation status of KMT2C promoter using a novel highly specific and sensitive real-time methylation-specific PCR (MSP) assay in: a) operable NSCLC: 48 fresh-frozen NSCLC tissues, their corresponding adjacent nonneoplastic tissues and 48 matched plasma samples; b) metastatic NSCLC: 91 plasma samples and c) 60 plasma samples from healthy donors (HD). KMT2C promoter methylation in plasma-cfDNA was detected in 7/48 (14.6%) patients with operable and in 18/91 (19.8%) patients with advanced NSCLC but in none (0/60, 0%) of the plasma samples from HD. In operable NSCLC, in corresponding adjacent non-neoplastic tissue samples, KMT2C promoter methylation was detected in 3/48 (6.3%) cases. Moreover, in operable NSCLC, KMT2C promoter methylation in plasma-cfDNA was related to reduced disease-free survival (DFS) (ΗR=0.239; p=0.001) and worse overall survival (OS) (HR=0.342, p=0.023). In metastatic NSCLC, KMT2C promoter methylation in plasma-cfDNA was related to worse progression-free survival (PFS) (HR=0.431; p=0.005) and worse OS (HR=0.306; p<0.001). Our data strongly suggest that detection of KMT2C promoter methylation in plasma cfDNA predicts poor prognosis in patients with both operable and metastatic NSCLC. KMT2C promoter methylation in plasma cfDNA therefore merits further evaluation and validation as a non-invasive circulating epigenetic biomarker.

DNA methylation analysis of tumor suppressor genes in liquid biopsy components of early stage NSCLC: a promising tool for early detection

“…Once isolated, plasma samples were centrifuged again at 2.000xg for 10 min, before transferring into clean 2-mL tubes and freezing at − 70 °C until time of processing. cfDNA was extracted from 2.00 mL plasma using the QIAamp® Circulating Nucleic Acid kit 50 (Qiagen®, Germany), as previously described [ 32 ].…”

Detection and relevance of epigenetic markers on ctDNA: recent advances and future outlook

“…Additionally, HOXA9 methylation levels were higher in squamous cell carcinoma than in adenocarcinoma [67]. Very recently, the detection of KMT2C (MLL3) promoter methylation was detected in plasma cfDNA of NSCLC patients at both early and advanced stages, but not in plasma of healthy individuals [68]. Promoter methylation of this gene in plasma cfDNA needs to be further evaluated in a large and well-defined patient cohort [68].…”

“…Very recently, the detection of KMT2C (MLL3) promoter methylation was detected in plasma cfDNA of NSCLC patients at both early and advanced stages, but not in plasma of healthy individuals [68]. Promoter methylation of this gene in plasma cfDNA needs to be further evaluated in a large and well-defined patient cohort [68]. Promoter methylation of two other genes, namely BRMS1 and SOX17, in plasma ctDNA from NSCLC patients has also been shown to be of prognostic significance [69,70].…”

Epigenetic Alterations and Inflammation as Emerging Use for the Advancement of Treatment in Non-Small Cell Lung Cancer

“…Hence, they were recognized as potential innovative markers that benefit the early-stage lung cancer diagnosis ( 166 ). The gene encoding MLL3 histone methyltransferase, KMT2C, promoter methylation of which in plasma cell‐free DNA (cfDNA) was found to can indicate unfortunate results in NSCLC and provide further assessment as a circulating epigenetic biomarker ( 167 ). Sun et al.…”