A Panel of Novel Detection and Prognostic Methylated DNA Markers in Primary Non–Small Cell Lung Cancer and Serum DNA

Abstract

To establish a novel panel of cancer-specific methylated genes for cancer detection and prognostic stratification of early-stage non-small cell lung cancer (NSCLC). Identification of differentially methylated regions (DMR) was performed with bumphunter on "The Cancer Genome Atlas (TCGA)" dataset, and clinical utility was assessed using quantitative methylation-specific PCR assay in multiple sets of primary NSCLC and body fluids that included serum, pleural effusion, and ascites samples. A methylation panel of 6 genes (, and ) was selected from TCGA dataset. Promoter methylation of the gene panel was detected in 92.2% (83/90) of the training cohort with a specificity of 72.0% (18/25) and in 93.0% (40/43) of an independent cohort of stage IA primary NSCLC. In serum samples from the later 43 stage IA subjects and population-matched 42 control subjects, the gene panel yielded a sensitivity of 72.1% (31/41) and specificity of 71.4% (30/42). Similar diagnostic accuracy was observed in pleural effusion and ascites samples. A prognostic risk category based on the methylation status of, and refined the risk stratification for outcomes as an independent prognostic factor for an early-stage disease. Moreover, the paralog group for HOXA9, predominantly overexpressed in subjects with methylation, showed poor outcomes. Promoter methylation of a panel of 6 genes has potential for use as a biomarker for early cancer detection and to predict prognosis at the time of diagnosis. .

Epigenetic biomarkers of promoter DNA methylation in the new era of cancer treatment

“…Digital PCR for CDO1 methylation (which can detect a 1/100 000 dilution of fully methylated CDO1 ) might be sufficient to detect cancer cells in plasma, as shown for VIMENTIN ( VIM ) gene hypermethylation in patients with CRC . However, CDO1 gene methylation was reported to be readily detected in the plasma of patients with lung cancer, where Q‐MSP detection of CDO1 methylation in plasma or serum showed 65% sensitivity with 74% specificity, and, when assessed in combination with the methylation of other HRMG, showed high sensitivity even in stage I disease. This extraordinarily high sensitivity of detection of cancer cells in plasma has been for the first time experienced in cancer clinics.…”

“…Relatively low specificity is a concern in lung cancer. Ooki et al selected a methylation panel of 6 genes ( CDO1 / HOXA9 , AJAP1 / PTGDR / UNCX / MARCH11 ) from the TOGA dataset. Even in serum samples from the stage IA subjects and population‐matched control subjects, the gene panel yielded a sensitivity of 72.1% and a specificity of 71.4%.…”

“…Ooki et al 48 In gynecological and urological cancer research, methylation markers were applied to the testing of cervical scrapings and urine specimens. Both tests are kinds of cytological assays, and various methylation markers showed superior clinical outcomes for diagnosis of the individual cancers as described below.…”

Aberrant methylation of mutL homolog 1 is associated with increased risk of non‐small cell lung cancer

“…A diagnostic test based on miRNA‐944 and miRNA‐3662 showed 75.7% sensitivity and 82.3% specificity (AUC = 0.898) in distinguishing NSCLC from healthy individuals . In addition, a panel of CDO1 , HOXA9, AJAP1 , PTGDR , UNCX , and MARCH11 methylation could be potential biomarkers for early detection of NSCLC with high sensitivity and specificity . And frequent simultaneous methylation of DLEC1 , ITGA9, and MLH1 in more than 50% NSCLC patients indicated the possibility of considering them as a panel of epigenetic markers in NSCLC .…”

“…36 In addition, a panel of CDO1, HOXA9, AJAP1, PTGDR, UNCX, and MARCH11 methylation could be potential biomarkers for early detection of NSCLC with high sensitivity and specificity. 37 And frequent simultaneous methylation of DLEC1, ITGA9, and MLH1 in more than 50% NSCLC patients indicated the possibility of considering them as a panel of epigenetic markers in NSCLC. 31 However, Geng et al 39 found no significant differences in MLH1 methylation between AC and SCC in Chinese population.…”