A Novel Epigenetic Signature for Early Diagnosis in Lung Cancer

Abstract

Purpose: Lung cancer remains as the leading cause of cancer-related death worldwide, mainly due to late diagnosis. Cytology is the gold-standard method for lung cancer diagnosis in minimally invasive respiratory samples, despite its low sensitivity. We aimed to identify epigenetic biomarkers with clinical utility for cancer diagnosis in minimally/noninvasive specimens to improve accuracy of current technologies. Experimental Design: The identification of novel epigenetic biomarkers in stage I lung tumors was accomplished using an integrative genome-wide restrictive analysis of two different large public databases. DNA methylation levels for the selected biomarkers were validated by pyrosequencing in paraffin-embedded tissues and minimally invasive and noninvasive respiratory samples in independent cohorts. Results: We identified nine cancer-specific hypermethylated genes in early-stage lung primary tumors. Four of these genes presented consistent CpG island hypermethylation compared with nonmalignant lung and were associated with transcriptional silencing. A diagnostic signature was built using multivariate logistic regression model based on the combination of four genes: BCAT1, CDO1, TRIM58, and ZNF177. Clinical diagnostic value was also validated in multiple independent cohorts and yielded a remarkable diagnostic accuracy in all cohorts tested. Calibrated and cross-validated epigenetic model predicts with high accuracy the probability to detect cancer in minimally and noninvasive samples. We demonstrated that this epigenetic signature achieved higher diagnostic efficacy in bronchial fluids as compared with conventional cytology for lung cancer diagnosis. Conclusions: Minimally invasive epigenetic biomarkers have emerged as promising tools for cancer diagnosis. The herein obtained epigenetic model in combination with current diagnostic protocols may improve early diagnosis and outcome of lung cancer patients. Clin Cancer Res; 22(13); 3361–71. ©2016 AACR.

Frequent silencing of the candidate tumor suppressor TRIM58 by promoter methylation in early-stage lung adenocarcinoma

“…The frequent inactivation of TRIM58 via hypermethylation observed even in early-stage cases from our panel of primary LADC cases was consistent with the findings of a very recent report [11] in which Diaz-Lagares et al . identified TRIM58 as one of four genes that consistently exhibited CGI hypermethylation in non-small cell lung cancers (NSCLCs) relative to non-malignant lung tissues.…”

“…identified TRIM58 as one of four genes that consistently exhibited CGI hypermethylation in non-small cell lung cancers (NSCLCs) relative to non-malignant lung tissues. In addition, Diaz-Lagares and colleagues found that this hypermethylation was associated with transcriptional silencing in early-stage (stage I) NSCLCs, regardless of smoking status, and identified a DNA methylation signature model based on those four genes that yielded high diagnostic accuracy for NSCLCs even in minimally invasive samples, such as bronchial fluids [11]. According to reference databases in which gene expression profiles of normal tissue have been generated using next-generation RNA sequencing technologies, such as RNA-seq Atlas (http://medicalgenomics.org/rna_seq_atlas) and RefEx (http://refex.dbcls.jp/), TRIM58 mRNA was not detected in most normal tissues although higher expression of this gene is observed in the lung relative to the levels in various other tissues.…”

QSEA—modelling of genome-wide DNA methylation from sequencing enrichment experiments

“…Figure 4B shows the 20 TSGs with largest differences in methylation between tumour and normal samples. The literature supports the detected methylation differences: Differential promoter methylation for cysteine dioxygenase 1 (CDO1, mean QSEA methylation level of 4% in normal and 78% in PDX) has already been described as part of a DNA methylation signature to detect minimally and non-invasive lung cancer (32–34). Other prominent methylation markers of NSCLC are, for example, paired box 6 (PAX6, mean QSEA methylation level of 7% in normal and 79% in PDX) whose promoter hypermethylation has been found to be significantly associated with poor overall survival (35) but also genes like CDX2, CEBPA, HOXB13 and SOX11, that are well described epigenetically regulated genes involved in tumourigenesis of several cancers (36–40).…”

Role of <em>p14^ARF</em> and <em>p15^INK4B</em> promoter methylation in patients with lung cancer: a systematic meta-analysis

“…A large number of studies have reported that genes with aberrant promoter methylation are significantly correlated with lung cancer 10–13. Located on the human chromosome 9p21, the INK4/ARF locus encodes three cell-cycle inhibitory proteins involving p15 INK4B , p14 ARF , and p16 INK4A ; p16 INK4A is encoded by cyclin-dependent kinase inhibitor 2A ( CDKN2A ), p14 ARF is encoded by an alternative reading frame of CDKN2A, and p15 INK4B is encoded by cyclin-dependent kinase inhibitor 2B ( CDKN2B ), which plays roles in the regulation of p53 and retinoblastoma pathways 14–16.…”