Correlation of SHOX2 Gene Amplification and DNA Methylation in Lung Cancer Tumors

Abstract

BackgroundDNA methylation in the SHOX2 locus was previously used to reliably detect lung cancer in a group of critical controls, including 'cytologically negative' samples with no visible tumor cell content, at a high specificity based on the analysis of bronchial lavage samples. This study aimed to investigate, if the methylation correlates with SHOX2 gene expression and/or copy number alterations. An amplification of the SHOX2 gene locus together with the observed tumor-specific hypermethylation might explain the good performance of this marker in bronchial lavage samples.MethodsSHOX2 expression, gene copy number and DNA methylation were determined in lung tumor tissues and matched morphologically normal adjacent tissues (NAT) from 55 lung cancer patients. Quantitative HeavyMethyl (HM) real-time PCR was used to detect SHOX2 DNA methylation levels. SHOX2 expression was assayed with quantitative real-time PCR, and copy numbers alterations were measured with conventional real-time PCR and array CGH.ResultsA hypermethylation of the SHOX2 locus in tumor tissue as compared to the matched NAT from the same patient was detected in 96% of tumors from a group of 55 lung cancer patients. This correlated highly significantly with the frequent occurrence of copy number amplification (p < 0.0001), while the expression of the SHOX2 gene showed no difference.ConclusionsFrequent gene amplification correlated with hypermethylation of the SHOX2 gene locus. This concerted effect qualifies SHOX2 DNA methylation as a biomarker for lung cancer diagnosis, especially when sensitive detection is needed, i.e. in bronchial lavage or blood samples.

Performance evaluation of the DNA methylation biomarker SHOX2 for the aid in diagnosis of lung cancer based on the analysis of bronchial aspirates

“…The CE marked in vitro diagnostic test Epi proLung BL Reflex Assay is comprised of the three individual kits Epi proLung BL DNA Preparation Kit for the preparation of bisulfite converted DNA using ammonium bisulfite chemistry (15), the Epi proLung BL real-time PCR Kit for quantitative and sensitive determination of SHOX2 DNA methylation, and the Epi proLung BL Work Flow Control Kit for controlling the whole work flow.…”

“…Hypermethylation of the human homeobox gene SHOX2 (short stature homeobox 2) has previously been shown to be frequently accompanied by gene amplification (15). The positive performance of the SHOX2 DNA methylation biomarker in plasma could be due to a correlation of DNA methylation and locus amplification in malignant cells (15).…”

“…The positive performance of the SHOX2 DNA methylation biomarker in plasma could be due to a correlation of DNA methylation and locus amplification in malignant cells (15). These accompanying effects render SHOX2 DNA methylation an attractive biomarker for malignant lung disease, particularly when sensitive detection is required (15).…”

Analysis of Gene Methylation Shox2, Tgfbr1, Mir-375 in Different Types of Lung Cancer

“…Увеличение числа копий гена SHOX2 было признано одним из самых распро-страненных и значимых хромосомных пере-строек при раке легкого [7][8][9][10][11]. В то же время, ненормальное метилирование гена SHOX2 является отличительной чертой раковых опухо-лей легких и коррелирует с увеличением числа копий участка локуса 3q25.3 [12,13].…”

Analysis of Prognostic Marker Panel for High-Grade Serous Ovarian Cancer through Age-Dependent DNA Methylation

“…The changes present in precancerous lesions [6] and some cancers [7] revealed that DNA methylation alterations play a key role in the early steps of human carcinogenesis. It has been a few decades now since Riggs, Holliday and Pugh proposed that DNA methylation was part of a system for controlling gene expression, and play an essential role in genome regulation, development and disease in mammalian cells [8,9]. Profiling of specific sites or panels of sites aberrantly methylated within tumor cells are currently being investigated as biomarkers for early prediction and prognostication, where cancer-associated methylation can be detected in tumor biopsy samples, cell-free serum, urine and peritoneal fluid [10][11][12].…”