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

Katja U Schneider1, Dimo Dietrich2*, Michael Fleischhacker3, Gunda Leschber4, Johannes Merk4, Frank Schäper4, Henk R Stapert5, Erik R Vossenaar5, Sabine Weickmann6, Volker Liebenberg7, Christoph Kneip8, Anke Seegebarth9, Fikret Erdogan10, Gudrun Rappold1 and Bernd Schmidt11

Author Affiliations

1 University Hospital Heidelberg, Institute of Human Genetics, Germany

2 Epigenomics AG, Berlin, Germany

3 Medizinische Klinik m.S. Onkologie Hämatologie, Charité-Universitätsmedizin, Berlin, Germany

4 ELK Berlin Chest Hospital, Germany

5 Biocartis B.V., Eindhoven, the Netherlands

6 Medizinische Klinik m.S. Infektiologie und Pneumologie, Pneumologie, Charité-Universitätsmedizin, Berlin, Germany

7 Metanomics Health GmbH, Berlin, Germany

8 Theracode GmbH, Mainz, Germany

9 Bavarian Nordic GmbH, Berlin, Germany

10 ATLAS Biolabs GmbH, Berlin, Germany

11 Universitätsklinik und Poliklinik für Innere Medizin I, Universitätsklinikum Halle (Saale), Halle, Germany

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BMC Cancer 2011, 11:102  doi:10.1186/1471-2407-11-102

Published: 22 March 2011



DNA 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.


SHOX2 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.


A 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.


Frequent 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.