title: Correlation of SHOX2 gene amplification and DNA methylation in lung cancer tumors.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: University Hospital Heidelberg, Institute of Human Genetics, Heidelberg, Germany.
authors.forename: Katja U
authors.initials: KU
authors.lastname: Schneider
authors.forename: Dimo
authors.initials: D
authors.lastname: Dietrich
authors.forename: Michael
authors.initials: M
authors.lastname: Fleischhacker
authors.forename: Gunda
authors.initials: G
authors.lastname: Leschber
authors.forename: Johannes
authors.initials: J
authors.lastname: Merk
authors.forename: Frank
authors.initials: F
authors.lastname: Schäper
authors.forename: Henk R
authors.initials: HR
authors.lastname: Stapert
authors.forename: Erik R
authors.initials: ER
authors.lastname: Vossenaar
authors.forename: Sabine
authors.initials: S
authors.lastname: Weickmann
authors.forename: Volker
authors.initials: V
authors.lastname: Liebenberg
authors.forename: Christoph
authors.initials: C
authors.lastname: Kneip
authors.forename: Anke
authors.initials: A
authors.lastname: Seegebarth
authors.forename: Fikret
authors.initials: F
authors.lastname: Erdogan
authors.forename: Gudrun
authors.initials: G
authors.lastname: Rappold
authors.forename: Bernd
authors.initials: B
authors.lastname: Schmidt
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D002277:Carcinoma / Q000175:diagnosis / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D055028:Comparative Genomic Hybridization; D019175:DNA Methylation / Q000502:physiology; D004252:DNA Mutational Analysis / Q000379:methods; D005784:Gene Amplification / Q000502:physiology*; D018628:Gene Dosage / Q000502:physiology; D018398:Homeodomain Proteins / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D006801:Humans; D008175:Lung Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D016555:Matched-Pair Analysis; D011110:Polymorphism, Genetic; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D014408:Biomarkers, Tumor; D018398:Homeodomain Proteins; C484664:SHOX2 protein, human