Potential of DNA methylation in rectal cancer as diagnostic and prognostic biomarkers.
BACKGROUND
Aberrant DNA methylation is more prominent in proximal compared with distal colorectal cancers. Although a number of methylation markers were identified for colon cancer, yet few are available for rectal cancer.


METHODS
DNA methylation differences were assessed by a targeted DNA microarray for 360 marker candidates between 22 fresh frozen rectal tumour samples and 8 controls and validated by microfluidic high-throughput and methylation-sensitive qPCR in fresh frozen and formalin-fixed paraffin-embedded (FFPE) samples, respectively. The CpG island methylator phenotype (CIMP) was assessed by MethyLight in FFPE material from 78 patients with pT2 and pT3 rectal adenocarcinoma.


RESULTS
We identified and confirmed two novel three-gene signatures in fresh frozen samples that can distinguish tumours from adjacent tissue as well as from blood with a high sensitivity and specificity of up to 1 and an AUC of 1. In addition, methylation of individual CIMP markers was associated with specific clinical parameters such as tumour stage, therapy or patients' age. Methylation of CDKN2A was a negative prognostic factor for overall survival of patients.


CONCLUSIONS
The newly defined methylation markers will be suitable for early disease detection and monitoring of rectal cancer.
Department of Surgery, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria.
Ruth
R
Exner
AIT-Austrian Institute of Technology GmbH, Health & Environment Department, Molecular Diagnostics, Muthgasse 11/2, A-1190 Vienna, Austria.
Walter
W
Pulverer
Clinical Institute of Pathology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria.
Martina
M
Diem
Clinical Institute of Pathology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria.
Lisa
L
Spaller
Clinical Institute of Pathology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria.
Laura
L
Woltering
Department of Obstetrics and Gynecology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria.
Martin
M
Schreiber
Department of Surgery, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria.
Brigitte
B
Wolf
AIT-Austrian Institute of Technology GmbH, Health & Environment Department, Molecular Diagnostics, Muthgasse 11/2, A-1190 Vienna, Austria.
Markus
M
Sonntagbauer
AIT-Austrian Institute of Technology GmbH, Health & Environment Department, Molecular Diagnostics, Muthgasse 11/2, A-1190 Vienna, Austria.
Fabian
F
Schröder
Clinical Institute of Pathology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria.
Judith
J
Stift
Clinical Institute of Pathology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria.
Fritz
F
Wrba
Department of Surgery, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria.
Michael
M
Bergmann
AIT-Austrian Institute of Technology GmbH, Health & Environment Department, Molecular Diagnostics, Muthgasse 11/2, A-1190 Vienna, Austria.
Andreas
A
Weinhäusel
Clinical Institute of Pathology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria.
Gerda
G
Egger
D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000235:genetics*; D018899:CpG Islands; D019941:Cyclin-Dependent Kinase Inhibitor p16; D019175:DNA Methylation; D004273:DNA, Neoplasm / Q000032:analysis; D005260:Female; D006801:Humans; D008297:Male; D008875:Middle Aged; D009363:Neoplasm Proteins / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D011379:Prognosis; D012004:Rectal Neoplasms / Q000235:genetics* / Q000473:pathology*; D016019:Survival Analysis
D014408:Biomarkers, Tumor; C000614131:CDKN2A protein, human; D019941:Cyclin-Dependent Kinase Inhibitor p16; D004273:DNA, Neoplasm; D009363:Neoplasm Proteins