Abstract
BackgroundIn colorectal cancer a distinct subgroup of tumours demonstrate the CpG island methylator phenotype (CIMP). However, a consensus of how to score CIMP is not reached, and variation in definition may influence the reported CIMP prevalence in tumours. Thus, we sought to compare currently suggested definitions and cut-offs for methylation markers and how they influence CIMP classification in colon cancer.MethodsMethylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), with subsequent fragment analysis, was used to investigate methylation of tumour samples. In total, 31 CpG sites, located in 8 different genes (RUNX3, MLH1, NEUROG1, CDKN2A, IGF2, CRABP1, SOCS1 and CACNA1G) were investigated in 64 distinct colon cancers and 2 colon cancer cell lines. The Ogino gene panel includes all 8 genes, in addition to the Weisenberger panel of which only 5 of the 8 genes included were investigated. In total, 18 alternative combinations of scoring of CIMP positivity on probe-, gene-, and panel-level were analysed and compared.ResultsFor 47 samples (71%), the CIMP status was constant and independent of criteria used for scoring; 34 samples were constantly scored as CIMP negative, and 13 (20%) consistently scored as CIMP positive. Only four of 31 probes (13%) investigated showed no difference in the numbers of positive samples using the different cut-offs. Within the panels a trend was observed that increasing the gene-level stringency resulted in a larger difference in CIMP positive samples than increasing the probe-level stringency. A significant difference between positive samples using ‘the most stringent’ as compared to ‘the least stringent’ criteria (20% vs 46%, respectively; p<0.005) was demonstrated.ConclusionsA statistical significant variation in the frequency of CIMP depending on the cut-offs and genes included in a panel was found, with twice as many positives samples by least compared to most stringent definition used.
Highlights
Cancer is a genetic disease caused by accumulation of molecular changes and modifications on DNA that drives tumorigenesis [1]
Colon cancer is a well investigated cancer model, for which tumours are separated into three phenotypical subgroups, depending on the predominant type of genetic aberrations: chromosomal instability (CIN) refers to changes at the chromosome level; microsatellite instability (MSI) refers to alterations in basepair-repeats, and; CpG island methylator phenotype (CIMP) denotes an aberrant methylation spectrum, compared to normal cells [2,3]
The largest variation was observed for probe 09-021965200 in CDKN2A, in which 8 patients (12%) were scored differently using the two different cutoffs
Summary
Cancer is a genetic disease caused by accumulation of molecular changes and modifications on DNA that drives tumorigenesis [1]. Proper molecular characterisation of the cancer geno- and phenotypes is important to reveal markers for early detection, prognostication or prediction, as well as increase the understanding of disease processes that may yield information for therapeutic intervention. While it is generally well accepted that etiologically and clinically distinct subgroups exist [13,14], a precise definition of CIMP remains to be established, both methodologically and on a molecular level [15]. The increasing use of high-throughput technologies for methylation studies have shown great impact and suggested several panels, e.g. to aid in the discrimination of colorectal tumour from epithelial cells, differentiate between disease stages, prognostic groups, and subgroups associated to other molecular features [16,17,18]. In colorectal cancer a distinct subgroup of tumours demonstrate the CpG island methylator phenotype (CIMP). We sought to compare currently suggested definitions and cut-offs for methylation markers and how they influence CIMP classification in colon cancer
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
