Comprehensive analysis of the promoter region in 480 patients with colorectal cancer and 1150 controls reveals new variants including one with a heritable constitutional epimutation.

BACKGROUND

Germline defects in , , and predisposing for Lynch syndrome (LS) are mainly based on sequence changes, whereas a constitutional epimutation of (CEM) is exceptionally rare. This abnormal promoter methylation is not hereditary when arising de novo, whereas a stably heritable and variant-induced CEM was described for one single allele. We searched for promoter variants causing a germline or somatic methylation induction or transcriptional repression.

METHODS

We analysed the promoter sequence in five different patient groups with colorectal cancer (CRC) (n=480) composed of patients with i) CEM (n=16), ii) unsolved loss of MLH1 expression in CRC (n=37), iii) CpG-island methylator-phenotype CRC (n=102), iv) patients with LS (n=83) and v) MLH1-proficient CRC (n=242) as controls. 1150 patients with non-LS tumours also served as controls to correctly judge the results.

RESULTS

We detected 10 rare promoter variants. One novel, complex variant c.-63_-58delins18 is present in a patient with CRC with CEM and his sister, both showing a complete allele-specific promoter methylation and transcriptional silencing. The other nine promoter variants detected in 17 individuals were not associated with methylation. For four of these, a normal, biallelic expression was found in the patients' cDNA.

CONCLUSION

We report the second promoter variant stably inducing a hereditary CEM. Concerning the classification of promoter variants, we discuss contradictory results from the literature for two variants, describe classification discrepancies between existing rules for five variants, suggest the (re-)classification of five promoter variants to (likely) benign and regard four variants as functionally unclear.