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Comprehensive analysis of the MLH1 promoter region in 480 patients with colorectal cancer and 1150 controls reveals new variants including one with a heritable constitutional MLH1 epimutation
  1. Monika Morak1,2,
  2. Ayseguel Ibisler3,
  3. Gisela Keller4,
  4. Ellen Jessen5,
  5. Andreas Laner2,
  6. Daniela Gonzales-Fassrainer2,
  7. Melanie Locher2,
  8. Trisari Massdorf1,
  9. Anke M Nissen2,
  10. Anna Benet-Pagès2,
  11. Elke Holinski-Feder1,2
  1. 1Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Bavaria, Germany
  2. 2Center of Medical Genetics, Medizinisch Genetisches Zentrum, Munich, Bavaria, Germany
  3. 3Department of Human Genetics, Ruhr University Bochum, Bochum, North Rhine-Westphalia, Germany
  4. 4Institute of Pathology, Technical University Munich, Munich, Bavaria, Germany
  5. 5Praxis für Humangenetik, Praxis für Humangenetik, Hamburg, Hamburg, Germany
  1. Correspondence to Professor Elke Holinski-Feder, Center of Medical Genetics, Medizinisch Genetische Zentrum, Munich 80335, Germany; elke.holinski-feder{at}


Background Germline defects in MLH1, MSH2, MSH6 and PMS2 predisposing for Lynch syndrome (LS) are mainly based on sequence changes, whereas a constitutional epimutation of MLH1(CEM) is exceptionally rare. This abnormal MLH1 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 MLH1 promoter variants causing a germline or somatic methylation induction or transcriptional repression.

Methods We analysed the MLH1 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 MLH1 promoter variants. One novel, complex MLH1 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 MLH1 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.

  • cancer: colon
  • epigenetics
  • genetics
  • genetic screening/counselling

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  • Contributors EH-F and MM designed the study, wrote the manuscript and are responsible for the content of the study. EH-F, AI, GK, EJ and DG-F provided patients clinical and molecular data and samples. Experiments were mainly performed by TM, supervised by MM; tumour analyses were also carried out by ML and AL. AB-P was responsible for NGS techniques and supervised AMN for bioinformatical analyses. EH-F, MM, AL, AB-P and AN were involved in data analyses and interpretation. EH-F and MM wrote the manuscript and are responsible for the content of the study. MM submitted the article.

  • Funding This work was supported by grants from the German Cancer Aid (Deutsche Krebshilfe) (#111222) and the Wilhelm Sander-Stiftung (#2012.081.1).

  • Competing interests None declared.

  • Patient consent Obtained.

  • Ethics approval Ethikkommission der Medizinischen Fakultät der LMU München.

  • Provenance and peer review Not commissioned; externally peer reviewed.

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