Dominantly Inherited Constitutional Epigenetic Silencing of MLH1 in a Cancer-Affected Family Is Linked to a Single Nucleotide Variant within the 5′UTR

Abstract

Constitutional epimutations of tumor suppressor genes manifest as promoter methylation and transcriptional silencing of a single allele in normal somatic tissues, thereby predisposing to cancer. Constitutional MLH1 epimutations occur in individuals with young-onset cancer and demonstrate non-Mendelian inheritance through their reversal in the germline. We report a cancer-affected family showing dominant transmission of soma-wide highly mosaic MLH1 methylation and transcriptional repression linked to a particular genetic haplotype. The epimutation was erased in spermatozoa but reinstated in the somatic cells of the next generation. The affected haplotype harbored two single nucleotide substitutions in tandem; c.-27C > A located near the transcription initiation site and c.85G > T. The c.-27C > A variant significantly reduced transcriptional activity in reporter assays and is the probable cause of this epimutation.

The MLH1 c.-27C>A and c.85G>T variants are linked to dominantly inherited MLH1 epimutation and are borne on a European ancestral haplotype

“…17,21 AQ data from mRNA was normalized to AQ data from parallel assays of genomic DNA to produce an allelic expression ratio: (allele 1 mRNA / allele 2 mRNA )/(allele 1 DNA /allele 2 DNA ).…”

“…[12][13][14][15] However, a handful of familial cases with an MLH1 epimutation have been reported in which transmission of the epimutation between generations has been shown to occur in both non-Mendelian 14 and autosomal dominant patterns, with the latter linked to localized cis-acting genetic anomalies. 16,17 In a Caucasian family from Western Australia (WA Family 16), dominant transmission of a mosaic MLH1 epimutation was demonstrated through three successive generations linked to a particular haplotype bearing two single-nucleotide variants (SNVs) in tandem; promoter substitution c. À27C4A and missense variant c.85G4T (p.A29S) (according to coding reference sequence NM_000249.2). 17 The mosaic nature of the epimutation was observed as variable levels of somatic methylation and partial allelic losses of transcription among different tissues and carriers in the family.…”

“…16,17 In a Caucasian family from Western Australia (WA Family 16), dominant transmission of a mosaic MLH1 epimutation was demonstrated through three successive generations linked to a particular haplotype bearing two single-nucleotide variants (SNVs) in tandem; promoter substitution c. À27C4A and missense variant c.85G4T (p.A29S) (according to coding reference sequence NM_000249.2). 17 The mosaic nature of the epimutation was observed as variable levels of somatic methylation and partial allelic losses of transcription among different tissues and carriers in the family. 17 Two other index cases have also been reported as carriers of the MLH1 c. À27C4A and c.85G4T SNVs.…”

“…17 The mosaic nature of the epimutation was observed as variable levels of somatic methylation and partial allelic losses of transcription among different tissues and carriers in the family. 17 Two other index cases have also been reported as carriers of the MLH1 c. À27C4A and c.85G4T SNVs. 7,10 In the first familial case ever reported (Family 1744), 7 no methylation or allelic expression studies were performed and so this allele was not linked to constitutional epimutation at the time.…”

“…However, comprehensive functional assays of the p.A29S protein variant encoded by this SNV showed normal protein activity, suggesting it is neutral. 7 The subsequent link between the c.[ À27C4A; 85G4T] haplotype and MLH1 epimutation in WA Family 16, 17 and thereafter the identification of another index case (Proband H) with this haplotype and concomitant MLH1 epimutation, 10 strongly suggests this haplotype confers cancer susceptibility through its propensity for soma-wide epigenetic silencing. The concurrence of both SNVs in distinct cases also raises the question of whether they are borne on a founder haplotype.…”