Disease-causing gene-flanking genomic rearrangements in HNPCC patients

Background

The molecular diagnosis of hereditary non-polyposis colorectal cancer (HNPCC) or Lynch-Syndrome is the detection of a pathogenic germline mutation in one of the DNA mismatch repair (MMR) genes. However, in ~10-20% of cases suspected of Lynch-syndrome no disease-causing mechanism can be detected. Genomic rearrangements such as gene-flanking deletions, inversions, duplications, or translocations might affect MMR genes - but are difficult to detect. We report here two different disease-causing rearrangement mechanisms in HNPCC patients flanking the gene in question.

Material and methods

37 patients with colorectal tumours lacking MMR protein staining were included if gene sequencing and deletion screening did not detect MMR germline mutations. The genomic situation was analyzed by oligo array, MLPA kits (P003, P248, P072) and abnormalities were investigated by Long-Range PCRs and sequencing. Additionally, cDNA analyses were performed.

Results

In one patients with loss of MLH1 oligo array analyses detected a deletion in LRRFIP2 exon 20-15, a gene located downstream of MLH1 with antisense-orientation. The deletion was verified by MLPA in LRRFIP2 exon 26, MLH1 exon 1-19 and it`s termination codon were unaffected. The deletion starting after MLH1 affecting LRRFIP2 could per se not explain the pathogenicity on the MLH1 gene. In cDNA analyses the coding SNP c.655A>G in MLH1 exon 8 showed biallelic expression amplifying exons 3-9, 6-9, 3-11, 7/8-14, but monoallelic c.655G in fragments from exon 1-19, 7/8-16, 7/8-18. Suspecting a paracentric inversion we identified two fusion transcripts: MLH1 exon 1-15 and LRRFIP2 exon 29 in frame, and LRRFIP2 exon 1-3 fused with MLH1 exon 16-19 in frame. The inversion breakpoints in MLH1 intron 15 and LRRFIP2 intron 3 with deletion of exons 4-28 were verified in genomic DNA.

A duplication of the complete MLH1 promoter region and exon 1-19 was found in a patient, his unaffected sister and affected mother. Duplication carriers all showed MLH1 promoter hypermethylation of 8-18% to 14-25% in DNA from blood, hair follice, colonic and buccal mucosa. We hypothesize that mosaic methylation is a consequence of transcriptional silencing. As cDNA analyses were not informative so far, quantification of MLH1 expression could not be investigated and no fusion transcripts detected.

Conclusion

We report disease-causing rearrangements in HNPCC patients: one appeared as a deletion of the LRRFIP2 gene downstream of MLH1 but revealed as a paracentric inversion between the two genes creating two new stable fusion transcripts, the other one is a silencing mechanism accompanied with promoter methylation caused by a duplication of the complete MLH1 gene and flanking region leaving the MLH1 gene and promotor per se intact. In the remaining unsolved HNPCC-suspected patients we expect further mechanisms in the genome to decommission the respective gene which might be detectable by new technologies.