Identification and characterization of a novel MLH1 genomic rearrangement as the cause of HNPCC in a Tunisian family: evidence for a homologous Alu-mediated recombination

Abstract

High rates of early colorectal cancers are observed in Tunisia suggesting high genetic susceptibility. Nevertheless, up to now no molecular studies have been performed. Hereditary nonpolyposis colorectal cancer (HNPCC) is the most frequent cause of inherited colorectal cancer. It is caused by constitutional mutations in the DNA mismatch repair (MMR) genes. Here, we investigated a Tunisian family highly suspected of hereditary nonpolyposis colorectal cancer (HNPCC). Six patients were diagnosed with a colorectal or an endometrial cancer at an early age, including one young female who developed a colorectal cancer at 22 years and we tested for germline mutations in MMR genes. MMR genes were tested for rearrangements by MLPA (MLH1, MSH2) and the presence of point mutations by sequencing (MLH1, MSH2, MSH6). Moreover, tumors were analyzed for microsatellite instability and expression of MMR proteins, as well as for somatic rearrangements in MLH1 and MSH2 by MLPA. MMR gene analysis by MLPA revealed the presence of a large deletion in MLH1 removing exon 6. Sequence analysis of the breakpoint region showed that this rearrangement resulted from a homologous unequal recombination mediated by a repetitive Alu sequence. Moreover, tumors harbored biallelic deletion of MLH1 exon 6 and loss of heterozygosity at MLH1 intragenic markers, suggesting duplication of the rearranged allele in the tumor. This germline MLH1 rearrangement was associated to a severe phenotype in this family. This is the first report of a molecular analysis in a Tunisian family with HNPCC.

Novel MLH1 duplication identified in Colombian families with Lynch syndrome

“…Previous reports of LS genomic rearrangements have highlighted the role of Alu-mediated homologous recombination as a common cause for these mutations but not recombination involving T stretches. 14,[17][18][19][20] Also, Alu-mediated homologous recombination seems to be more involved in MSH2 genomic rearrangements, whereas MLH1 rearrangements may originate from alternative mechanisms. 20,21 This LS genetic alteration was found in the MLH1 gene, whereas genomic rearrangements in MMR genes have been found more frequently in MSH2.…”

Contribution of Large Genomic Rearrangements in Italian Lynch Syndrome Patients: Characterization of a Novel Alu-Mediated Deletion

“…A systematic study on genomic rearrangement in Lynch Syndrome showed that MLH1 and MSH2 are the most frequently targeted MMR genes for this type of mutation [14]. Furthermore, molecular characterisation of the breakpoints involved in large rearrangements within MLH1 and MSH2 genes showed that the majority are caused by homologous recombination between Alu repeats [15–17]. These mutations are not usually detected by conventional methods of mutation analysis, such as denaturing high-performance liquid chromatography (DHPLC) and direct DNA sequencing, but they are detectable by a simple and robust technique such as the Multiplex Ligation-Probe Dependent Amplification (MLPA) [18, 19] assay.…”

Homozygous deletion of the STK11/LKB1 locus and the generation of novel fusion transcripts in cervical cancer cells

“…In addition to driving genome evolution, ARMDs also contribute to human disease. ARMDs occurring within the germline have been observed in several inherited disorders including α-thalassaemia, familial hypercholesterolaemia, Lesch–Nyhan syndrome, and Tay–Sachs disease [42], and have been implicated in the inactivation of tumor suppressor genes in familial cancers including CDH1 in hereditary diffuse gastric cancer [43], MLH1 in hereditary nonpolyposis colorectal cancer [44], MEN1 in multiple endocrine neoplasia type 1 [45], and BRCA1 in hereditary breast and ovarian cancer [46]. Alternatively, ARMDs of tumor suppressor genes have also been observed to occur somatically in tumor tissues such as TMPRSS2/ERG in prostate cancer [47], CAD in hepatoma [48], and TSC2 in tuberous sclerosis [49].…”