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Germline, Somatic and Epigenetic Events Underlying Mismatch Repair Deficiency in Colorectal and HNPCC-Related Cancers

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Germline, Somatic and Epigenetic Events Underlying Mismatch Repair Deficiency in Colorectal and HNPCC-Related Cancers Oncogene (2002) 21, 7585 – 7592 ª 2002 Nature Publishing Group All rights reserved 0950 – 9232/02 $25.00 www.nature.com/onc Germline, somatic and epigenetic events underlying mismatch repair deficiency in colorectal and HNPCC-related cancers Siu Tsan Yuen*,1,3, Tsun Leung Chan1, Judy WC Ho2,3, Annie SY Chan1, Lap Ping Chung1, Polly WY Lam4, Chun Wah Tse5, Andrew H Wyllie6 and Suet Yi Leung*,1 1Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong; 2Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Hong Kong; 3Hereditary Gastrointestinal Cancer Registry, The University of Hong Kong, Queen Mary Hospital, Hong Kong; 4Department of Pathology, Queen Elizabeth Hospital, Hong Kong; 5Department of Surgery, Queen Elizabeth Hospital, Hong Kong; 6Department of Pathology, Cambridge University, UK High-frequency microsatellite instability (MSI-H) results wild-type RNA by as yet undiscovered mechanisms, or from deficiency in nucleotide mismatch repair. It no detectable abnormality in any of these parameters. contributes significantly to carcinogenesis in the human Evidence is presented to indicate that methylation in colorectal mucosa. Here we study 41 colorectal and three proximal region of the hMLH1 promoter is a more other HNPCC-related cancers with MSI-H to provide reliable correlate of transcriptional silencing in colorectal comprehensive information on the mechanisms of cancers than methylation in upstream region. These inactivation of the two major proteins involved, hMLH1 observations have significant implications for manage- and hMSH2. Seventeen of the patients had family ment of patients with MSI-H tumours. histories meeting the criteria for Bethesda grades 1, 2 Oncogene (2002) 21, 7585 – 7592. doi:10.1038/sj.onc. or 3. Of these familial cases, 14 (83%) had early-onset 1205968 disease, defined on the basis of diagnosis prior to the age of 50, but in three the disease was of late onset (450 Keywords: microsatellite instability; promoter methyla- years). A second subset of 20 patients had early onset tion; mismatch repair gene mutation; colorectal cancer; disease without family history. The remaining seven HNPCC patients were selected to allow comparisons with sporadic, late-onset disease, the molecular basis of which has been extensively reported elsewhere. We stratified the tumours initially on the basis of hMLH1 or hMSH2 protein deficiency, detected by immunohistochemistry, High frequency microsatellite instability (MSI-H) is the and then by analysis of germline and somatic mutation, phenotypic manifestation of mismatch repair defect. In mRNA transcription, loss of heterozygosity (LOH) at colorectal carcinomas most MSI-H is associated with the hMLH1 and hMSH2 loci, and methylation status in inactivation of either hMSH2 or hMLH1, genes that two regions of the hMLH1 promoter. The functional encode proteins involved early in the process of significance of several of these changes in the MSI-H mismatch repair (MMR) (Peltomaki and Vasen, tumours was confirmed by comparisons with 16 tumours 1997). Whilst germline MMR gene mutation is the with low-frequency microsatellite instability and 56 major mechanism responsible for the mismatch repair tumours with stable microsatellites. As anticipated, deficiency in hereditary non-polyposis colorectal cancer patients with family histories usually showed germline (HNPCC) kindreds, the majority of sporadic late-onset mutation of hMSH2 or hMLH1. In many cases the MSI-H colorectal cancer were attributed to hMLH1 residual normal allele was silenced in their tumours by promoter hypermethylation (Kane et al., 1997; Herman loss of heterozygosity (LOH). The small subset of late- et al., 1998; Cunningham et al., 1998; Kuismanen et onset, sporadic cases confirmed the preponderance in this al., 2000). Cancers with MSI-H constitute a high group of biallelic hMLH1 promoter methylation. In the proportion of those arising in the colon and rectum of early-onset, apparently sporadic subset there were 11 younger patients, and whilst many of these have clear tumours with hMLH1 deficiency, five with hMSH2 family histories of cancer, several do not. Relatively deficiency and four with no detectable abnormality in little is known of the molecular origins of the MMR expression of either protein. These showed a complex deficiency in such apparently sporadic early-onset mixture of lesions, including germline and somatic cancers, although we and others have shown that some mutations, promoter methylation, LOH, suppression of arise on a background of germ-line mutation in hMSH-2 or hMLH1, despite the absence of family history (Liu et al., 1995; Chan et al., 1999a). A comprehensive understanding of the mechanisms *Correspondence: SY Leung; E-mail: [email protected] and ST Yuen; E-mail: [email protected] underlying MSI, in particular distinguishing between Received 1 May 2002; revised 8 August 2002; accepted 8 August germline and somatic or epigenetic events, could 2002 significantly influence both the management of the Basis of MSI in colorectal cancer ST Yuen et al 7586 patients and the level of surveillance required for their Figure 1. Methylation-specific PCR, which assessed relatives. There is good reason to believe that the MSI- methylation status of CpG sites located in bases 7694, H phenotype requires bi-allelic (‘two hit’) inactivation 7688, 7674, 7672, 7600, 7598 and 7588 (referred of the responsible MMR gene. In practice, however, to here as region 1), was successfully performed in 40 only a single inactivating event was identified in up to MSI-H, 15 MSI-L and 26 MSS tumours. hMLH1 65% of currently reported MSI-H colorectal tumours promoter methylation was detected in 12 of 22 MSI-H (Hemminki et al., 1994; Konishi et al., 1996; cases with hMLH1 protein loss, but also in several Tannergard et al., 1997; Leung et al., 1998; Chan et tumours in which hMLH1 expression was normal: two al., 1999b). This may reflect the restricted number of of 12 MSI-H cases with hMSH2 protein loss, two of inactivation mechanisms that were directly investi- six MSI-H cases with no MMR protein loss, two of 15 gated. Moreover, there are technical limitations to the MSI-L cases, and zero of 26 MSS cases. The incidence detection of mutations, be they germline or somatic, in of promoter methylation was significantly different the MMR genes. These large genes have no mutation between cases with (12/22) and without (6/59) loss of hot spots and hence no simple strategy can detect all hMLH1 protein (P50.0001), but the clear evidence of mutations. The simple detection of hMLH1 promoter region one methylation in six tumours with normal hypermethylation also suffers from several drawbacks. expression of hMLH1 protein prompted search for Firstly, it does not distinguish between mono-allelic or other promoter regions with which the association of bi-allelic inactivation in primary cancer tissue. methylation and protein expression was more specific. Secondly, the specificity of promoter methylation and When bisulphite sequencing was used to identify hence its functional significance varies according to the methylation in a region more proximal to the methods used and the CpG sites examined (Deng et al., transcription start site, covering bases 7178 to 1999). These limitations are particularly important for 7248 (referred to here as region 2), two distinct the group of sporadic early-onset colorectal cancer patterns emerged. DNA extracted from the tumour with MSI, where so far there is no comprehensive was either unmethylated in all eight CpG sites study addressing the relative contributions of germline, (hereafter referred to as the unmethylated pattern), somatic and epigenetic events. Here we characterize the or showed methylation close to or in excess of 50% of basis of MSI-H in a substantial number of MSI-H total DNA at all eight CpG sites (referred to as the colorectal cancers, including familial, sporadic late- methylated pattern) (Figure 2). Of the six tumours onset and sporadic early-onset cases, the latter group with normal expression of hMLH1 protein but with shows an exceptionally high incidence in Hong Kong methylation in region 1 of the hMLH1 promoter, all (Yuen et al., 1997; Chan et al., 1999a). For both showed an unmethylated pattern in region 2. Of the hMSH2 and hMLH1 we sought to identify loss of 12 tumours with loss of hMLH1 expression and protein expression, germline and somatic mutations, methylated region 1, however, seven also showed the mRNA expression and LOH. Methylation was exam- methylated pattern in region 2. Amongst the remain- ined in various regions of the hMLH1 promoter. The ing five tumours, only two (L6, L20) failed to show data show that different mechanisms of MMR clear evidence of bi-allelic inactivation of hMLH1 by deficiency predominate in these three groups. means other than methylation (i.e. somatic or germ- The results of immunohistochemical staining for line mutation together with LOH), and none failed to hMSH2 and hMLH1, and the family or personal show at least one somatic or germline mutation histories of cancer of 44 individuals with MSI-H (Figure 2B,C). In contrast, of the seven cases with tumours are shown in Table 1 and summarized in region 2 methylation, five showed a predominance of Figure 1. In the majority of these tumours (38/44, methylated DNA in region 2 on bisulphite sequencing 86%) one or other of the hMLH1 or hMSH2 proteins and absence of other germline or somatic inactivation was undetectable. In contrast, both proteins were events. Real time quantitative PCR of these cases readily identified in a nuclear location in all of 16 demonstrated significantly lowered hMLH1 transcript tumours with low levels of microsatellite instability when compared with 10 randomly selected MSS (MSI-L) and 56 tumours with stable microsatellites colorectal cancers (Figure 3). These results strongly (MSS). When the MSI-H tumours were classified on support transcriptional silencing of hMLH1 in these the basis of age and family history into familial cases by bi-allelic promoter methylation in region 2.
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