A novel sensitive method to detect frameshift mutations in exonic repeat sequences of cancer-related genes

Polymorphisms of short tandem repeat of genes and breast cancer susceptibility

AIM

To explore the relationship of short tandem repeat polymorphisms and breast cancer susceptibility.

METHODS

We searched the MEDLINE database (up to June 2006) with the keywords of tandem repeat sequences, gene polymorphisms, breast cancer, cancer susceptibility and microsatellite instability. We reviewed the literature on gene polymorphisms, especially the relationship of short tandem repeat and breast cancer risk.

RESULTS

We focused on the candidate genes sex hormones, steroid hormone and receptors, carcinogen metabolism, cell proliferation regulation and other genes.

CONCLUSIONS

The functional effects of short tandem repeat polymorphisms on cancer susceptibility, especially on breast cancer risk, are identified. The importance of short tandem repeat polymorphisms on development and progression of breast cancer are discussed.

Does tumorigenesis select for or against mutations of the DNA repair-associated genes BRCA2 and MRE11?: considerations from somatic mutations in microsatellite unstable (MSI) gastrointestinal cancers

Background

The BRCA2 and MRE11 proteins participate in the repair of double-strand DNA breaks by homologous recombination. Germline BRCA2 mutations predispose to ovarian, breast and pancreatic cancer, while a germline MRE11 mutation is associated with an ataxia telangiectasia-like disorder. Somatic mutations of BRCA2 are rare in typical sporadic cancers. In tumors having microsatellite instability (MSI), somatic truncating mutations in a poly [A] tract of BRCA2 are reported on occasion.

Results

We analyzed gastrointestinal MSI cancers by whole gene BRCA2 sequencing, finding heterozygous truncating mutations in seven (47%) of 15 patients. There was no cellular functional defect in RAD51 focus-formation in three heterozygously mutated lines studied, although other potential functions of the BRCA2 protein could still be affected. A prior report of mutations in primary MSI tumors affecting the IVS5-(5–15) poly [T] tract of the MRE11 gene was confirmed and extended by analysis of the genomic sequence and protein expression in MSI cancer cell lines. Statistical analysis of the published MRE11 mutation rate in MSI tumors did not provide evidence for a selective pressure favoring biallelic mutations at this repeat.

Conclusion

Perhaps conflicting with common suspicions, the data are not compatible with selective pressures during tumorigenesis promoting the functional loss of BRCA2 and MRE11 in MSI tumors. Instead, these data fit closely with an absence of selective pressures acting on BRCA2 and MRE11 gene status during tumorigenesis.

Heterozygous ATR Mutations in Mismatch Repair–Deficient Cancer Cells Have Functional Significance

ATR (ataxia telangiectasia and Rad3-related) function is necessary for the proper response to commonly used chemotherapeutic agents. Heterozygous truncating mutations in exon 10 of the ATR gene have been described in numerous cancers exhibiting microsatellite instability. We show that truncating mutations of ATR are capable of acting in a dominant-negative manner to abrogate ATR-dependent Chk1 phosphorylation and cell-cycle arrests after DNA damage. In addition, endometrial cell lines harboring ATR mutations are defective for ATR-dependent responses. These findings imply that ATR mutations play an important role in the development and clinical behavior of a subset of microsatellite instability-positive endometrial, colon, and stomach cancers.

Genomic instability in oral squamous cell carcinoma: relationship to betel-quid chewing

Genomic instability in repeated DNA sequences is exhibited by a variety of cancer types, including oral squamous cell carcinoma. Exposure to carcinogenic compounds may further increase the instability. We have used Inter-Simple Sequence Repeat (Inter-SSR) PCR methodology to detect genetic alterations in 37 oral cancer patients who had chewed betel-quid. Thirty-eight percent of DNA from tumors had genomic alterations in the sequences flanked by (CA)(8) and (GT)(8) repeats. Patients with tumor DNAs harboring genomic alterations had a two-fold higher consumption of betel-quid than patients without alterations in tumor DNA. Matched normal and tumor DNAs were also screened for microsatellite instability where four patients (10.8%) showed alterations in at least one microsatellite marker but there was no relationship between this phenotype and betel-quid chewing. These data indicate that exposure to carcinogens present in the betel-quid may contribute to genomic instability detected by inter-SSR PCR in a subset of oral tumors.

Genetic alterations and MSI status in primary, synchronous, and metachronous tumors in a family with hereditary nonpolyposis colorectal cancer (HNPCC)

In colorectal cancer, different levels of microsatellite instability (MSI) have been described: high-frequency MSI, low-frequency MSI, and stable microsatellites. MSI-H characterizes a unique clinical and pathologic phenotype known as hereditary nonpolyposis colorectal cancer syndrome (HNPCC). In this case, an increased incidence of synchronous and metachronous tumors has been reported, but there are few reports with standardized criteria of MSI in HNPCC-associated tumors. The authors attempted to establish whether tumors of the HNPCC spectrum with different levels of MSI could predict the development of metachronous carcinomas. We have examined the levels of MSI at loci frequently affected in colorectal cancers in primary, synchronous, and metachronous tumors in a family that fulfils the Amsterdam criteria for HNPCC. This family presents colorectal cancers, HNPCC-extracolonic tumors (endometrial and ureter), and tumors (breast and bladder) not described in the HNPCC spectrum. The tumors exhibited MSI-H, irrespective of their location and regardless whether they were primary, synchronous, or metachronous, with the only exception of both endometrial tumors that showed low-frequency MSI tumors (MSI-L). Our results suggest that not only colorectal tumors with MSI-H result in a potential marker for the determination of high-risk individuals for metachronous and synchronous tumors, but also MSI-L endometrial tumors might be considered as indicative of high-risk individuals.

Mutation frequency in coding and non-coding repeat sequences in mismatch repair deficient cells derived from normal human tissue

Repetitive tracts within the coding regions of TGFBR2 and BAX are frequently mutated in mismatch repair deficient tumours and are implicated in tumour progression. However, there has been little study of the balance between selection pressure and inherent instability at sequences within these genes. To determine whether TGFBR2 and BAX are inherently prone to mutations in the presence of MMR defects, we studied MMR deficient cells derived from B-lymphocytes. By analysing cells derived from normal tissue we aimed to minimize the effects of selection pressures that bias the apparent frequency of mutation. We definitively show that certain sequences, usually repaired by MMR, are inherently unstable. Using a small pool PCR technique we confirmed these cells exhibit microsatellite instability. Additionally, we demonstrate that MMR deficiency results in an excess of mutations, specifically at the poly(A)(10) tract compared to other regions of the TGFBR2 gene (P<0.001). Conversely, an excess of mutations does not appear to arise at the poly(G)(8) tract of the BAX gene. These studies provide insight into the mechanism by which TGFBR2 and BAX genes become mutated during tumorigenesis. These findings invoke the notion of "unmasking" specific hypermutable sequences in particular genes adding further complexity to the concept of the mutator phenotype.

Clinicopathologic and immunohistochemical features and microsatellite status of endometrial cancer of the uterine isthmus

To clarify the clinicopathologic, molecular, and immunohistochemical characteristics of uterine isthmic endometrial cancer (UIE), we examined 13 cases of UIE and compared them with 33 cases of endometrial cancer of the uterine corpus (UCE) with respect to clinicopathologic factors, the expression of p53, the estrogen receptor (ER) and the progesterone receptor (PR) status, DNA ploidy, and microsatellite instability (MSI). Five (38.4%) of the UIE patients had stage I, two (15.4%) had stage II, and six (46.2%) had stage III disease (FIGO 1988). Myometrial invasion was confirmed in 92.3% of the UIE patients, and these patients had a higher (p < 0.05) frequency of > 50% myometrial invasion (46.2%) than the patients with UCE (15.2%). Moreover, the UIE patients had a higher frequency of positive peritoneal cytology (p < 0.05) and pelvic lymph node metastases (p < 0.05). No UIE tumors exhibited MSI, and the tumors in these patients had a higher expression of p53 (p < 0.01), a lower expression of ER (p < 0.05) and PR (p < 0.05), and a higher frequency of DNA aneuploidy (p < 0.01) than the UCE tumors. These findings suggest that the UIE is clearly different from UCE in the clinicopathologic, immunohistochemical features, and microsatellite status.

Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair-deficient cancer cells

Microsatellite instability (MSI) caused by deficient DNA mismatch-repair functions is a hallmark of cancers associated with the hereditary nonpolyposis colorectal cancer (HNPCC) syndrome but is also found in about 15% of all sporadic tumors. Most affected microsatellites reside in untranslated intergenic or intronic sequences. However, recently few genes with coding microsatellites were also shown to be mutational targets in MSI-positive cancers and might represent important mutation targets in their pathogenesis. The systematic identification of such genes and the analysis of their mutation frequency in MSI-positive cancers might thus reveal major clues to their functional role in MSI-associated carcinogenesis. We therefore initiated a systematic database search in 33,595 distinctly annotated human genes and identified 17,654 potentially coding mononucleotide repeats (cMNRs) and 2,028 coding dinucleotide repeats (cDNRs), which consist of n > or = 6 and n > or = 4 repeat units, respectively. Expression pattern and mutation frequency of 19 of these genes with the longest repeats were compared between DNA mismatch repair-deficient (MSI(+)) and proficient (MSS) cancer cells. Instability frequencies in these coding microsatellite genes ranged from 10% to 100% in MSI-H tumor cells, whereas MSS cancer cells did not show mutations. RT-PCR analysis further showed that most of the affected genes (10/15) were highly expressed in tumor cells. The approach outlined here identified a new set of genes frequently affected by mutations in MSI-positive tumor cells. It will lead to novel and highly specific diagnostic and therapeutic targets for microsatellite unstable cancers.

Molecular pathology of endometrial hyperplasia and carcinoma

Four different genetic abnormalities may occur in endometrioid adenocarcinomas of the endometrium (mircosatellite instability and mutations in the PTEN, k-RAS and beta-catenin genes), whereas nonendometrioid carcinomas of the endometrium often have p53 mutations and loss of heterozygosity on several chromosomes. Occasionally, a nonendometrioid carcinoma may develop as a result of dedifferentiation of a preexisting endometrioid carcinoma; in such a case, the tumor exhibits overlapping clinical, morphologic, immunohistochemical, and molecular features of the 2 types. The insaturation of microsatellite instability in endometrial carcinogenesis seems to occur late in the transition from complex hyperplasia to carcinoma, and it is preceded by progressive inactivation of MLH-1 by promoter hypermethylation. Moreover, the endometrioid adenocarcinomas that exhibit microsatellite instability show a stepwise progressive accumulation of secondary mutations in oncogenes and tumor suppressor genes that contain short-tandem repeats in their coding sequences. Mutations in the PTEN and k-RAS genes are also frequent in endometrioid adenocarcinomas of the endometrium, particularly in the tumors that exhibit microsatellite instability, whereas beta-catenin mutations do not seem to be associated with such a phenomenon.

The Hedgehog signalling pathway and cancer

The Hedgehog signalling pathway is important in embryological development and is highly conserved through evolution. Recently Patched, a member of the pathway, was found to be important in Gorlin's syndrome. Inherited Patched gene mutations underlie the syndrome, in which a key feature is multiple basal cell carcinomas (BCCs). The gene is also mutated in sporadic BCCs as well as in sporadic occurrences of other tumours seen in Gorlin's syndrome. The precise mechanism whereby Patched gene mutation leads to tumour development is not known, but BCC is characterized by relentless local invasion and only rarely metastasizes. This suggests that abnormalities of the Hedgehog pathway account for these features. This proposal is discussed in the context of what is already known about the normal function of the Hedgehog pathway and its deregulation in cancer.