Inherited predisposition to colorectal adenomas caused by multiple rare alleles of MUTYH but not OGG1, NUDT1, NTH1 or NEIL 1, 2 or 3.

BACKGROUND: MUTYH-associated polyposis (MAP) is a recessive trait characterised by multiple colorectal adenomas and a high risk of colorectal cancer. MUTYH functions in the DNA base excision repair pathway and has a key role in the repair of oxidative DNA damage. OBJECTIVES: To assess the contribution of inherited variants in genes involved in base excision repair and oxidative DNA damage including MUTYH, OGG1, NEIL1, NEIL2, NEIL3, NUDT1 and NTH1 to the multiple colorectal adenoma phenotype. METHODS: Inherited variants of MUTYH, OGG1, NEIL1, NEIL2, NEIL3, NUDT1 and NTH1 were sought in 167 unrelated patients with multiple colorectal adenomas whose family histories were consistent with recessive inheritance. These variants were also characterised in approximately 300 population controls. RESULTS: Thirty-three patients (20%) and no controls were MUTYH homozygotes or compound heterozygotes (ie, carried two mutations) and therefore had MAP. Eight different pathogenic MUTYH mutations were identified, of which four were novel. MAP cases had significantly more adenomas than non-MAP cases (p = 0.0009; exact test for trends in proportions) and presented earlier (p = 0.013; analysis of variance). Twenty-four protein-altering variants were identified upon screening of OGG1, NEIL1, NEIL2, NEIL3, NUDT1 and NTH1. However, all combinations of two (or more) variants that were identified at an individual locus in patients were also seen in controls, and no variants were significantly over-represented (or under-represented) in cases. CONCLUSION: Multiple rare alleles of MUTYH are associated with autosomal recessive MAP, while OGG1, NEIL1, NEIL2, NEIL3, NUDT1 and NTH1 do not contribute significantly to autosomal recessive polyposis.

Genetic counselling and consent for tumour testing in HNPCC.

Molecular pathological tests are performed on stored tumour material in order to identify individuals with hereditary non-polyposis colorectal cancer. We have previously identified that there is widespread use of this testing and now describe what counselling occurs prior to testing and the approaches in seeking consent. A respondent from every cancer genetic centre in UK offering microsatellite instability and/or immunohistochemistry testing (n= 20, response rate = 100%) was interviewed in order to ascertain pre-test counselling and consent protocols. Individuals providing consent are not always seen in person prior to providing consent but few services had supporting written information. Nine (of 19) consent forms documented consent to perform genetic testing, while the majority (14/19) sought consent to release pathology samples to the genetic service. Less than half of the services routinely seek consent to test samples from a deceased individual. Concerns were raised about spousal consent when the implications of results are for blood relatives. The differences identified between genetic counselling for testing of tumour tissue and for germ-line genetic testing suggest that counselling protocols specific for somatic testing should be developed. The results are discussed in the context of a changing legal environment and anticipated growing demand for testing.

Variability and inequity in testing of somatic tissue for hereditary cancer: a survey of UK clinical practice.

A growing body of literature demonstrates the benefits of molecular pathological investigations of tumour material in the identification of individuals with hereditary non-polyposis colorectal cancer and debates the best detection strategies. This testing is novel as it is the first widespread use of somatic tissue testing to inform genetic analysis and requires the co-ordination of both histopathology and molecular genetics laboratories. However, the clinical use and experience of microsatellite instability (MSI) testing and immunohistochemical analysis have not been reported. A respondent from every cancer genetics centre in the UK (n= 24, response rate 100%) and laboratory performing MSI testing (n= 5, response rate 100%) was interviewed by telephone to ascertain test availability, testing methods, eligibility criteria and post-test management. Twenty centres (83%) offer eligible clients at least one form of tumour testing, and all use tumour testing to determine who should have access to germ line genetic testing. However, no two laboratories used the same testing methods, seven different testing strategies were applied and there was considerable variation in eligibility criteria. The implications of these variations are considered, and recommendations for the development of a consistent service for testing of somatic tissue offered.

Systematic review of genetic influences on the prognosis of colorectal cancer.

BACKGROUND: In terms of genetics, colorectal cancer is one of the best understood of all malignant diseases. Genetic influences on prognosis may have far-reaching implications, especially for the design of surgical and chemoradiotherapeutic regimens. However, their significance in determining prognosis remains unclear. This study aimed to review the literature on the specific role of key genes in determining the survival of patients with colorectal cancer. METHODS: A Medline search was carried out to identify all original scientific papers relating colorectal cancer genetics to patient survival, up to December 2002. Cochrane and Embase databases were also searched. Identified articles were retrieved and searched carefully for additional information. This review includes K-ras, p53, DCC, NM23 and DNA mismatch repair genes. RESULTS AND CONCLUSION: Conflicting evidence exists as to the prognostic significance of genes commonly implicated in the pathogenesis of colorectal carcinoma. Possible causes for such discrepancy include differences in study methods and laboratory techniques, variable duration of follow-up, statistical differences in study power, and heterogeneity in study populations. Future studies should adopt standardized protocols to define clinically relevant genetic observations.

The spectrum of p53 mutations in colorectal adenomas differs from that in colorectal carcinomas.

BACKGROUND: p53 mutations are frequently observed in colorectal carcinomas but they have also been found in colorectal adenomas, although considerably less frequently. AIMS: To explore p53 mutations in benign tumours, we have screened 70 colorectal adenomas for allelic loss at, and point mutations in, TP53 by analysis of selected microdissected cell populations. RESULTS: Sixteen (22.8%) adenomas were found to have allelic loss, of which 11 (15.7%) had p53 mutations. In adenomas with mild, moderate, or severe dysplasia, mutation or allelic loss occurred in 4.8%, 16.7%, and 52.6%, respectively (p<0.001). Seven different mutations were found, all missense changes or inframe deletions: one (Thr150Arg) has not been found before while three (Gln144His, Gly245Arg, and Glu285Gln) have not been described previously in colorectal tumours. The other three mutations (Arg175Gly, DeltaPro190, and Gly245Ser) have been found in colorectal carcinomas, the last commonly. Adenomas harboured a spectrum of p53 mutations which was significantly different from cancers as regards the position in the gene and a higher frequency of G-->C/C-->G changes. CONCLUSIONS: Combining our data on adenomas with data already published and in comparison with the spectrum of mutations in colorectal carcinomas, it is suggested that some p53 mutations have a weaker effect than others and are therefore more likely to be found in adenomas which have not progressed to carcinomas.

Methods of molecular analysis: mutation detection in solid tumours.

Most mutation detection techniques are unsuitable for routine use on solid tumours. Important parameters include sensitivity, specificity, efficiency, use of existing resources, and cost. In the UK, < 0.2% of service genetics laboratory activity involves mutation analysis in tumours (usually for family studies), mainly because it is time consuming/labour intensive (thus expensive) and DNA extracted from formalin fixed, paraffin wax embedded tissue is of low quality and yield. The small size of DNA fragments obtained from tissue blocks limits the polymerase chain reaction, the basis of most mutation detection methods. Other, biological, factors include: (1) heterogeneity of mutations within and between tumours, (2) variation in type and site of mutations in any one gene, (3) normal tissue harbouring mutations, (4) few genes are mutated in most of any one tumour type, and (5) few clinically useful correlations with genetic changes have been found. Present research is centred on correlating single gene mutations with various clinicopathological features, but the pattern of mutations in a combination of genes will probably prove more useful. Microsatellite instability, however, appears to be worth testing for in both familial and sporadic tumours, particularly of the colorectum.

Desmoids in familial adenomatous polyposis are monoclonal proliferations.

Desmoids are poorly-understood, locally aggressive, non-metastasizing fibromatoses that occur with disproportionate frequency in patients with familial adenomatous polyposis (FAP). Their nature is controversial with arguments for and against a neoplastic origin. Neoplastic proliferations are by definition monoclonal, whereas reactive processes originate from a polyclonal background. We examined clonality of 25 samples of desmoid tissue from 11 female FAP patients by assessing patterns of X-chromosome inactivation to calculate a clonality ratio. Polymerase chain reaction (PCR) amplification of a polymorphic CAG short tandem repeat (STR) sequence adjacent to a methylation-sensitive restriction enzyme site within the human androgen receptor (HUMARA) gene using fluorescent-labelled primers enabled analysis of PCR products by Applied Biosystems Genescan II software. Twenty-one samples from nine patients were informative for the assay. Samples from all informative cases comprised a median of 66% (range 0-75%) clonal cells but from the six patients with a clonality ratio < or =0.5 comprised a median of 71% (65-75%) clonal cells. FAP-associated desmoid tumours are true neoplasms. This may have implications in the development of improved treatment protocols for patients with these aggressive tumours.

Attenuated adenomatous polyposis coli: the role of ascertainment bias through failure to dye-spray at colonoscopy.

PURPOSE: The aim of this study is to show that the diagnosis of attenuated adenomatous polyposis coli must be made with caution and certainly only after adequate colonic examination with dye-spray. METHODS: Four patients thought to have attenuated adenomatous polyposis coli on the basis of family history and the identification of fewer than 100 polyps on simple colonoscopy underwent colonoscopy with dye-spray. RESULTS: All four individuals were found to have more than 100 polyps when dye-spray was used, confirming a diagnosis of classical familial adenomatous polyposis. CONCLUSIONS: The diagnosis of familial adenomatous polyposis may be missed altogether or incorrectly assigned as attenuated adenomatous polyposis coli if dye-spray is not used at colonoscopy. Patients with a family history of familial adenomatous polyposis or colorectal cancer should be considered for dye-spray before the diagnosis of familial adenomatous polyposis is excluded or one of attenuated adenomatous polyposis coli is made.

Germline PTEN mutations in Cowden syndrome-like families.

Cowden syndrome (CS) or multiple hamartoma syndrome (MIM 158350) is an autosomal dominant disorder with an increased risk for breast and thyroid carcinoma. The diagnosis of CS, as operationally defined by the International Cowden Consortium, is made when a patient, or family, has a combination of pathognomonic major and/or minor criteria. The CS gene has recently been identified as PTEN, which maps at 10q23.3 and encodes a dual specificity phosphatase. PTEN appears to function as a tumour suppressor in CS, with between 13-80% of CS families harbouring germline nonsense, missense, and frameshift mutations predicted to disrupt normal PTEN function. To date, only a small number of tumour suppressor genes, including BRCA1, BRCA2, and p53, have been associated with familial breast or breast/ovarian cancer families. Given the involvement of PTEN in CS, we postulated that PTEN was a likely candidate to play a role in families with a "CS-like" phenotype, but not classical CS. To answer these questions, we gathered a series of patients from families who had features reminiscent of CS but did not meet the Consortium Criteria. Using a combination of denaturing gradient gel electrophoresis (DGGE), temporal temperature gel electrophoresis (TTGE), and sequence analysis, we screened 64 unrelated CS-like subjects for germline mutations in PTEN. A single male with follicular thyroid carcinoma from one of these 64 (2%) CS-like families harboured a germline point mutation, c.209T-->C. This mutation occurred at the last nucleotide of exon 3 and within a region homologous to the cytoskeletal proteins tensin and auxilin. We conclude that germline PTEN mutations play a relatively minor role in CS-like families. In addition, our data would suggest that, for the most part, the strict International Cowden Consortium operational diagnostic criteria for CS are quite robust and should remain in place.

The APC variants I1307K and E1317Q are associated with colorectal tumors, but not always with a family history.

Classical familial adenomatous polyposis (FAP) is a high-penetrance autosomal dominant disease that predisposes to hundreds or thousands of colorectal adenomas and carcinoma and that results from truncating mutations in the APC gene. A variant of FAP is attenuated adenomatous polyposis coli, which results from germ-line mutations in the 5' and 3' regions of the APC gene. Attenuated adenomatous polyposis coli patients have "multiple" colorectal adenomas (typically fewer than 100) without the florid phenotype of classical FAP. Another group of patients with multiple adenomas has no mutations in the APC gene, and their phenotype probably results from variation at a locus, or loci, elsewhere in the genome. Recently, however, a missense variant of APC (I1307K) was described that confers an increased risk of colorectal tumors, including multiple adenomas, in Ashkenazim. We have studied a set of 164 patients with multiple colorectal adenomas and/or carcinoma and analyzed codons 1263-1377 (exon 15G) of the APC gene for germ-line variants. Three patients with the I1307K allele were detected, each of Ashkenazi descent. Four patients had a germ-line E1317Q missense variant of APC that was not present in controls; one of these individuals had an unusually large number of metaplastic polyps of the colorectum. There is increasing evidence that there exist germ-line variants of the APC gene that predispose to the development of multiple colorectal adenomas and carcinoma, but without the florid phenotype of classical FAP, and possibly with importance for colorectal cancer risk in the general population.

Appearances can be deceptive: an APC 1893del4 mutation with unusual properities. Mutations in brief no. 171. Online.

During a systematic search for germ-line APC mutations causative of familial adenomatous polyposis, we discovered what appeared to be an insertion mutation while simply checking exon 14PCR products by agarose gel electrophoresis (AGE). On AGE, exon 14PCR product from the known affected member of this family gave two bands: one of normal length, the other retarded on the gel equivalent to an increase in length of some 20-25 bp. Direct sequencing of DNA purified from the two bands gave identical results, and was consistent with amplification from the same two alleles: one wild-type, and the other having an 1893del4 mutation. This suggested that the normal length band on AGE consisted of DNA homoduplexes (normal:normal and mutant:mutant) and the retarded band consisted of DNA heteroduplexes (normal:mutant and mutant:normal). This hypothesis was tested by subjecting purified material from each of the two bands alone to a single cycle of heat denaturation and annealing, which showed that either band was equally capable of regenerating both bands. Because the anomalous migration of the heteroduplexes is observed in the presence of ethidium bromide, it implies that they have a cruciform of cruciform-like structure. This case illustrates the necessity to be aware of anomalous DNA migration and always sequence all putative mutations.

Allele loss in colorectal cancer at the Cowden disease/juvenile polyposis locus on 10q.

The genes that are mutated in inherited cancer syndromes are often involved in the pathogenesis of sporadic cancers of the types that characterize those syndromes. In colorectal cancer such loci include the familial adenomatous polyposis (APC) gene and the hereditary nonpolyposis colorectal cancer (DNA mismatch repair) genes. Juvenile hamartomatous polyposis syndromes, which include Juvenile Polyposis and Cowden disease, also predispose to colorectal cancer. The gene for Cowden disease has recently been localized to chromosome 10q22-q23, and a juvenile polyposis locus, JP1, has been reported as mapping to the same location. We have studied up to 70 cases of sporadic colorectal cancer for allele loss at markers predominantly on the long arm of chromosome 10, including loci flanking the putative Cowden Disease/JP1 locus. Frequencies of allele loss of about 35% were found close to this locus, whereas low frequencies of allele loss were found elsewhere on 10q. Mutations at the putative Cowden Disease/JP1 locus may therefore be important in sporadic colorectal cancer and fine mapping of allele loss on 10q in sporadic colon cancers may help to refine the position of this gene.

Frequency of germline hereditary non-polyposis colorectal cancer gene mutations in patients with multiple or early onset colorectal adenomas.

BACKGROUND: The hereditary non-polyposis colorectal cancer (HNPCC) syndrome is caused by germline mutations in mismatch repair genes and predisposes individuals to cancers of the colon and other specific sites. On theoretical grounds, it is expected that patients with HNPCC also develop more colorectal adenomas than the general population. In essence, if the mutation rate is raised owing to mutations at a mismatch repair locus, more mutations are expected at loci such as APC (adenomatous polyposis coli) and more adenomas will start to grow. Not all data support this expectation, however. AIM: To search for germline mutations at HNPCC loci in patients with multiple adenomas. SUBJECTS: Twenty five patients (without known APC mutations) who have developed colorectal adenomas in unusually large numbers and, in some cases, at an early age. METHODS: Germline APC mutations were excluded using the protein truction test for exon 15 and mismatch chemical cleavage analysis for remaining exons. Germline HNPCC mutations were detected by using PCR and single strand conformation polymorphism analysis. RESULTS: Just one germline HNPCC mutation was found (4% of cases) and this was of uncertain functional effect. CONCLUSIONS: In general, germline HNPCC mutations are not responsible for the phenotype of patients with multiple colonic adenomas. It is possible that patients with HNPCC tend to develop adenomas more frequently and earlier than the general population, but that this effect is relatively subtle. These results suggest that individuals with colorectal adenomas only should not strictly be classified as "affected" in HNPCC families (although they should certainly not be classified as "unaffected" either and may warrant intensive screening). In the absence of a personal or strong family history of colorectal cancer, it is probably not worthwhile performing diagnostic or predictive genetic testing for HNPCC mutations in subjects with colorectal adenomas. Although undetected APC mutations may be responsible for some of the phenotypes in this sample, as yet uncharacterised adenoma predisposing genes probably exist.

APC mutations in familial adenomatous polyposis families in the Northwest of England.

We have investigated a series of FAP patients in the Northwest of England in order to identify and characterise the specific APC mutations. Using SSCP, we found 27 mutations in a total of 50 families investigated. The mutations were predominantly frameshift or nonsense mutations and there were two splice site changes. We have described two patients with severe Gardner's phenotype from different ethnic backgrounds who share the same mutation at codon 1537. Although the frequency of the most common mutation appears low, it is not dissimilar to that reported by other groups.

Induction of murine O6-alkylguanine-DNA-alkyltransferase in response to ionising radiation is p53 gene dose dependent.

Expression of both the DNA repair protein O6-alkylguanine-DNA-alkyltransferase (ATase) and the p53 tumour suppressor protein are inducible by a number of DNA damaging agents. It is probable that DNA strand breaks are the common inducing signals. This similarity, and the function of p53 as a transcription factor lead us to reason that p53 might be involved in ATase inducibility. We now report that the induction of ATase activity in mouse tissues following gamma-radiation is p53 gene dose dependent. While the extent and kinetics of induction in p53 wildtype mice are consistent with previous reports (a 2-3-fold peak increase at 36 h), no induction is observed in p53 null animals. Importantly the heterozygous mice show an intermediate response but the same kinetics. The basal levels of expression in all tissues examined are unaffected by p53 status. These data represent the first report of a discrete DNA repair function being p53 regulated in vivo and their potential clinical implications are discussed.

Searching for mutations : familial adenomatous polyposis as a case study.

The molecular diagnosis of a genetic disease can be made by demonstrating linkage of suitable markers to the disease allele. However, it is generally agreed that it is better to define the mutation responsible. There is a plethora of techniques available for the detection of mutations within genes. No one method is predominant, although single-stranded conformational polymorphism (SSCP) may be the single most widely used technique. The choice in any given situation is a complex function of a particular method's efficiency (i.e., the proportion of all mutations in a given set that are detected), reproducibrhty, ease, speed, and cost, coupled with local considerations, such as the equipment, expertise, and budget available. Factors specific to the disease and gene(s) concerned also play an important part: genes can vary greatly in size; mutations may be clustered in regions or occur in "hot spots"; some specific mutations may occur at a high frequency in a particular population; mutations may be mostly either mis-sense or non-sense; some diseases may have a high new mutation rate. In addition, the nature of the material available for diagnosis (e.g., stored DNA or lymphoblastoid cell line, formalin-fixed, or frozen tissue) may be a deciding factor. The priorities of providing a clinical service may be somewhat different from those of a research laboratory, but any laboratory's decision on the methods it employs will be governed by the costtobenefit ratio. All these points are illustrated when considering the molecular diagnosis of familial adenomatous polyposis (FAP). For service laboratories, however, there is the special consideration regarding whether the expense of mutation detection can be justified by the clinical benefit, but a discussion on the assessment of this is beyond the scope of this chapter. Climcally, FAP is characterized by the development of multiple gastromtestmal (GI) adenomas, usually hundreds to thousands, one or more of which if left untreated inevitably progress to carcinomas.

Evidence for the simultaneous expression of alternatively spliced alkylpurine N-glycosylase transcripts in human tissues and cells.

We have isolated a novel human alkylpurine N-glycosylase (APNG) cDNA from a placental library by screening with an oligonucleotide based on the published sequence of the human liver cDNA encoding this protein. The nucleotide sequences of the two cDNAs were essentially identical, but the 5' untranslated region of the new sequence was truncated and the 5'-terminal 92 nucleotides of the novel cDNA were different, indicating the possibility of alternative transcripts. This region included a portion of the open reading frame, so that the predicted protein was truncated and the seven N-terminal amino acids differed from the published sequence for APNG. PCR amplification of reverse transcribed mRNA, using 5' primers unique to the two cDNAs and a common 3' primer showed that the alternative transcripts can be co-expressed in the same cells and tissues.