Characterization of 19 novel and six recurring APC mutations in Italian adenomatous polyposis patients, using two different mutation detection techniques

Germline mutations of the adenomatous polyposis coli (APC) gene in Algerian familial adenomatous polyposis cohort: first report

BACKGROUND

Familial adenomatous polyposis (known also as classical or severe FAP) is a rare autosomal dominant colorectal cancer predisposition syndrome, characterized by the presence of hundreds to thousands of adenomatous polyps in the colon and rectum from an early age. In the absence of prophylactic surgery, colorectal cancer (CRC) is the inevitable consequence of FAP. The vast majority of FAP is caused by germline mutations in the adenomatous polyposis coli (APC) tumor suppressor gene (5q21). To date, most of the germline mutations in classical FAP result in truncation of the APC protein and 60% are mainly located within exon 15.

MATERIAL AND METHODS

In this first nationwide study, we investigated the clinical and genetic features of 52 unrelated Algerian FAP families. We screened by PCR-direct sequencing the entire exon 15 of APC gene in 50 families and two families have been analyzed by NGS using a cancer panel of 30 hereditary cancer genes.

RESULTS

Among 52 FAP index cases, 36 had 100 or more than 100 polyps, 37 had strong family history of FAP, 5 developed desmoids tumors, 15 had extra colonic manifestations and 21 had colorectal cancer. We detected 13 distinct germline mutations in 17 FAP families. Interestingly, 4 novel APC germline pathogenic variants never described before have been identified in our study.

CONCLUSIONS

The accumulating knowledge about the prevalence and nature of APC variants in Algerian population will contribute in the near future to the implementation of genetic testing and counseling for FAP patients.

Contribution of APC and MUTYH mutations to familial adenomatous polyposis susceptibility in Hungary

Familial adenomatous polyposis (FAP) is a colorectal cancer predisposition syndrome with considerable genetic and phenotypic heterogeneity, defined by the development of multiple adenomas throughout the colorectum. FAP is caused either by monoallelic mutations in the adenomatous polyposis coli gene APC, or by biallelic germline mutations of MUTYH, this latter usually presenting with milder phenotype. The aim of the present study was to characterize the genotype and phenotype of Hungarian FAP patients. Mutation screening of 87 unrelated probands from FAP families (21 of them presented as the attenuated variant of the disease, showing <100 polyps) was performed using DNA sequencing and multiplex ligation-dependent probe amplification. Twenty-four different pathogenic mutations in APC were identified in 65 patients (75 %), including nine cases (37.5 %) with large genomic alterations. Twelve of the point mutations were novel. In addition, APC-negative samples were also tested for MUTYH mutations and we were able to identify biallelic pathogenic mutations in 23 % of these cases (5/22). Correlations between the localization of APC mutations and the clinical manifestations of the disease were observed, cases with a mutation in the codon 1200-1400 region showing earlier age of disease onset (p < 0.003). There were only a few, but definitive dissimilarities between APC- and MUTYH-associated FAP in our cohort: the age at onset of polyposis was significantly delayed for biallelic MUTYH mutation carriers as compared to patients with an APC mutation. Our data represent the first comprehensive study delineating the mutation spectra of both APC and MUTYH in Hungarian FAP families, and underscore the overlap between the clinical characteristics of APC- and MUTYH-associated phenotypes, necessitating a more appropriate clinical characterization of FAP families.

A novel pathogenic germline mutation in the adenomatous polyposis coli gene in a Tunisian family with FAP

Familial adenomatous polyposis (FAP) is an autosomal dominant disorder which typically presents with colorectal cancer in early adult life, secondary to extensive adenomatous polyps of the colon. In addition to the colonic manifestations, the syndrome presents several extracolonic features including, congenital hypertrophy of the retinal pigment, osteomata and desmoid tumors. In this study, we aimed to investigate the clinical and genetic features in a Tunisian family with FAP. Sequence of the APC gene (Adenomatous Polyposis Coli) revealed a novel mutation (c.2016-2017 del TA) in exon 15, present in all affected individuals in an heterozygous state. The frameshift mutation generates a premature stop codon at amino acid 677 of the APC protein (p. H672Qfs X5). The unaffected family members did not harbor this mutation, however, a first degree relative of the patient aged of 32-year-old was phenotypically normal but carries the c.2016-2017 del TA mutation. This discrepancy can be explained by the effect of modifier gene which can affect the expressivity of the disease.

Inactivation of promoter 1B of APC causes partial gene silencing: evidence for a significant role of the promoter in regulation and causative of familial adenomatous polyposis

Familial adenomatous polyposis (FAP) is caused by germline mutations in the adenomatous polyposis coli (APC) gene. Two promoters, 1A and 1B, have been recognized in APC, and 1B is thought to have a minor role in the regulation of the gene. We have identified a novel deletion encompassing half of this promoter in the largest family (Family 1) of the Swedish Polyposis Registry. The mutation leads to an imbalance in allele-specific expression of APC, and transcription from promoter 1B was highly impaired in both normal colorectal mucosa and blood from mutation carriers. To establish the significance of promoter 1B in normal colorectal mucosa (from controls), expression levels of specific transcripts from each of the promoters, 1A and 1B, were examined, and the expression from 1B was significantly higher compared with 1A. Significant amounts of transcripts generated from promoter 1B were also determined in a panel of 20 various normal tissues examined. In FAP-related tumors, the APC germline mutation is proposed to dictate the second hit. Mutations leaving two or three out of seven 20-amino-acid repeats in the central domain of APC intact seem to be required for tumorigenesis. We examined adenomas from mutation carriers in Family 1 for second hits in the entire gene without any findings, however, loss of the residual expression of the deleterious allele was observed. Three major conclusions of significant importance in relation to the function of APC can be drawn from this study; (i) germline inactivation of promoter 1B is disease causing in FAP; (ii) expression of transcripts from promoter 1B is generated at considerable higher levels compared with 1A, demonstrating a hitherto unknown importance of 1B; (iii) adenoma formation in FAP, caused by impaired function of promoter 1B, does not require homozygous inactivation of APC allowing for alternative genetic models as basis for adenoma formation.

The Italian external quality control program for familial adenomatous polyposis of the colon: five years of experience

Familial adenomatous polyposis is a rare autosomal dominant inherited disease (incidence, 1/8000). More than 90% of families affected by familial adenomatous polyposis have a mutation in the tumor suppressor gene adenomatous polyposis coli (APC). Mutations in this gene are characterized by 100% penetrance, although there is a variation in phenotypic expression of the disease. According to a 2004 survey of the Italian Human Genetic Society, about 264 APC gene molecular genetic tests were performed by Italian laboratories per year. The Italian External Quality Assessment (IEQA), financially supported by the Ministry of Health and coordinated by the Istituto Superiore di Sanità, was started in 2000 to improve the quality of molecular genetic tests in Italy. In the frame of the IEQA, about 50% of public laboratories performing APC gene tests have been monitored. The number of responding public laboratories during the 5 years was 6, 7, 7, 7, and 5 from 2001 to 2006, respectively; on average, 96.3% of samples completely analyzed were correctly genotyped. Methods used by laboratories to detect mutation were direct sequencing, single-strand conformation polymorphism, protein truncation test, and denaturing high-performance liquid chromatography. Written reports were not homogeneous among laboratories, although a new form of written report was proposed to laboratories in 2004. It will be interesting to monitor the effects of the reporting model and the output of this educational action in the future.

May the APC gene somatic mutations in tumor tissues influence the clinical features of Chinese sporadic colorectal cancers?

The APC gene plays an important role in colorectal carcinogenesis. The impact of APC mutations on the clinical features in sporadic CRC remains to be uncovered. The APC gene was screened for mutations with systematic analysis techniques including DHPLC, PTT, MLPA and DNA sequencing in 43 Chinese sporadic CRC patients. Twenty nine somatic mutations (in 17 different types) in APC gene were found in 18 of 43 sporadic CRC patients. Of those, nine were novel mutations. Higher frequency of somatic APC mutations was found in younger CRC patients than that in elder ones. The biallelic somatic mutations of APC gene were identified in four CRC patients whose tumors had more invasive clinical features. The nonsense mutation Arg1114X in APC gene was found in five of 43 CRC tumor tissues. A higher cancer metastasis rate was uncovered in CRC patients with this mutation. The somatic mutations of APC gene may influence the clinical features of sporadic CRC. Arg1114X in APC gene, as a hot spot mutation in Chinese CRC, may predispose to the cancer metastasis of sporadic CRC.

Novel APC mutations in Czech and Slovak FAP families: clinical and genetic aspects

Background

Germline mutations in the adenomatous polyposis gene (APC) result in familial adenomatous polyposis (FAP). FAP is an autosomal dominantly inherited disorder predisposing to colorectal cancer. Typical FAP is characterized by hundreds to thousands of colorectal adenomatous polyps and by several extracolonic manifestations. An attenuated form of polyposis (AFAP) is characterized by less than 100 adenomas and later onset of the disease.

Methods

Here, we analyzed the APC gene for germline mutations in 59 Czech and 15 Slovak FAP patients. In addition, 50 apparently APC mutation negative Czech probands and 3 probands of Slovak origin were screened for large deletions encompassing the APC gene. Mutation screening was performed using denaturing gradient gel electrophoresis and/or protein truncation test. DNA fragments showing an aberrant electrophoretic banding pattern were sequenced. Screening for large deletions was performed by multiplex ligation dependent probe amplification. The extent of deletions was analyzed using following microsatellite markers: D5S299, D5S82, D5S134 and D5S346.

Results

In the set of Czech and Slovak patients, we identified 46 germline mutations among 74 unrelated probands. Total mutation capture is 62,2% including large deletions. Thirty seven mutations were detected in 49 patients presenting a classical FAP phenotype (75,5%) and 9 mutations in 25 patients with attenuated FAP (36%). We report 20 novel germline APC mutations and 3 large deletions (6%) encompassing the whole-gene deletions and/or exon 14 deletion. In the patients with novel mutations, correlations of the mutation localization are discussed in context of the classical and/or attenuated phenotype of the disease.

Conclusion

The results of the molecular genetic testing are used both in the establishment of the predictive diagnosis and in the clinical management of patients. In some cases this study has also shown the difficulty to classify clinically between the classical and the attenuated form of FAP according to the established criteria. Interfamilial and/or intrafamilial phenotype variability was also confirmed in some cases which did not fit well with predicted genotype-phenotype correlation. All these findings have to be taken into consideration both in the genetic counselling and in the patient care.

APC genotype is not a prognostic factor in familial adenomatous polyposis patients with colorectal cancer

PURPOSE

Several studies have shown that the clinical phenotype of patients with familial adenomatous polyposis is influenced by the position of the associated germline mutation in the APC gene. The aim of this work was to assess whether the site of the APC mutation may also predict the survival of familial adenomatous polyposis patients with a confirmed diagnosis of colorectal cancer.

METHODS

A total of 387 familial adenomatous polyposis patients with colorectal cancer were examined. Of these, 287 (74 percent) belonged to families with an identified mutation, whereas 100 (26 percent) were from families in which no detectable APC mutation had been found by standard screening methods. The subjects were subdivided into four groups, according to the presence and localization of the identified mutation: with mutation before (a), at (b), or beyond codon 1309 (c), and without identified mutation (d).

RESULTS

The cumulative five-year survival estimate of all cases included in the study was 0.56 (95 percent confidence interval, 0.51-0.61). No difference was observed in survival probability among patients from families with mutations before (0.56; 95 percent confidence interval, 0.49-0.63), at (0.58; 95 percent confidence interval, 0.43-0.72), or beyond (0.52; 95 percent confidence interval, 0.31-0.73) codon 1309 or those from families that were mutation negative (0.58; 95 percent confidence interval, 0.48-0.68) (log-rank test, P = 0.9). Survival analysis did not reveal any significant advantage for patients carrying a mutation in a specific region of the APC gene, after adjustment for age, gender, site, and stage.

CONCLUSION

These data do not support the hypothesis that APC mutation may influence the outcome of familial adenomatous polyposis cases affected by colorectal cancer.

Profuse familial adenomatous polyposis with an adenomatous polyposis coli exon 3 mutation

The attenuated form of familial adenomatous polyposis coli (AAPC) is associated with mutations in the adenomatous polyposis coli (APC) gene which cluster in the 5' region of the gene. It has been proposed that a 'genotype-phenotype boundary' exists at codons 159-163, and mutations that are 5' of this boundary will produce AAPC. Herein we document a three-generation family with an exon 3 mutation well to the 5' side of the proposed boundary, in which two affected individuals have had, in their 40s, a profuse form of familial adenomatous polyposis coli. We conclude that the codon 159-163 'boundary' is indicative rather than definitive. These two patients also had postoperative intra-abdominal adhesions, severely so in one.

Phenotype variability of two FAP families with an identical APC germline mutation at codon 1465: a potential modifier effect?

We report the cases of two familial adenomatous polyposis (FAP) families who presented with the same 2 base pair deletion (AG) at codon 1465 of the adenomatous polyposis coli (APC) gene, but showed phenotypic variability. The mutation was revealed by a simple nonradioactive method using a heteroduplex analysis and identified by a sequence analysis. This observation suggests the responsibility of modifier genes in FAP patients' phenotype.

Genotype and phenotype factors as determinants of desmoid tumors in patients with familial adenomatous polyposis

Desmoids represent the most important cause of death, after colorectal cancer, in patients affected with familial adenomatous polyposis (FAP), an inherited disease due to mutations in the APC gene. The aims of our study were to estimate the risk of developing desmoids in FAP patients and to evaluate the association between desmoids and different risk factors. The occurrence of desmoids, colorectal cancer and other extra-colonic manifestations were assessed in 897 FAP patients, 653 of whom were also investigated for APC mutations. Odds ratios (OR) and corresponding 95% confidence intervals (CI) were computed using an unconditional multiple logistic regression model. Desmoids developed in 107 patients (11.9%), with a cumulative risk of 20.6%. Females had a significantly higher risk than males (OR = 2.1; 95% CI 1.4-3.1). Family history of desmoids (OR = 8.75; 95% CI 5.66-13.51), osteomas (OR = 2.9; 95% CI 1.8-4.8) and epidermoid cysts (OR = 1.8; 95% CI 1.1-3.2) was also significantly associated with the occurrence of disease. Subjects with APC mutations beyond codon 1444 had a 12-fold increased risk, compared with patients with mutations located upstream. Mutations beyond codon 1309 conferred a 17-fold higher risk, compared with mutations upstream codon 452. Multivariate analysis identified as independent predictors mutation beyond codon 1444 (OR = 6.2; 95% CI 2.5-15.8), family history of desmoids (OR = 5.8; 95% CI 3.1-10.6), female gender (OR = 2.1; 95% CI 1.1-3.8) and the presence of osteomas (OR = 1.9; 95% CI 1.1-3.4). Our results indicate that integrating genetic and clinical data is helpful in defining subgroups of patients at higher risk for desmoids, who may benefit from specific prevention programs.

Genotype and phenotype factors as determinants for rectal stump cancer in patients with familial adenomatous polyposis. Hereditary Colorectal Tumors Registry

OBJECTIVE

To identify factors influencing the occurrence of cancer in the rectal remnant in patients with familial adenomatous polyposis (FAP) after colectomy and ileorectal anastomosis (IRA).

SUMMARY BACKGROUND DATA

The risk for rectal cancer in patients with FAP after colectomy and IRA remains a major concern.

METHODS

Between 1955 and 1997, 371 patients (206 men, 165 women) from the Registry of Hereditary Colorectal Tumors underwent colectomy and IRA as a primary surgical procedure. Survival was estimated using the Kaplan-Meier method. Cox proportional hazard models were fitted to assess the relative excess risk of rectal cancer and to control for confounding factors. A multivariate analysis was performed to assess the relation between cancer risk in the rectum and sex, age, number of rectal polyps, colon cancer, and APC germline mutation.

RESULTS

Median follow-up was 81 months. Eighty-nine patients (24%) had colon cancer at the time of surgery. The APC mutation was found in 200 patients. In 27 patients, cancer developed in the retained rectum 1 to 26 years after surgery. The incidence of rectal carcinoma appears to increase with time: at 10, 15, and 20 years after surgery, the cumulative risk was 7.7%, 13.1%, and 23.0%, respectively. Multivariate analysis identified as independent predictors the presence of colon cancer at IRA and a mutation occurring between codons 1250 and 1464; both factors increased the risk nine times.

CONCLUSIONS

The presence of cancer at IRA and APC mutation type are the most important risk factors for the future development of cancer in the rectal remnant in patients with FAP.

Congenital hypertrophy of the retinal pigment epithelium and APC mutations in two Chinese families with familial adenomatous polyposis

PURPOSE

Congenital hypertrophy of the retinal pigment epithelium (CHRPE) exists almost exclusively among familial adenomatous polyposis (FAP) patients with adenomatous polyposis coli (APC) mutations between codon 413 in exon 9 and codon 1387 in exon 15. We investigated the locality of APC mutations in relationship to the occurrence of CHRPE in two Chinese families with FAP.

METHODS

Genomic DNA of available members of two unrelated Chinese FAP families was investigated for sequence alteration in the APC gene by polymerase chain reaction and direct sequencing. All subjects were examined by binocular indirect ophthalmoscopy (BIO) for CHRPE.

RESULTS

A mutation in exon 6, Arg216Stop, was identified in one patient with FAP and CHRPE. An Arg283Stop mutation in exon 8 was found in 5 members in another family; 4 of them had FAP and all had small hypopigmented white lesions, probably a new type of CHRPE.

CONCLUSIONS

We found two mutations, Arg216Stop and Arg283Stop, upstream of codon 413 in FAP patients presenting with CHRPE. Arg283Stop has not previously been reported in such patients. A large-scale study on CHRPE and APC mutations in Chinese FAP patients is required to affirm their inter-relationships and the significance of the hypopigmented white lesions.

Apc1638T: a mouse model delineating critical domains of the adenomatous polyposis coli protein involved in tumorigenesis and development

The adenomatous polyposis coli (APC) gene is considered as the true gatekeeper of colonic epithelial proliferation: It is mutated in the majority of colorectal tumors, and mutations occur at early stages of tumor development in mouse and man. These mutant proteins lack most of the seven 20-amino-acid repeats and all SAMP motifs that have been associated with down-regulation of intracellular beta-catenin levels. In addition, they lack the carboxy-terminal domains that bind to DLG, EB1, and microtubulin. APC also appears to be essential in development because homozygosity for mouse Apc mutations invariably results in early embryonic lethality. Here, we describe the generation of a mouse model carrying a targeted mutation at codon 1638 of the mouse Apc gene, Apc1638T, resulting in a truncated Apc protein encompassing three of the seven 20 amino acid repeats and one SAMP motif, but missing all of the carboxy-terminal domains thought to be associated with tumorigenesis. Surprisingly, homozygosity for the Apc1638T mutation is compatible with postnatal life. However, homozygous mutant animals are characterized by growth retardation, a reduced postnatal viability on the B6 genetic background, the absence of preputial glands, and the formation of nipple-associated cysts. Most importantly, Apc1638T/1638T animals that survive to adulthood are tumor free. Although the full complement of Apc1638T is sufficient for proper beta-catenin signaling, dosage reductions of the truncated protein result in increasingly severe defects in beta-catenin regulation. The SAMP motif retained in Apc1638T also appears to be important for this function as shown by analysis of the Apc1572T protein in which its targeted deletion results in a further reduction in the ability of properly controlling beta-catenin/Tcf signaling. These results indicate that the association with DLG, EB1, and microtubulin is less critical for the maintenance of homeostasis by APC than has been suggested previously, and that proper beta-catenin regulation by APC appears to be required for normal embryonic development and tumor suppression.

Novel germline APC variants in patients with multiple adenomas

Chain-terminating germline APC mutations are responsible for adenomatous polyposis coli (APC). In the present work, we tested the hypothesis that germline APC mutations may be present in some patients with a milder phenotype, i.e., multiple synchronous colorectal adenomas. Eighteen patients with 3 or more colorectal adenomas at endoscopy (within a 6-month period) were ascertained from a series of subjects undergoing endoscopic examination. Their blood DNAs were analysed for the presence of germline mutations in the APC coding region by single-strand polymorphism analysis. Ten unrelated polyp-free subjects and 101 unrelated APC patients were used as controls in the molecular analyses. Five of the eighteen patients carried novel germline APC variants or rare polymorphisms. These were various in site (from the splice acceptor site of intron 7 to the end of exon 15) and type (splice-site, missense, and chain-terminating mutations). Only one of ten polyp-free individuals carried a silent APC variant and none of these variants was found in the 101 APC controls. A first- or second-degree family history of colorectal cancer was reported by 4 of the 5 patients carrying a germline APC variant. In conclusion, novel APC germline variants were detected in patients with multiple synchronous adenomas. This suggests that the development of sporadic adenomas, in some instances, is associated with the presence of minor germline variants of the APC gene and that the spectrum of germline APC functional mutations may be larger than previously thought.