Systematic meta-analyses and field synopsis of genetic association studies in colorectal adenomas

BackgroundLow penetrance genetic variants, primarily single nucleotide polymorphisms, have substantial influence on colorectal cancer (CRC) susceptibility. Most CRCs develop from colorectal adenomas (CRA). Here we report the first comprehensive field synopsis that catalogues all genetic association studies on CRA, with a parallel online database [http://www.chs.med.ed.ac.uk/CRAgene/].MethodsWe performed a systematic review, reviewing 9750 titles, and then extracted data from 130 publications reporting on 181 polymorphisms in 74 genes. We conducted meta-analyses to derive summary effect estimates for 37 polymorphisms in 26 genes. We applied the Venice criteria and Bayesian False Discovery Probability (BFDP) to assess the levels of the credibility of associations.ResultsWe considered the association with the rs6983267 variant at 8q24 as 'highly credible', reaching genome-wide statistical significance in at least one meta-analysis model. We identified 'less credible' associations (higher heterogeneity, lower statistical power, BFDP > 0.02) with a further four variants of four independent genes: MTHFR c.677C>T p.A222V (rs1801133), TP53 c.215C>G p.R72P (rs1042522), NQO1 c.559C>T p.P187S (rs1800566), and NAT1 alleles imputed as fast acetylator genotypes. For the remaining 32 variants of 22 genes for which positive associations with CRA risk have been previously reported, the meta-analyses revealed no credible evidence to support these as true associations.ConclusionsThe limited number of credible associations between low penetrance genetic variants and CRA reflects the lower volume of evidence and associated lack of statistical power to detect associations of the magnitude typically observed for genetic variants and chronic diseases. The CRA gene database provides context for CRA genetic association data and will help inform future research directions

Systematic meta-analyses, field synopsis and global assessment of the evidence of genetic association studies in colorectal cancer

Objective: To provide an understanding of the role of common genetic variations in colorectal cancer (CRC) risk, we report an updated field synopsis and comprehensive assessment of evidence to catalogue all genetic markers for CRC (CRCgene2). Design: We included 869 publications after parallel literature review and extracted data for 1063 polymorphisms in 303 different genes. Meta-Analyses were performed for 308 single nucleotide polymorphisms (SNPs) in 158 different genes with at least three independent studies available for analysis. Scottish, Canadian and Spanish data from genome-wide association studies (GWASs) were incorporated for the meta-Analyses of 132 SNPs. To assess and classify the credibility of the associations, we applied the Venice criteria and Bayesian False-Discovery Probability (BFDP). Genetic associations classified as â € positive' and â € less-credible positive' were further validated in three large GWAS consortia conducted in populations of European origin. Results: We initially identified 18 independent variants at 16 loci that were classified as â € positive' polymorphisms for their highly credible associations with CRC risk and 59 variants at 49 loci that were classified as â € less-credible positive' SNPs; 72.2% of the â € positive' SNPs were successfully replicated in three large GWASs and the ones that were not replicated were downgraded to â € less-credible' positive (reducing the â € positive' variants to 14 at 11 loci). For the remaining 231 variants, which were previously reported, our meta-Analyses found no evidence to support their associations with CRC risk. Conclusion: The CRCgene2 database provides an updated list of genetic variants related to CRC risk by using harmonised methods to assess their credibility.</p

Molecular genetic of colorectal cancer : association between P53 restricted over expression and mismatch repair deficiency

The first question addressed in this work pertains to evaluating the relevance of p53 immunohistochemistry in phenotyping colorectal tumors in the daily practice of the pathologist. Further, we attempt to shed light on the relationship between alterations in p53-MDM2-p14ARF pathway and DNA mismatch repair sytem (MMR) deficiency in colorectal cancer (CRC). We demonstrated the existence of a particular pattern of p53 immunohistochemical expression that we defined as “restricted p53 overexpression”, characterized by a limited number of homogenously scattered and strongly positive tumor cells. We clearly demonstrated that this pattern of p53 expression is distinct from the two classical p53 immunostaining profiles usually described in the literature, namely the diffuse p53 overexpression associated with TP53 missense mutations and the negative p53 immunostaining associated with truncating TP53 mutations. We showed that the restricted pattern of p53 overexpression is significantly associated with microsatellite instability high (MSI-H) phenotype, suggesting that this pattern of p53 immunostaining could be an additional morphological feature of MSI-H CRCs. Although the restricted p53 overexpression pattern is also observed in a subset of microsatellite stable (MSS) CRCs and does not predict the origin of MMR deficiency, our data point to a significant role of p53 immunohistochemistry in the routine practice of the pathologist, as assessing the pattern of p53 protein expression could provide a more refined tumor classification and help the pathologist in categorizing CRCs in large scale screening. Despite the known relationship between wild-type TP53 and MMR deficiency, we showed that restricted p53 overexpression inversely correlated with TP53 mutation irrespective of MSI-status. We found that restricted p53 overexpression pattern is strongly associated with concomitant MDM2 overexpression and inversely correlated with p21 loss, independently of MSI-status. Moreover, while hypermethylation of proximal CpG sites within the 5’CpG island of p14ARF promoter flanking exon 1β seems to be a rare event in CRCs, this epigenetic event was more likely observed in CRCs displaying the restricted pattern of p53 overexpression, irrespective of MSI-status. Our results indicate a significant alternative mechanism of p53-MDM2-p14ARF axis deregulation in a subgroup of CRCs, including the majority of colorectal tumors evolving through the MSI-pathway. Taken together, the findings from this work could provide a more refined classification of colorectal tumors in the future, which would significantly impact the therapeutic management of CRC patients.(SBIM 3) -- UCL, 201

High risk for neoplastic transformation of endometriosis in a carrier of lynch syndrome.

Lynch syndrome is an autosomal dominant cancer-susceptibility disorder caused by mutations in DNA mismatch repair genes. Women with Lynch syndrome have an increased lifetime risk for endometrial and ovarian cancers. While there is evidence of efficacy for prophylactic surgery, no standard recommendations have been developed to support screening for premalignant endometrial and ovarian epithelial lesions in high-risk women. Here, we report a case of a healthy woman carrying a germline mutation in MLH1 gene with endometrial intra-epithelial neoplasia and ovarian endometriotic lesions exhibiting a loss of MLH1 protein expression. This case report illustrates the malignant potential of endometriosis, and highlights the need for a meticulous management of gynecologic premalignant precursor lesions in reducing cancer risk among related Lynch syndrome women

Hypermethylation of the 5′ CpG island of the <it>p14</it>^ARF flanking exon 1β in human colorectal cancer displaying a restricted pattern of p53 overexpression concomitant with increased MDM2 expression

<p>Abstract</p> <p>Background</p> <p>It has been suggested that inactivation of <it>p14</it>^ARF, a tumor suppressor central to regulating p53 protein stability through interaction with the MDM2 oncoprotein, abrogates p53 activity in human tumors retaining the wild-type <it>TP53</it> gene. Differences in expression of tumor suppressor genes are frequently associated with cancer. We previously reported on a pattern of restricted p53 immunohistochemical overexpression significantly associated with microsatellite instability (MSI), low <it>TP53</it> mutation frequency, and MDM2 overexpression in colorectal cancers (CRCs). In this study, we investigated whether <it>p14</it>^ARF alterations could be a mechanism for disabling the p53 pathway in this subgroup of CRCs.</p> <p>Results</p> <p>Detailed maps of the alterations in the <it>p14</it>^ARF gene were determined in a cohort of 98 CRCs to detect both nucleotide and copy-number changes. Methylation-specific PCR combined with bisulfite sequencing was used to evaluate the prevalence and distribution of <it>p14</it>^ARF methylation. <it>p14</it>^ARF alterations were then correlated with MSI status, <it>TP53</it> mutations, and immunohistochemical expression of p53 and MDM2. The frequency of <it>p14</it>^ARF mutations was extremely low (1/98; 1%), whereas coexistence of methylated and unmethylated alleles in both tumors and normal colon mucosa was common (91/98; 93%). Only seven of ninety-eight tumors (7%) had a distinct pattern of methylation compared with normal colon mucosa. Evaluation of the prevalence and distribution of <it>p14</it>^ARF promoter methylation in a region containing 27 CpG sites in 35 patients showed a range of methylated CpG sites in tumors (0 to 25 (95% CI 1 to 13) versus 0 to 17 (95% CI 0 to 2)) in adjacent colon mucosa (<it>P</it> = 0.004). Hypermethylation of the <it>p14</it>^ARF promoter was significantly correlated with the restricted p53 overexpression pattern (<it>P</it> = 0.03), and MDM2 overexpression <it>(P</it> = 0.02), independently of MSI phenotype. Although no significant correlation between <it>p14</it>^ARF methylation and <it>TP53</it> mutational status was seen (<it>P</it> = 0.23), methylation involving the proximal CpG sites within the 5′ CpG flanking exon 1β was present more frequently in tumors with restricted p53 overexpression than in those with diffuse p53 overexpression (range of methylated clones 17 to 36% (95% CI 24 to 36%) versus range 0 to 3% (95% CI 0 to 3%), <it>P</it> = 0. 0003).</p> <p>Conclusion</p> <p><it>p14</it>^ARF epigenetic silencing may represent an important deregulating mechanism of the p53-MDM2-p14^ARF pathway in CRCs exhibiting a restricted p53 overexpression pattern.</p

Distinctive patterns of p53 protein expression and microsatellite instability in human colorectal cancer

Although evidence suggests an inverse relationship between microsatellite instability and p53 alterations in colorectal cancer, no study has thoroughly examined the use of p53 immunohistochemistry in phenotyping colorectal cancers. We investigated the value of p53 immunohistochemistry in microsatellite instability-positive colorectal cancers prescreening and attempted to clarify the relationship between DNA mismatch repair system and p53 pathway. In a series of 104 consecutive colorectal cancers, we performed p53 immunohistochemistry, TP53 mutational analysis, DNA mismatch repair system efficiency evaluation (DNA mismatch repair system immunohistochemistry, microsatellite instability status, MLH1/MSH2 germ line, and BRAF, murine double minute 2, and p21 immunohistochemistry. Microsatellite instability high was observed in 25 of 104 colorectal cancers, with DNA mismatch repair system protein loss (24/25) and germ line (8/25) or BRAF mutations (8/25). p53 immunohistochemistry revealed 3 distinct patterns of expression: complete negative immunostaining associated with truncating TP53 mutations (P < .0001), diffuse overexpression associated with missense TP53 mutations (P < .0001), and restricted overexpression characterized by a limited number of homogenously scattered strongly positive tumor cells in 36.5% of colorectal cancers. This latest pattern was associated with wild-type TP53 and microsatellite instability high colorectal cancers (P < .0001) including all Lynch tumors (8/8), but its presence among 22% of DNA mismatch repair system-competent colorectal cancers decreased its positive predictive value (55.2% [95% confidence interval, 45%-65%]). It was also correlated with murine double minute 2 overexpression (P < .0001) and inversely with p21 loss (P = .0002), independently of microsatellite instability status. In conclusion, a restricted pattern of p53 overexpression is preferentially associated with microsatellite instability high phenotype and could, therefore, be of clinical use as signal for microsatellite instability analysis in a large-scale tumor screening. Its association with concomitant murine double minute 2 overexpression suggests an alternative mechanism of p53 pathway deregulation

Restricted overexpression of p53 immunohistochemistry (p53IHC RO) as prognostic after colorectal cancer (CRC) resection

Background: p53IHC RO was previously described as a distinct pattern from the negative or diffuse p53 IHC expression. p53IHC RO is characterized by a limited number of homogenously scattered strongly positive CRC cells and is associated with some clinico-pathologic CRC feature. The prognostic impact of p53IHC RO remains unknown. Methods: p53 and MMR (MLH1, MSH2, MSH6 and PMS2) proteins IHC expression were performed on CRC primary tumors from an unselected cohort of patients who underwent surgery at the Cliniques St-Luc between 1995 and 2000. p53 IHC results were defined as negative, diffuse or restricted expression. Clinico-pathologic CRC characteristics and patients follow-up were available for this analysis. Comparisons of numerical and categorical clinico-pathological data were evaluated respectively by ANOVA and Fisher exact tests between p53 expression groups. Progression-Free Survival (PFS) and Overall Survival (OS) analyses were performed using Kaplan-Meier method and compared with the log-rank test (Bonferroni correction applied for multiplicity). Uni and multivariate PFS and OS regression were performed using a Cox Proportional Hazard model. Results: Among 100 CRCs (99 patients), p53 IHC expression was categorized as restricted (n=36), diffuse (n= 46) or negative (n=18). p53IHC RO (total n=36, defective MMR n=20, proficient MMR n=16) was associated with age (≥60y), proximal location, poor differentiated CRC, and a lowest lymph node ratio (LNR) (p<0.05). Among the analysed defective MMR CRCs, 20/24 was p53IHC RO (p<0.001). After a mean follow-up of 13 years after CRC resection, median PFS and OS were significantly higher in the p53IHC RO group as compared with the diffuse and negative p53 IHC expression (median PFS respectively not reached vs 40.9 vs 22.8 months, p<0.001 and median OS respectively not reached vs 70.7 vs 48.0 months, p=0.009). LNR, synchronous metastases and p53IHC RO were significantly associated with a better PFS in multivariate analysis (p<0.05). Conclusions: p53IHC RO is a prognostic factor after CRC resection. These results must be confirmed on a larger cohort but could be clinically relevant for prognosis