Circulating tumor DNA in patients with colorectal adenomas: assessment of detectability and genetic heterogeneity.

Improving early detection of colorectal cancer (CRC) is a key public health priority as adenomas and stage I cancer can be treated with minimally invasive procedures. Population screening strategies based on detection of occult blood in the feces have contributed to enhance detection rates of localized disease, but new approaches based on genetic analyses able to increase specificity and sensitivity could provide additional advantages compared to current screening methodologies. Recently, circulating cell-free DNA (cfDNA) has received much attention as a cancer biomarker for its ability to monitor the progression of advanced disease, predict tumor recurrence and reflect the complex genetic heterogeneity of cancers. Here, we tested whether analysis of cfDNA is a viable tool to enhance detection of colon adenomas. To address this, we assessed a cohort of patients with adenomas and healthy controls using droplet digital PCR (ddPCR) and mutation-specific assays targeted to trunk mutations. Additionally, we performed multiregional, targeted next-generation sequencing (NGS) of adenomas and unmasked extensive heterogeneity, affecting known drivers such as APC, KRAS and mismatch repair (MMR) genes. However, tumor-related mutations were undetectable in patients' plasma. Finally, we employed a preclinical mouse model of Apc-driven intestinal adenomas and confirmed the inability to identify tumor-related alterations via cfDNA, despite the enhanced disease burden displayed by this experimental cancer model. Therefore, we conclude that benign colon lesions display extensive genetic heterogeneity, that they are not prone to release DNA into the circulation and are unlikely to be reliably detected with liquid biopsies, at least with the current technologies.

Quantitative assessment of the association between APC promoter methylation and breast cancer.

Adenomatous polyposis coli (APC) is an important tumor suppressor gene in breast cancer. However, there were inconsistent conclusions in the association between APC promoter methylation and breast cancer. Hence, we conducted a meta-analysis to quantitatively assess the clinicopathological significance and diagnosis role of APC methylation in breast cancer. In total, 3172 samples from 29 studies were performed in this study. The odds ratio (OR) of APC methylation was 5.92 (95% CI = 3.16-11.07) in breast cancer cases compared to controls,. The APC promoter methylation was associated with cancer stage (OR = 0.47, 95% CI = 0.28-0.80, P = 0.006), lymph node metastases (OR = 0.55, 95% CI = 0.36-0.84, P = 0.005) and ER status (OR = 1.34, 95% CI = 1.03-1.73, P = 0.003) in breast cancer. Furthermore, the sensitivity and specificity for all included studies were 0.444 (95% CI: 0.321-0.575, P < 0.0001) and 0.976 (95% CI: 0.916-0.993, P < 0.0001), respectively. These results suggested that APC promoter methylation was associated with breast cancer risk, and it could be a valuable biomarker for diagnosis, treatment and prognosis of breast cancer.

Familial adenomatous polyposis in pediatrics: natural history, emerging surveillance and management protocols, chemopreventive strategies, and areas of ongoing debate.

Familial adenomatous polyposis (FAP) is a hereditary condition with a near 100 % lifetime risk of colorectal cancer without prophylactic colectomy. Most patients with FAP have a mutation in the adenomatous polyposis coli gene on chromosome 5q22. This condition frequently presents in children with polyps developing most frequently in the second decade of life and surveillance colonoscopy is required starting at age ten. Polyps are found not only in the colon, but in the stomach and duodenum. Knowledge of the natural history of FAP is important as there are several extra-colonic sequelae which also require surveillance. In infants and toddlers, there is an increased risk of hepatoblastoma, while in teenagers and adults duodenal carcinomas, desmoid tumors, thyroid cancer and medulloblastoma are more common in FAP than in the general population. Current chemopreventive strategies include several medications and natural products, although to this point there is no consensus on the most efficacious and safe agent. Genetic counseling is an important part of the diagnostic process for FAP. Appropriate use and interpretation of genetic testing is best accomplished with genetic counselor involvement as many families also have concerns regarding future insurability or discrimination when faced with genetic testing.

Knowledge, attitudes and behavior of physicians regarding predictive genetic tests for breast and colorectal cancer.

BACKGROUND: Genetic testing for cancer susceptibility is an emerging technology in medicine. This study assessed the knowledge, attitudes and professional behavior of Italian physicians regarding the use of predictive genetic tests for breast and colorectal cancer, including the BRCA1/2 and APC tests. METHODS: A cross-sectional survey of a random sample of Italian physicians was performed in 2010 through a self-administered questionnaire. RESULTS: A response rate of 69.6% (1079 questionnaires) was achieved. A significant lack of knowledge was detected, particularly for APC testing. Less than half of the physicians agreed on the importance of efficacy and cost-effectiveness evidence in the selection of predictive genetic tests to be offered to the patients. Multiple logistic regression analyses showed that education had a positive influence on knowledge, attitudes and, to a lesser extent, professional use. The factor most strongly related to the physicians' use of genetic testing was patients requests for breast (odds ratio=12.65; 95% confidence interval 7.77-20.59) or colorectal cancer tests (odds ratio=7.02; 95% confidence interval 3.61-13.64). A high level of interest for specific training was reported by almost all physicians surveyed. CONCLUSIONS: Targeted educational programs are needed to improve the expertise of physicians, and, ultimately, to enhance the appropriate use of genetic tests in clinical practice.

Insertional mutagenesis identifies multiple networks of cooperating genes driving intestinal tumorigenesis.

The evolution of colorectal cancer suggests the involvement of many genes. To identify new drivers of intestinal cancer, we performed insertional mutagenesis using the Sleeping Beauty transposon system in mice carrying germline or somatic Apc mutations. By analyzing common insertion sites (CISs) isolated from 446 tumors, we identified many hundreds of candidate cancer drivers. Comparison to human data sets suggested that 234 CIS-targeted genes are also dysregulated in human colorectal cancers. In addition, we found 183 CIS-containing genes that are candidate Wnt targets and showed that 20 CISs-containing genes are newly discovered modifiers of canonical Wnt signaling. We also identified mutations associated with a subset of tumors containing an expanded number of Paneth cells, a hallmark of deregulated Wnt signaling, and genes associated with more severe dysplasia included those encoding members of the FGF signaling cascade. Some 70 genes had co-occurrence of CIS pairs, clustering into 38 sub-networks that may regulate tumor development.

Quantitative assessment of DNA hypermethylation in the inflammatory and non-inflammatory breast cancer phenotypes.

In this study, a comparative quantitative methylation profiling of inflammatory breast cancer (IBC) and non-IBC was set up for the identification of tumor-specific methylation patterns. Methylation ratios of six genes (DAPK, TWIST, HIN-1, RASSF1A, RARbeta2 and APC) were measured in benign breast tissues (n = 9) and in tumor samples from non-IBC (n = 81) and IBC (n = 19) patients using quantitative methylation-specific PCR. Median methylation ratios observed in breast cancer (n = 100) were significantly higher than those observed in benign breast tissues for five of six genes (TWIST, HIN-1, RASSF1A, RARbeta2 and APC). Only one of the individual genes studied, RARbeta2, showed differential methylation ratios in IBC and non-IBC (p = 0.016). Using the maximal methylation ratio observed in benign breast tissue as a threshold, the methylation frequency of two genes, RARbeta2 and APC, was significantly increased in IBC (n = 19) when compared to non-IBC (n = 81): 53 vs. 23% for RARbeta2 (p = 0.012) and 84 vs. 54% for APC (p = 0.017). Using hierarchical clustering, methylation patterns could not classify breast cancers according to their phenotype. The finding of differential frequencies of methylation in IBC and non-IBC for two out of six genes suggests that gene-specific patterns of methylation could provide a basis for molecular classification of IBC. Testing for additional genes could help to define the IBC phenotype based on patterns of aberrant gene promoter methylation.

How the I1307K adenomatous polyposis coli gene variant contributes in the assessment of risk of colorectal cancer, but not stomach cancer, in a Turkish population.

Germline and somatic truncating mutations of the adenomatous polyposis coli gene (APC) are thought to initiate colorectal tumor formation in familial adenomatous polyposis syndrome and sporadic colorectal carcinogenesis, respectively. Recently, an isoleucine-lysine polymorphism at codon 1307 (I1307K) of the APC gene has been identified in 6-7% of the Ashkenazi Jewish population. To assess the risk of this common APC allelic variant in colorectal carcinogenesis, a cohort of unselected Turkish subjects with stomach or colorectal cancer (or both) was analyzed for the APC I1307K polymorphism. Genomic DNA was extracted from patients by obtaining all stomach and colon malign polipose tissues using nuclei lysis methods. Detection of the I1307K mutation was performed using the commercial Pronto APC kit according to the manufacturer's instructions. The APC I1307K allele was identified in 7 of 57 stomach carcinoma patients (12.3%; P > 0.05) and 30 of 56 colon carcinoma patients (53.6%; P < 0.05) using antigen-anticor interaction methods. Comparing the frequencies of the two separate population control groups, the APC I1307K allele is associated with an estimated relative risk of 1.9 for colorectal neoplasia. Furthermore, APC I1307K carriers had greater numbers of adenomas and colorectal cancers per patient than noncarriers. The conclusion is that the APC I1307K variant leads to increased adenoma formation and colorectal cancer. The estimated relative risk for carriers may justify specific clinical screening for Turkish people expected to harbor this allele, and genetic testing in the long term may significantly promote colorectal cancer prevention in this population.

PCR-based assessment of the recovery rate of exfoliated colonocytes or cancer cells from fecal samples depends on the storage conditions after defecation.

BACKGROUND AND AIMS: We recently developed a new methodology for isolating colonocytes from fecal samples. We then applied a DNA-based analysis to the isolated colonocytes to detect colorectal cancer cells originating from any part of the colorectum. The purpose of the present study was to determine how long after defecation and at what temperature the fecal samples should be stored to isolate the colonocytes successfully. METHODS: Fecal samples were collected from 6 patients with colorectal cancer and 6 healthy volunteers soon after defecation at the National Cancer Center Hospital. The fecal samples were stored at 4 degrees C, room temperature or 40 degrees C for 0, 24 or 48 hours. Colonocytes were then isolated from the fecal samples, and the DNA was purified. Finally, PCR for p53, K-ras and APC was conducted to determine whether the corresponding PCR products could be obtained. RESULTS: The colonocyte recovery rate was not reduced, when compared with the data for successful PCR amplification, if the fecal samples were kept at 4 degrees C after defecation and if the colonocytes were isolated within 48 hours after defecation. CONCLUSIONS: The present data provided important clinical knowledge regarding the storage of fecal samples for future mass screening tests.

The I1307K adenomatous polyposis coli gene variant does not contribute in the assessment of the risk for colorectal cancer in Ashkenazi Jews.

Ashkenazi Jews with the I1307K adenomatous polyposis coli gene variant were suggested to confer a higher risk for colorectal cancer (CRC). We assessed the clinical importance of this polymorphism in Israeli Jews at average and elevated risk for CRC. Among 1,370 consecutive subjects that were examined, 975 Ashkenazi Jews were stratified into those at average risk (no personal or family history of colorectal neoplasia) and those at high risk. DNA was obtained from peripheral leukocytes and amplified by PCR, with primers designed to detect the I1307K variant. Overall, I1307K polymorphism was found in 7.1% (9.1% among Ashkenazi and 1.7% among non-Ashkenazi Jews). The carrier rate was 8.3 and 9.3% in average and high-risk Ashkenazim, respectively (P = 0.65). The overall odds ratio for neoplasia in carriers was 1.43 (95% confidence interval, 0.89-2.30). Age, gender, and the histopathological features of adenomas and cancers did not differ between carriers and noncarriers. No interaction on the CRC risk was found between I1307K variant and lifestyle modifiers (such as cigarette smoking, alcohol consumption, high body mass index, low physical activity, and vitamins/antioxidant intake). The I1307K adenomatous polyposis coli gene variant is not an important marker for increased risk for CRC. It confirms previous reports of a slight nonsignificant increase (OR, 1.4) in the risk of CRC in these carriers. There is no interaction effect on the risk of colorectal neoplasia between the I1307K variant and various lifestyle risk factors. The usual recommended screening and surveillance strategies should be used for carriers of this polymorphism.