sodium-bisulfite and Colorectal-Neoplasms

The genome of cancer cells accumulates numerous genetic and epigenetic somatic alterations ultimately conferring capabilities for unrestrained growth, invasion of local tissues, migration, and colonization of distant organs. Many of these new capabilities require the disruption of the cell-to-cell interactions between the cancer cell and its microenvironment. These interactions are mediated, among other factors, by the activity of extracellular enzymes that reshape not only the extracellular compartment of the cancer cells but also that of the neighboring non-cancerous stroma cells. Cell surface metallopeptidases play a crucial role in this process, by cleaving and modifying fundamental components of the extracellular compartment. The transcriptional profile of cell surface metallopeptidases becomes deregulated in several human cancers by genetic and epigenetic alterations, contributing to the tumor phenotype. In this article, we describe two common strategies to analyze somatic epigenetic alterations of cell surface metallopeptidases, i.e., high-resolution single locus analysis and high-throughput multi-loci analysis, presenting several illustrative analyses performed on our CRC collection. These analyses demonstrate that cell surface metallopeptidases, particularly those belonging to the ADAMTS gene family, frequently undergo somatic DNA hypermethylation in CRC suggesting the existence of an underlying mechanism or a strong selection process favoring the transcriptional silencing of these genes.

Topics: ADAMTS Proteins; Cell Line, Tumor; Cell Membrane; Colorectal Neoplasms; CpG Islands; Databases, Genetic; DNA Methylation; DNA Mutational Analysis; Epigenesis, Genetic; Gene Expression Regulation, Neoplastic; Humans; Mutagens; Mutation; Sulfites

Methylation-sensitive high-resolution melting (MS-HRM) is a new technique for assaying DNA methylation, but its feasibility for assaying stool in patients with colorectal cancer (CRC) is unknown.. First, the MS-HRM and methylation-specific PCR (MSP) detection limits were tested. Second, the methylation statuses of SFRP2 and VIM were analyzed in stool samples by MS-HRM, and in matching tumor and normal colon tissues via bisulfite sequencing PCR (BSP). Third, a case-control study evaluated the diagnostic sensitivity and specificity of MS-HRM relative to results obtained with MSP and the fecal immunochemical test (FIT). Finally, the linearity and reproducibility of MS-HRM were assessed.. The detection limits of MS-HRM and MSP were 1% and 5%, respectively. The diagnostic sensitivities of MS-HRM (87.3%, 55/63) in stool and BSP in matching tumor tissue (92.1%, 58/63) were highly consistent (κ=0.744). The MS-HRM assay detected 92.5% (37/40) methylation in CRCs, 94.4% (34/36) in advanced adenomas, and 8.8% (5/57) in normal controls. The results of MS-HRM analysis were stable and reliable and showed fairly good linearity for both SFRP2 (P<0.001, R(2)=0.957) and VIM (P<0.001, R(2)=0.954).. MS-HRM shows potential for CRC screening.

Topics: Adult; Aged; Aged, 80 and over; Biomarkers, Tumor; Colorectal Neoplasms; DNA Methylation; Feces; Female; Humans; Male; Membrane Proteins; Methylation; Middle Aged; Occult Blood; Polymerase Chain Reaction; Reproducibility of Results; Sulfites; Vimentin

Epigenetic alterations have been reported in colorectal neoplasia which can either complement or in some cases be predisposed to genetic alterations such as K-ras mutations. We examined the promoter methylation status of the CDKN2A and O6-methylguanine-DNA methyltransferase (MGMT) genes, after sodium bisulfite conversion and DNA amplification with methylation specific PCR. Moreover, we searched for G to A transitions in codons 12 and 13 of the K-ras oncogene in normal colorectal mucosae, aberrant crypt foci (ACF, early premalignant lesions) and carcinomas. CDKN2A hypermethylation was an infrequent event in ACF (2 of 26, 7.7%). On the contrary, MGMT hypermethylation was found in the normal mucosae (3 of the 12 samples, 25%), in 14 of the 26 ACF (53.8%) and in 7 of the 9 (77.8%) carcinomas examined. K-ras mutations were evident in 6 ACF (23%) and in 3 carcinomas (33.3%), mostly associated with MGMT promoter hypermethylation. These findings strongly support the hypothesis that epigenetic mechanisms play an important role in the early steps of colorectal carcinogenesis.

Topics: Aged; Aged, 80 and over; Carcinoma; Cell Transformation, Neoplastic; Colorectal Neoplasms; Cyclin-Dependent Kinase Inhibitor p16; DNA Methylation; Epigenesis, Genetic; Female; Gene Expression Regulation, Neoplastic; Genes, ras; Humans; Intestinal Mucosa; Male; Middle Aged; Mutation; O(6)-Methylguanine-DNA Methyltransferase; Promoter Regions, Genetic; Sequence Analysis, DNA; Sulfites

Accurate assessment of gene methylation in formalin-fixed, paraffin-embedded archived tissue (FF-PEAT) by microdissection remains challenging because the tissue volume is small and DNA is damaged. In addition, methods for methylation assessment, such as methylation-specific PCR (MSP), require sodium bisulfite modification (SBM) on purified DNA, which causes major loss of DNA. On-slide SBM, in which DNA is modified in situ before isolation of tumor cells, eliminates DNA purification steps and allows histology-oriented assessment of gene methylation. This study describes a protocol and use of on-slide SBM using 20 FF-PEAT of colorectal cancers with intratumoral adenoma components to detect accumulation of gene methylation during colorectal malignant transformation. Deparaffinized tissue sections were incubated in sodium bisulfite solution for 8 hours at 60 degrees C, stained with hematoxylin, and then microdissected. Proteinase K lysate was directly used as a template in subsequent PCR. Using on-slide SBM, 282-bp-long bisulfite direct sequencing was possible. Yield of modified DNA was 2.6-fold greater than standard SBM on average. The mean conversion rate was 97%, and false-positive or false-negative results were not observed in subsequent MSP. Intratumoral heterogeneity by accumulation of p16 and Ras association domain family protein 1a methylation during malignant transformation were shown by MSP comparing cancer with adenoma parts within a single section. On-slide SBM is applicable in most methylation studies using FF-PEAT. It allows detailed, intratumoral analysis of methylation heterogeneity within solid tumors. On-slide SBM will significantly improve our approach and understanding of epigenetic events in minimal disease and the carcinogenic process.

Topics: Alu Elements; Base Sequence; Cell Transformation, Neoplastic; Colorectal Neoplasms; DNA Methylation; DNA-Cytosine Methylases; Estrogen Receptor alpha; Female; Genes, p16; Humans; Male; Molecular Sequence Data; Polymerase Chain Reaction; Promoter Regions, Genetic; Sulfites; Thymine DNA Glycosylase; Tumor Suppressor Proteins

We report in silico identification and characterisation of a novel member of the ras association domain family 1 (RASSF1)/NORE1 family, namely, RASSF2, located at chromosomal region 20p13. It has three isoforms, all contain a ras association domain in the C-terminus. The longest isoform RASSF2A contains a 5' CpG island. RASSF2A was cloned from a brain cDNA library and directly sequenced, confirming the genomic gene structure. In previous reports, we and others have demonstrated that RASSF1A is epigenetically inactivated in a variety of cancers, including sporadic colorectal cancer (CRC). In the present report, we analysed the methylation status of RASSF2A promoter region CpG island in sporadic CRC and compared it to K-ras mutation status. RASSF2A promoter region CpG island was hypermethylated in a majority of colorectal tumour cell lines (89%) and in primary colorectal tumours (70%), while DNA from matched normal mucosa was found to be unmethylated (tumour-specific methylation). RASSF2A expression was reactivated in methylated tumour cell lines after treatment with 5-aza 2-deoxycytidine. RASSF2A methylation is an early event, detectable in 7/8 colon adenomas. Furthermore, 75% of colorectal tumours with RASSF2A methylation had no K-ras mutations (codons, 12 and 13) (P=0.048), Fisher's exact test). Our data demonstrate that RASSF2A is frequently inactivated in CRCs by CpG island promoter hypermethylation, and that epigenetic (RASSF2A) and genetic (K-ras) changes are mutually exclusive and provide alternative pathways for affecting Ras signalling.

Topics: Base Sequence; Brain; Cell Line, Tumor; Cloning, Molecular; Colonic Neoplasms; Colorectal Neoplasms; DNA Primers; Female; Gene Expression Regulation, Neoplastic; Gene Library; Humans; Male; Mutation; Neoplasm Staging; Promoter Regions, Genetic; Proteins; Sulfites; Tumor Suppressor Proteins

ID4 gene is a member of the inhibitor of DNA binding (ID) family proteins that inhibit DNA binding of basic helix-loop-helix transcription factors. The epigenetic inactivation of ID4 gene on colorectal cancer (CRC) development and its clinical significance was assessed.. In CRC cell lines, ID4 methylation status of the promoter region was assessed by methylation-specific PCR and bisulfite sequencing. The mRNA expression level was assessed by quantitative real-time reverse transcription-PCR. The methylation status of 9 normal epithelia, 13 adenomas, 92 primary CRCs, and 26 liver metastases was assessed by methylation-specific PCR. ID4 protein expression was assessed by immunohistochemistry analysis of tissue specimen.. CRC cell lines were shown to be hypermethylated, and mRNA expression was suppressed and could be restored by 5-aza-cytidine treatment. In clinical specimens from normal epithelia, adenomas, primary CRCs, and liver metastases, the frequency of ID4 hypermethylation was 0 of 9 (0%), 0 of 13 (0%), 49 of 92 (53%), and 19 of 26 (73%), respectively, with a significant elevation according to CRC pathological progression. Methylation status of primary CRCs significantly correlated with histopathological tumor grade (P = 0.028). Immunohistochemistry analysis showed ID4 expression of normal colon epithelia, adenomas, and unmethylated primary CRCs but not hypermethylated CRC specimens. Among 76 American Joint Committee on Cancer stage I to IV patients who had undergone curative surgical resection, overall survival was significantly poorer in patients with hypermethylated ID4 bearing tumors (P = 0.0066).. ID4 gene is a potential tumor suppressor gene for which methylation status may play an important role in the CRC progression.

Topics: Adult; Aged; Aged, 80 and over; Azacitidine; Carcinoma; Cell Differentiation; Cell Line, Tumor; Colon; Colorectal Neoplasms; Disease Progression; DNA Methylation; DNA Primers; DNA-Binding Proteins; Female; Humans; Immunohistochemistry; Inhibitor of Differentiation Protein 2; Male; Middle Aged; Models, Genetic; Neoplasms; Polymerase Chain Reaction; Prognosis; Repressor Proteins; Risk; RNA, Messenger; Sequence Analysis, DNA; Sulfites; Time Factors; Transcription Factors

Death-associated protein (DAP)-kinase is frequently inactivated by promoter methylation in human cancers. To understand the involvement of the DAP-kinase gene in colorectal cancer (CRC), we investigated the methylation of the DAP-kinasegene in primary CRC to define the frequency of this epigenetic aberration and the clinicopathological significance. For this reason, methylation-specific polymerase chain reaction (MSP) was used to detect DAP-kinase gene methylation in DNA from 122 cases of CRC and 18 paired serum samples. Methylation of the DAP-kinase gene was found in 67 of 122 (55%) cases of primary CRC. Study of the serum DNA from 14 patients exhibiting methylated DAP-kinase gene revealed aberrant methylation in three patients (21%). False positives were not obtained in any of the patients who did not exhibit methylation. No association was found between the promoter methylation of the DAP-kinase gene in primary CRC and gender, localization, tumor differentiation, invasion depth, regional lymph node involvement, or tumor stage. In conclusion, methylation of the DAP-kinase gene is common in CRC. The detection of the methylation of the DAP-kinase gene has a potential clinical application as a diagnostic tumor marker for CRC.

Topics: Apoptosis Regulatory Proteins; Blotting, Western; Calcium-Calmodulin-Dependent Protein Kinases; Colorectal Neoplasms; Death-Associated Protein Kinases; DNA; DNA Methylation; Female; Humans; Male; Polymerase Chain Reaction; Promoter Regions, Genetic; Sulfites

ASC/TMS1, a proapoptotic activator of procaspase-1, was reported to be aberrantly methylated in human breast cancer. We found that ASC was methylated in three of five human colon cancer cell lines lacking ASC protein expression. Demethylation treatment of these cell lines lacking ASC with 5-aza-2'-deoxycytidine partially restored ASC expression. Methylated ASC was also detected in six of ten colorectal cancer tissues. Although clear down-regulation of ASC in the whole region of a tumor tissue was hardly observed by immunostaining with anti-ASC mAb, complete suppression of ASC was identified in a minor population of the colorectal tumor cells. The biological significance of ASC methylation inducible ASC suppression in colorectal cancer will be discussed.

Topics: Adult; Aged; Aged, 80 and over; Apoptosis; Azacitidine; CARD Signaling Adaptor Proteins; Case-Control Studies; Caspase 1; Caspases; Colorectal Neoplasms; Cytoskeletal Proteins; DNA (Cytosine-5-)-Methyltransferases; DNA Methylation; DNA Primers; DNA, Neoplasm; Down-Regulation; Enzyme Activation; Enzyme Inhibitors; Enzyme Precursors; Female; Gene Expression Regulation, Neoplastic; Gene Silencing; Humans; Male; Middle Aged; Polymerase Chain Reaction; Proteins; Sulfites; Tumor Cells, Cultured

Cytosine-5 DNA methylation occurs in the context of CpG dinucleotides in vertebrates. Aberrant methylation of CpG islands in human tumors has been shown to cause transcriptional silencing of tumor-suppressor genes. Most methods used to analyze cytosine-5 methylation patterns require cumbersome manual techniques that employ gel electrophoresis, restriction enzyme digestion, radiolabeled dNTPs or hybridization probes. The development of high-throughput technology for the analysis of DNA methylation would significantly expand our ability to derive molecular information from clinical specimens. This study describes a high-throughput quantitative methylation assay that utilizes fluorescence-based real-time PCR (TaqMan) technology that requires no further manipulations after the PCR step. MethyLight is a highly sensitive assay, capable of detecting methylated alleles in the presence of a 10,000-fold excess of unmethylated alleles. The assay is also highly quantitative and can very accurately determine the relative prevalence of a particular pattern of DNA methylation. We show that MethyLight can distinguish between mono-allelic and bi-allelic methylation of the MLH1 mismatch repair gene in human colorectal tumor specimens. The development of this technique should considerably enhance our ability to rapidly and accurately generate epigenetic profiles of tumor samples.

Topics: Adaptor Proteins, Signal Transducing; Adenocarcinoma; Adult; Aged; Aged, 80 and over; Alleles; Carrier Proteins; Colorectal Neoplasms; CpG Islands; DNA Methylation; DNA Repair; Female; Humans; Male; Middle Aged; MutL Protein Homolog 1; Neoplasm Proteins; Nuclear Proteins; Oligonucleotide Probes; Polymerase Chain Reaction; Reproducibility of Results; Sensitivity and Specificity; Sulfites

We report here on a quantitative technique called COBRA to determine DNA methylation levels at specific gene loci in small amounts of genomic DNA. Restriction enzyme digestion is used to reveal methylation-dependent sequence differences in PCR products of sodium bisulfite-treated DNA as described previously. We show that methylation levels in the original DNA sample are represented by the relative amounts of digested and undigested PCR product in a linearly quantitative fashion across a wide spectrum of DNA methylation levels. In addition, we show that this technique can be reliably applied to DNA obtained from microdissected paraffin-embedded tissue samples. COBRA thus combines the powerful features of ease of use, quantitative accuracy, and compatibility with paraffin sections.

Topics: Base Sequence; Colorectal Neoplasms; Dinucleoside Phosphates; DNA; DNA Methylation; DNA, Neoplasm; Genome, Human; Humans; Indicators and Reagents; Polymerase Chain Reaction; Receptors, Estrogen; Restriction Mapping; Sensitivity and Specificity; Sulfites