Heterogeneity of DNA methylation status analyzed by bisulfite-PCR-SSCP and correlation with clinico-pathological characteristics in colorectal cancer.

Aberrant DNA methylation has been identified as an important mechanism for inactivation of tumor suppressor genes and mismatch repair genes during carcinogenesis. We used bisulfite treatment and the PCR-single strand conformation polymorphism (SSCP) (BiPS) technique to analyze methylation status of the promoter regions of the hMLH1, p16, and HIC1 genes in several cancer cell lines and colorectal cancer tissues. The methylation of the hMLH1, p16 and HIC1 genes was observed in 2, 8, and 13 of 13 cancer cell lines, respectively. The SSCP for p16 and HIC1 in each of the methylation-positive cell lines were similar, indicating relative homogeneity of methylation status and complete methylation in the cell lines. Methylation was observed in 8, 5, and 21 of 25 colorectal cancer tissues for the hMLH1, p16, and HIC1 genes, respectively. The methylated bands revealed by BiPS analysis of the hMLH1 gene were homogeneous, whereas those of the p16 and HIC1 genes were different in each case. The methylation of the promoter region of the HIC1 gene in colorectal cancer was observed most frequently and could serve as a sensitive marker for colorectal cancer. Methylation status of the hMLH1 and p16 gene promoters was correlated with microsatellite instability status, tumor location, and differentiation but not with K-ras mutation or allelic loss of p53.

Enhanced detection of deleterious and other germline mutations of hMSH2 and hMLH1 in Japanese hereditary nonpolyposis colorectal cancer kindreds.

Hereditary nonpolyposis colorectal cancer (HNPCC) is an autosomal, dominantly inherited cancer-prone syndrome. Here, we describe a novel and efficient approach for screening mutations of two major HNPCC susceptibility genes, hMSH2 and hMLH1. The system consists of RNA extraction from whole blood treated with the translation inhibitor, followed by long RT-PCR of the entire coding regions combined with direct sequencing. In analysis of 15 kindreds suspicious for HNPCC, 8 samples were subjected to analysis after puromycin treatment and 7 samples were analyzed without puromycin treatment. Three deleterious mutations were detected in the kindreds with puromycin treatment, while none were observed in those without puromycin. Signals from mutated alleles were enhanced after puromycin treatment and easily distinguished from the wild-type allele, achieved by suppression of nonsense-mediated mRNA decay. Furthermore, 12 other mutations were detected in 15 kindreds. The system is considered to be a reliable and useful approach for detecting germline mutations of hMSH2 and hMLH1 in HNPCC kindreds.

Allelic loss on chromosome 9 in bladder cancer tissues and urine samples detected by blunt-end single-strand DNA conformation polymorphism.

Allelic loss on chromosome 9 is the most frequent and earliest genetic event in bladder carcinogenesis, and its detection in urine samples would be useful for detecting bladder cancer. A highly sensitive method to detect loss of heterozygosity (LOH) at 5 polymorphic loci on chromosome 9p and 9q was developed by the use of blunt-end single-strand DNA conformation polymorphism (blunt-end SSCP) analysis. Tumor tissues, urine samples and peripheral blood lymphocytes from 34 patients with transitional cell carcinoma of the bladder were analyzed. LOHs on 9p and/or 9q were found in 24 (71%) of 34 tumor samples and 23 (70%) of 33 urine samples, while no allelic loss was detected in 20 urine samples from benign urothelial diseases. The frequency of allelic loss in tumor tissues was 67%, 71% and 80% in the pTa, pT1 and > or = pT2 stages and 50%, 80% and 79% in G1, G2 and G3 tumors, respectively. In comparison with a urine cytological examination, LOH on chromosome 9 was detected in 70% of urine samples diagnosed as transitional cell carcinoma, 67% of those as atypia and 70% of those as no malignant cells. Thus, detection of LOH on chromosome 9 from urine samples by blunt-end SSCP is a more sensitive diagnostic modality than cytologic examination for detecting bladder cancer. It would be useful for postoperative management of bladder cancer, particularly when the allelic loss is revealed in the tumor tissues obtained at first surgery.

Detection of K-ras gene mutations at codon 12 in the pancreatic juice of patients with intraductal papillary mucinous tumors of the pancreas.

BACKGROUND: The authors previously found specific mutations of the K-ras gene at codon 12 in the pancreatic juice of 67% of patients (6 of 9) with pancreatic ductal carcinoma, and the detection of these mutations was useful for diagnosis. This study was performed to detect and evaluate K-ras mutations in pancreatic juice from patients with intraductal papillary mucinous tumor of the pancreas, which is considered a low grade malignancy. The results were interpreted from the viewpoint of clinical significance. METHODS: K-ras mutations were examined using seminested polymerase chain reaction analysis combined with restriction enzyme digestion, followed by nonradioisotopic single strand DNA conformation polymorphism. RESULTS: Twelve of thirteen cases (92%) of intraductal papillary mucinous tumor of the pancreas, confirmed histologically (9 adenomas and 4 carcinomas), and 26 of 43 cases (60%) of ductal carcinoma showed specific K-ras gene mutations in the pancreatic juice. Furthermore, 4 of 22 patients (18%) with chronic pancreatitis, followed for more than 1 year without a sign of pancreatic tumor, showed K-ras mutations. In contrast, no mutations of the K-ras gene were detected in the pancreatic juice from 28 normal controls. CONCLUSIONS: K-ras mutations were found in the pancreatic juice of all but one patient with intraductal papillary mucinous tumor of the pancreas, but they were not useful for distinguishing carcinoma from adenoma. The authors concluded that K-ras mutations are not a specific marker for pancreatic neoplasms because similar mutations were detected in the pancreatic juice from patients with chronic pancreatitis. At the present time, the detection of K-ras mutations in pancreatic juice should be used clinically as an adjunct diagnostic modality for pancreatic diseases.

Polymerase chain reaction-based approaches for detection of allelic loss in the p53 tumor suppressor gene in colon neoplasms.

OBJECTIVES: Inactivation of the p53 tumor suppressor gene is considered to be a late event involved in the malignant transformation of colorectal adenoma to cancer. Thus, its detection is thought to provide useful information for the clinical management of colorectal neoplasms. We devised a rapid screening test for allelic loss of the p53 gene by non-radioisotopic single-strand conformation polymorphism analysis. METHODS: Biopsy materials from 119 colorectal tumors obtained at endoscopy were examined. Three intragenic polymorphic sites were amplified by polymerase chain reaction using DNA extracted from these materials, and amplified DNA fragments were subjected to non-radioisotopic single-strand conformation polymorphism. RESULTS: This method can detect a loss of heterozygosity (LOH) of the p53 locus from samples containing over 40% tumor derived DNA, and the combination of the three polymorphic markers encompassed 62.4% of Japanese patients as informative. In adenocarcinoma, an LOH was detected in 51.5% (17 of 33) of the samples and in 12.2% (4 of 33) of tubular and/or tubulovillous adenomas. The p53 gene was mutated only in samples carrying an LOH, that is 64.7% (11 of 17) of carcinomas and 25.0% (1 of 4) of adenomas, but there were no mutation in samples retaining both alleles. The presence of an LOH was statistically correlated both with p53 mutation and malignant histology (chi 2 test, p < 0.05). CONCLUSIONS: This method can detect LOH from biopsy material obtained at endoscopy. LOH in the p53 locus precedes mutation of the p53 gene, and its detection provides useful information of malignancy in colorectal tumors.

Detection of K-ras point mutations in mesenteric venous blood from colorectal cancer patients by enriched polymerase chain reaction and single-strand conformation polymorphism analysis.

In order to confirm the presence of cancer cells in mesenteric venous blood and to examine their relationship with the occurrence of liver metastases, we attempted to detect K-ras codon 12 point mutations in perioperative mesenteric blood using enriched polymerase chain reaction and single-strand conformation polymorphism (PCR-SSCP) analysis in 25 patients with primary colorectal tumors carrying K-ras point mutations. Among these patients, three with synchronous liver metastases were included. The same K-ras point mutation (substitution of GAT for GGT) was detected in both the blood and the primary tumor in a Dukes' C patient. We confirmed this result by colony hybridization and estimated the tumor-to-normal cell ratio to be 1:400. This patient has no liver metastases two years after surgery and her carcinoembryonic antigen (CEA) level remains normal. We demonstrated that considerable numbers of cancer cells can be found in mesenteric venous blood during colorectal cancer surgery. However, their potential role in the formation of liver metastases remains unclear.

Sensitive detection of loss of heterozygosity in the TP53 gene in pancreatic adenocarcinoma by fluorescence-based single-strand conformation polymorphism analysis using blunt-end DNA fragments.

We have developed a fluorescence-based single-strand conformation polymorphism analysis to detect Haelil-sensitive polymorphic sites in intron 1 of the TP53 gene. It is important to treat the PCR products with Klenow fragment to remove a 3'-protruding nucleotide from the amplified DNA fragments added during the reaction in order to obtain a single peak for each allele. A comparison of the signal profiles of two alleles with those of normal heterozygotes by data processing using computer software has enabled sensitive detection of loss of heterozygosity (LOH) from clinical materials with a fraction of tumor cells below 10%. In analysis of 14 pancreatic carcinomas in which the proportion of the tumor cells is usually low due to the abundance of the stromal component, 7 samples (50%) were informative and 5 of the 7 (71.4 %) were positive for LOH at the TP53 locus. This approach would be useful for allelotyping tumors with low cellularity, as well as other clinical samples such as biopsied specimens and paraffin embedded tissues.

Analysis of Ki-ras codon 12 mutations in the duodenal juice of patients with pancreatic cancer.

BACKGROUND & AIMS: Point mutations of the Ki-ras gene at codon 12 have been frequently identified in pure pancreatic juice of patients with pancreatic cancer in studies examining pancreatic cancer tissues. The aim of this study was to examine mutations of the Ki-ras codon 12 in the duodenal juice collected from patients with various pancreatic disorders. METHODS: The duodenal juice was collected through a Dreiling tube installed in the duodenum during a secretin test. Analysis of the Ki-ras mutations was performed using the enriched polymerase chain reaction--single-strand conformation polymorphism technique. RESULTS: Point mutations were detected in 12 of 19 patients with pancreatic cancer; of the 12 patients, 10 had ductal tubular adenocarcinoma and 2 intraductal papillary adenocarcinoma. Mutational patterns included GAT (n = 4), GTT (n = 3), CGT (n = 1), and double mutations of GTT and GAT (n = 3) and GAT and CGT (n = 1). In 41 patients with benign pancreatic disorders, a point mutation was detected in only 1 patient with chronic pancreatitis. CONCLUSIONS: Analysis of the Ki-ras codon 12 mutations in the duodenal juice is useful in the diagnosis of pancreatic cancer.

Single-strand conformation polymorphism analysis by perpendicular temperature-gradient gel electrophoresis.

Using a newly developed temperature-gradient gel electrophoresis apparatus, mutations in the K-ras oncogene and p53 tumor suppressor gene were analyzed for single-strand conformation polymorphism (SSCP). The mobilities of single-stranded DNAs, carrying various mutations, change--depending on the gel temperature during electrophoresis. Therefore, temperature-gradient single-strand conformation polymorphism (TG-SSCP) analysis can provide useful information concerning the optimum temperature for SSCP and may also be used to screen for various mutations or polymorphisms in a single electrophoretic run.

Detection of point mutations in the K-ras oncogene at codon 12 in pure pancreatic juice for diagnosis of pancreatic carcinoma.

BACKGROUND: Mutations in the K-ras oncogene at codon 12 are detected at a remarkably high frequency in pancreatic carcinomas and are believed to be a critical event in oncogenesis. The authors attempted to detect K-ras mutations in DNA obtained from pure pancreatic juice collected endoscopically, as a novel diagnostic approach to pancreatic carcinoma. METHODS: K-ras mutations were examined using the two-step polymerase chain reaction (PCR) combined with restriction enzyme digestion, followed by nonradioisotopic single-strand conformation polymorphism (SSCP) analysis. RESULTS: Specific mutations of the K-ras gene at codon 12 were found in six of nine (67%) duct cell carcinomas, all of which were negative by cytodiagnosis of the same pure pancreatic juice. K-ras mutations were not detected in the pancreatic juice from 14 healthy control subjects, 10 patients with chronic pancreatitis, or 3 patients with islet cell tumors. CONCLUSIONS: Detection of K-ras mutation at codon 12 in pancreatic juice is highly specific for diagnosing pancreatic duct cell carcinoma and may be a valuable diagnostic modality for pancreatic carcinoma and for differentiating chronic pancreatitis from carcinoma.

[Sensitive detection of K-ras oncogene codon 12 mutations by nested PCR using mismatched primers and selective digestion of non-mutated PCR fragments with restriction enzyme].

Sensitive detection of K-ras oncogene mutation at codon 12 using nested polymerase chain reactions (PCR) with mismatched primers combined with selective digestion of nonmutated DNA fragments after the first PCR amplification was reported by Levi S, et al. (Cancer Res 51:3497-3502, 1991). We examined the usefulness of this novel technique in cell lines carrying various K-ras codon 12 mutations and clinical samples such as colon carcinoma tissue, corresponding normal colonic mucosa and pancreatic juice obtained from the patients with pancreatic carcinoma undergoing endoscopic retrograde pancreatography (ERP). In analysis of tumor cell lines carrying mutated K-ras at codon 12, the fragment length of the amplified DNA was 135 bp after digestion using restriction enzyme BstN1, whereas those of nonmutated cell lines were 106 bp. This method was highly sensitive to detect mutant DNA diluted at a ratio of 2048 fold with normal DNA samples obtained from peripheral blood lymphocytes. In analysis of clinical samples, 4 out of 10 colorectal carcinoma tissues were positive for K-ras gene mutation at codon 12, however, no mutations were detected in corresponding normal colonic mucosa. In analysis of pancreatic juice taken from the patients with pancreatic carcinoma, 1 out of 3 samples were positive for K-ras mutation at codon 12. Thus, this novel approach was thought to be useful for detection of minimum number of cancer cells from compound samples containing larger amounts of normal cells.

Methods in laboratory investigation. Rapid and simple detection of c-Ki-ras2 gene codon 12 mutations by nonradioisotopic single-strand conformation polymorphism analysis.

BACKGROUND: To achieve simple and rapid detection of codon 12 mutations of the c-Ki-ras2 gene, we developed a nonradioisotopic single-strand conformation polymorphism analysis using silver stain. EXPERIMENTAL DESIGN: After a conventional polymerase chain reaction, amplified DNA fragments were mixed with formamide, heated and subjected to electrophoresis for 1.5 hours using minigels of polyacrylamide. The gels were then silver stained and single-strand DNA fragments were visualized directly. RESULTS: Electrophoresis and subsequent silver staining were completed within 2.5 hours. Plasmids carrying various codon 12 mutations of the c-Ki-ras2 gene were used as controls of Nonradioisotopic single-strand confirmation polymorphism analysis, and all six mutations were successfully separated from the normal allele in a single electrophoretic run. In the analysis of tumor cell lines and tumor samples, the results were identical with those of conventional dot blot hybridization using 32P-labeled oligonucleotide probes. Of 10 colorectal carcinoma tissues examined, 4 tumors were shown to carry codon 12 mutations of the c-Ki-ras2 gene. CONCLUSIONS: We conclude that this novel technique is a rapid, simple and useful method that may replace conventional methods.