Molecular changes in the Ki-ras and APC genes in primary colorectal carcinoma and synchronous metastases compared with the findings in accompanying adenomas.

AIMS: To compare the molecular genetic changes in the Ki-ras and adenomatous polyposis coli (APC) genes between colorectal carcinomas and synchronous metastases, and then to compare and contrast those changes with previously reported changes in the two genes between these carcinomas and accompanying adenomas. This expanded comparison would provide greater understanding of the progression of molecular changes in neoplastic tissue during the development of malignancy from a benign adenoma to carcinoma and then to metastatic spread of the malignancy. METHODS: DNA was extracted from paraffin wax embedded tissue. This was followed by polymerase chain reaction and gel electrophoresis for mutations in the Ki-ras gene using single stranded conformational polymorphism analysis. Amplification of a CA repeat marker was used to assess loss of heterozygosity (LOH) at the APC gene. RESULTS: The findings for the Ki-ras gene in 42 paired carcinomas and synchronous metastases were identical, regardless of whether or not the carcinoma and its companion adenoma had identical Ki-ras findings. The results of APC LOH for 39 paired carcinomas and synchronous metastases were also identical, whether or not the carcinoma and its companion adenoma had identical APC LOH findings. Results were uninformative for three pairs. CONCLUSIONS: With respect to these two genes, a carcinoma may be discordant from its companion adenoma, but the metastasis remains consistent with the colonic carcinoma.

Molecular changes in the Ki-ras and APC genes in colorectal adenomas and carcinomas arising in the same patient.

The purpose of this study was to compare the molecular genetic changes in the Ki-ras and adenomatous polyposis coli (APC) genes between adenomas and carcinomas removed from the same patients. This comparison of benign and malignant tissue would enhance understanding of the progression of molecular changes during the development of colorectal malignancy and similarities between paired lesions could be indicative of a common aetiology. The basic procedures used were DNA extraction from wax blocks of removed tissue, followed by polymerase chain reaction (PCR) and gel electrophoresis for mutations in the Ki-ras gene using single strand conformational polymorphism (SSCP); amplification of a CA repeat marker was used to assess for loss of heterozygosity (LOH) of the APC gene. The main findings in 100 adenoma and carcinoma pairs for the Ki-ras gene were as follows: the frequency of Ki-ras mutation in the adenomas increased with increasing villous component, but did not vary in the paired carcinomas; the frequency of Ki-ras mutation in villous adenomas was greater than in carcinomas; and when both paired lesions had Ki-ras mutations, only 44% had the identical mutation. For the APC gene, the incidence of LOH in the adenomas did not vary by histological type; the LOH status of the adenoma was associated with that of the paired carcinoma; but when both paired lesions had LOH of the APC gene, only 50% had LOH for the same allele. In conclusion, these data on paired adenomas and carcinomas suggest that a Ki-ras mutation is not a consistent finding between the adenoma and carcinoma from the same bowel. The development of LOH of the APC gene is a slightly more consistent finding between the pair, but is not always allelic-specific.

K-ras mutation and loss of heterozygosity of the adenomatous polyposis coli gene in patients with colorectal adenomas with in situ carcinoma.

BACKGROUND: The majority of colorectal carcinomas, if not all, arise from a benign adenoma. The DNA of the carcinomatous cells frequently has mutations in several genes. However, it is not exactly clear when during the neoplastic process each mutation develops. An adenoma with an area of in situ carcinoma provides an opportunity to evaluate genetic changes within a single neoplasia whose separate areas are comprised of both the benign adenoma as well as the malignant carcinoma. METHODS: Thirty-seven neoplasms with areas of both benign adenoma and in situ carcinoma were studied. Both portions were evaluated for loss of heterozygosity (LOH) of the adenomatous polyposis coli (APC) gene and for mutations in codons 12/13 of the K-ras oncogene using the polymerase chain reaction technique. RESULTS: Twenty-eight neoplasms showed no LOH in either portion whereas both portions of 4 neoplasms revealed a loss of heterozygosity. In three lesions the APC gene was normal in the adenomatous portion but LOH was present in the carcinomatous portion. Two neoplasms were uninformative for LOH of the APC gene. Thirteen neoplasms showed the wild-type pattern for the K-ras oncogene whereas 15 contained the identical mutation in both portions. Of the remaining nine neoplasms, six had a K-ras mutation in the adenomatous portion only and three had one pattern in the adenomatous portion and a different pattern in the in situ carcinoma portion. CONCLUSIONS: LOH of the APC gene is an early and persistent feature in the evolution of a benign colorectal adenoma into an in situ carcinoma. There is less consistency regarding K-ras mutations; one in five in situ carcinomas contains a K-ras mutation different from that observed in the adenomatous portion.

Comparison of allelic ratios from paired blood and paraffin-embedded normal tissue for use in a polymerase chain reaction to assess loss of heterozygosity.

BACKGROUND: One method to assess loss of heterozygosity (LOH) of various genes is the amplification of DNA from neoplastic tissue by using microsatellite markers. LOH can best be considered on a quantitative basis as a comparison of allelic ratios of neoplastic tissue to that of the normal control. We will illustrate through quantitative methods the importance of using the appropriate controls when determining allelic loss. METHODS AND RESULTS: DNA extracted from 28 paired blood and formalin-fixed, paraffin-embedded normal mucosal tissue was amplified using the DP1 microsatellite marker, consisting of a variable number of CA repeats. This marker is located within the D5S346 (DP1) region on chromosome 5 and is linked to the adenomatous polyposis coli gene. Allelic ratios were calculated after scanning autoradiographs on a densitometer. Ratio values approaching 1 were observed when the two alleles were close in molecular weight, whereas ratios less than 1 were detected when the two alleles had very different molecular weights. This discrepancy was more pronounced in paraffin-embedded tissue than with blood samples. CONCLUSION: For LOH amplification assays, it is best to use normal control samples that are of the same tissue source as the neoplastic sample being analyzed. When assessing LOH in neoplastic tissue, a quantitative value rather than visual assessment of the alleles should be considered. The values may be normalized by dividing the ratio of the two tumor alleles by the ratio of the two normal alleles.

Conformational properties of Z-forming DNA oligomers bearing terminal unpaired bases.

Three sets of semi-self-complementary deoxyribonucleotide decamers with the sequence XX-(5meCG)4, (5meCG)4-XX, or Y-(5meCG)4-Y, where XX = AA, CC, GG, or TT and Y = A, C, G, or T, were synthesized along with the self-complementary octamer (5meCG)4. The 8-mer duplex readily undergoes a B-to-Z conformational conversion upon increasing the NaCl concentration with a transitional midpoint of approximately 1.1 M NaCl. The 10-mers should form 8-bp duplexes a with core sequence of [(5meCG)4]2 with 5'-XX overhangs, 3'-XX overhangs, or 5',3'-Y/Y mismatches. Circular dichroism was employed to determine the conformations of all oligomers. Salt titrations were performed to measure the effect of overhangs and terminal mismatches on the B-to-Z conversion. In general, the presence of 5'-XX overhangs results in a transition midpoint equal to or slightly higher than the control, whereas the presence of 3'-XX overhangs results in a transition midpoint slightly lower than the control. The 3'-CC and 5'-GG overhangs are exceptions, with transition midpoints much higher than the control. These oligomers apparently form duplexes with 5',3'-C/C or 5',3'-G/G mismatches abutting a [(G5meC)4]2 duplex core. The presence of terminal mismatches in the third set of oligomers results in transition midpoints higher than the control. Ultraviolet absorbance methods were used to evaluate the effect of the various stacking motifs of the 10-mers on the thermodynamics of melting relative to the 8-mer for both B and Z conformations. We found that in both the B and Z conformations, the presence of an overhang stabilizes the [(5meCG)4]2 duplex, with the 5' overhangs having a greater stabilizing effect relative to the 3' overhangs. The presence of 5',3'-Y/Y mismatches also imparts a stabilizing effect on the control 8-mer in both the B and Z conformations. These results are discussed in terms of stacking interactions of the terminal unpaired bases.

Sequence and environmental effects on the self-assembly of DNA oligomers possessing GxT2Gy segments.

It is well-known that DNA oligomers possessing contiguous guanine bases can assume non-Watson-Crick type structures through the formation of four-stranded species. The architecture of these four-stranded structures is highly dependent upon the sequence of the DNA and the conditions (e.g., buffer, pH, ionic strength, cations present, and temperature) under which the DNA is prepared. This lab has previously reported the self-assembly of DNA oligomers of sequence C4T4G4T1-4G4 into multistranded high molecular weight species [Dai, T.-Y., Marotta, S. P., & Sheardy, R. D. (1995) Biochemistry 34, 3655-3662]. In order to further investigate the sequence and environmental effects on the self-assembly of DNA oligomers possessing GxT2Gy (where x = 1, 3, or 4 and y = 2-5) segments, the synthesis of a number of such oligomers was undertaken. DNA samples were prepared in standard phosphate buffer (10 mM phosphate, pH 7.0) and NaCl, KCl and/or MgCl2 added to different concentrations in order to evaluate the influence of the cations and their concentrations on the self-assembly of the DNA oligomers. The self-assembly of these oligomers was monitored by nondenaturing polyacrylamide gel electrophoresis and circular dichroism studies. Electrophoresis of the oligomers in either 100 mM K+ or 50 mM Na+ with 50 mM K+ indicated the formation of one or two molecular species for these oligomers. In contrast, electrophoresis of these oligomers in the presence of both 100 mM K+ and 20 mM Mg2+ give a ladder of multiple bands of high molecular weight indicative of multistanded DNA structure formation. The results presented here indicate that self-assembly into high molecular weight species is favored by the presence of Mg2+ as well as the presence of four or more bases in the terminal Gy segment. These results also suggest that the structure of telomeric DNA, which possesses similar sequences, may be quite unusual.

Self-assembly of DNA oligomers into high molecular weight species.

Thermal denaturation, gel electrophoresis, and circular dichroism methods were used to characterize DNA oligomers possessing one or two segments of four contiguous G bases in order to investigate their environmentally dependent conformational properties. The sequences of the oligomers studied were the following: HP1-T series, C4T4G4T5-8; HP1-TG series, C4T4G4T1-4G4. In NaCl at concentrations up to 200 mM, the melting profiles of these oligomers are characterized by single inflection points whose Tm values are independent of DNA concentration. In addition, these oligomers run as single bands in polyacrylamide gels under those same conditions as well as in 100 mM K+ or 20 mM Mg2+. These data suggest that these oligomers exist as intramolecular hairpins comprised of four G:C base pairs in the stems, loops of four T bases, and 3'-overhangs of T5-8 or T1-4G4. In the presence of 100 mM K+ plus 20 mM Mg2+, however, gel electrophoresis indicates that oligomers of the HP1-T series exist as equilibria between parent hairpins and four-stranded structures (i.e., quadraplexes). Quadraplex formation for any member of the HP1-T series requires unfolding of the hairpin, exposing the G4 segment prior to quadraplexation. Members of the HP1-TG series self-assemble into multistranded species of high molecular weight in the presence of 100 mM K+ plus 20 mM Mg2+. For this series of oligomers, the data suggest that these higher order species arise from successive additions of parent oligomer to an initially formed quadraplex.(ABSTRACT TRUNCATED AT 250 WORDS)