Single-step direct PCR amplification from solid tissues

Extracción de adn con resina chelex en el análisis de la amplificación oncogénica en carcinomas de cabeza y cuello

DNA extraction from tissues can be the most laborious and complex step in amplifying DNA by PCR when phenol-choroform procedure is used. We compare this lengthy, slow and expensive extraction method with other two based in the use of Chelex-100 resin. This chelating resin has been applied for extracting DNA from different tissues to use with the PCR. These procedures are simple, rapid and do not require multiple steps. In this study we compared DNA extraction from 30 head and neck squamous cell carcinomas (HNSCC) using organic solvent precipitation, Chelex 100 resin with and without proteinase K pretreatment. The results show that proteinase K-Chelex 100 procedure is as efficient as the phenol-chloroform one.

Novel method for simultaneous analysis of p53 and K-ras mutations and p53 protein expression in single histologic sections

BACKGROUND AND OBJECTIVE

Abnormal protein expression and gene mutation should be examined on exactly identified lesions. To perform simultaneous analyses of oncogene or tumor suppressor gene mutations and related protein expression in single histologic sections, we have developed a novel method using an antigen-retrieval solution for a polymerase chain reaction template before immunohistochemical staining.

METHODS

Using 20 cases of sporadic colorectal carcinoma, several kinds of antigen-retrieval solutions were tested after heating rehydrated, 4-microm-thick, formalin-fixed, paraffin-embedded histologic sections at 96 degrees C for 20 minutes. Polymerase chain reaction-single-strand conformation polymorphism analysis was conducted for p53 (exons 5 through 9) and K-ras (exons 1 and 2), and the histologic sections were then immunostained with monoclonal antibody against p53.

RESULTS

DNA analysis of antigen-retrieval solutions was possible in all 20 cases and revealed completely consistent results (100%) with fresh cancer tissue and microdissected cancer tissue of paraffin-embedded histologic sections. With this method, K-ras mutations were positive in 10 of 20 cases (exon 1 in 9 cases and exon 2 in 1 case) and p53 mutations were positive in 9 of 20 cases (exon 5 in 4 cases, exon 6 in 1, exon 7 in 3, and exon 8 in 1 case), with 8 of the 9 p53 mutation cases showing diffuse p53 protein expression on immunostaining. Base alterations of all abnormal conformers were confirmed with direct sequencing. For polymerase chain reaction-single-strand conformation polymorphism analysis, sodium citrate buffer (pH 6.0) was found to be the optimal antigen-retrieval solution.

CONCLUSIONS

This newly developed method can be used for routine immunostaining and genetic analysis with single histologic sections.

Comparative genomic hybridization studies in hydatidiform moles and choriocarcinoma: amplification of 7q21-q31 and loss of 8p12-p21 in choriocarcinoma

Comparative genomic hybridization (CGH) was utilized to investigate genetic changes from archived cases of choriocarcinoma (n = 12) and hydatidiform moles (n = 7). Test DNA was extracted from paraffin-embedded tissues, amplified using total universal PCR, and co-hybridized with control DNA to normal metaphases. Comparative genomic hybridization findings showed chromosomal imbalances in 9 of 12 cases of choriocarcinoma. By contrast, all hydatidiform moles showed normal CGH profiles. Consistent findings in choriocarcinoma included deletion at 8p (5 cases) and amplification at 7q (4 cases). A tumor suppressor gene (e.g., N33) at 8p and/or a growth regulator at 7q could play a role in the initiation of choriocarcinoma and its progression. This is the first study showing specific alterations in choriocarcinomas by CGH, and illustrates the utility of this technique in elucidating genetic changes in gynecological tumors.

Rapid microsatellite analysis of paraffin embedded tumour specimens from patients with hereditary non-polyposis colorectal cancer

In screening for hereditary non-polyposis colorectal cancer (HNPCC)--an autosomal dominant disorder characterised by mutations in mismatch repair genes--detection of microsatellite instability is an important diagnostic criterion. The mono- or dinucleotide repeat DNA sequences are usually amplified from formalin fixed, paraffin embedded tissue by polymerase chain reaction after numerous time consuming steps including deparaffinisation, DNA extraction, and purification. A rapid single step method for direct DNA analysis is described, based on preincubation of paraffin embedded tissue with Triton X-100 followed by DNA amplification with fluorescence labelled primers and electrophoresis in an automated sequencer. This procedure allows precise allele sizing and analysis of genetic instability, is more efficient and time saving, reduces the risk of contamination, and is therefore of particular interest in screening for HNPCC.

Frequency and clinico-pathological associations of ras mutations in colorectal cancer in the Victorian population

BACKGROUND

Mutations in the oncogene ras occur in 20-50% of colorectal cancers. The presence of these mutations allows screening tests to be developed based on the identification of mutant DNA in cells derived from cancers. A study of the prevalence and clinicopathological associations of ras mutations was undertaken.

METHODS

The frequency of mutations in codons 12 and 13 of the K-ras gene was investigated in 103 colorectal carcinomas using restriction fragment length polymorphism.

RESULTS

Mutations were detected in 32% (33/103) of the tumours, predominantly in codon 12 (25/33). No mutations were detected in normal-appearing mucosa from the same patients.

CONCLUSIONS

Analysis of the frequency of ras mutations compared with various independent clinical variables revealed a sex-linked relationship between the presence of a ras mutation and nodal status but no correlation with any other clinical parameter was found. The findings suggest that screening tests based on ras mutation detection may lack sensitivity because of the presence of mutations in only 32% of tumours.