Loss of heterozygosity detected in formalin-fixed, paraffin-embedded tissue of colorectal carcinoma using a microsatellite located within the deleted in colorectal carcinoma gene

Short tandem repeat (STR) instability in the oral mucosa of patients submitted to fixed orthodontic therapy: a limitation of STR profile quality for human identification

The purpose of this study was to evaluate changes in short tandem repeat (STR) profile quality before and after fixed orthodontic therapy. Samples of oral epithelial cells were obtained from 28 volunteers who had an indication for orthodontic treatment. The samples were collected before and three months after starting orthodontic treatment with fixed appliances. DNA extraction and integrity were evaluated by electrophoresis, and STR profiles were obtained by polymerase chain reaction amplification and STR typing via capillary electrophoresis. DNA electrophoresis showed a higher proportion (7/28, 25%) of DNA degradation in the samples collected after fixed orthodontic treatment compared to those obtained before starting orthodontic therapy (3/28, 11%), however, changes in DNA were not significant (p=0.289). In concordance all STR profiles showed complete genotyping; however, imbalances in the size of heterozygotes and in the signal were detected in 25% of STR profiles after orthodontic therapy. Moreover, STR instability was demonstrated by an increase in stutter bands detected in 60% of the DNA profiles after treatment and a spurious allele of the D195433 marker was found in one sample after treatment. The STR profiles of samples obtained from the oral cavity with orthodontic appliances should be interpreted with caution. STR instability increases the incidence of artifacts that could compromise the quality of the results of tests performed in forensic DNA laboratories.

A comparative microsatellite analysis of colorectal cancer in patients <35 years and >50 years of age

OBJECTIVE

This study was undertaken to investigate microsatellite instability and allelic imbalance in a cohort of young patients (<35 yr) and older patients (>50 yr) with sporadic colorectal carcinomas in the Kwa-Zulu Natal region of South Africa.

METHODS

Normal and tumor DNA was isolated from formalin-fixed, paraffin-embedded tissue from 32 patients <35 yr and from 50 patients >50 yr of age. Tumors were staged using the modified Astler-Coller classification. Fluorescent-based DNA technology using an automated DNA sequencer (Alf Express Automated DNA Sequencer) was employed. CY5 labeled primers for microsatellite markers in chromosomes 18, 3, and 2 (DCC, D18S34, D18S58, D3S659, D3S1255, and D2S123) were used. The data were captured and analyzed using the Fragment Manager Software.

RESULTS

The informativity of the microsatellite markers ranged from 50% to 71.8%. Microsatellite instability was seen in 44 of 82 cases (53.7%) for at least one of the six markers. Low frequency MSI (MSI-L) was seen in 28 of 82 cases (34.2%) and high frequency MSI (MSI-H) in 16 of 82 cases (19.5%). In the <35-yr age group, MSI-L was seen in six cases (18.8%) and MSI-H in 10 cases (31.3%). In the >50 yr age group, MSI-L was seen in 22 cases (44%) and MSI-H in six cases (12%). Twelve cases showed AI for DCC, seven showed AI for D18S34, and four showed AI for D18S58. MSI was found in 13, 10, and 16 cases for each of these markers, respectively. Allelic imbalance for the D3S659, D2S123, and D3S1255 loci was 3 of 82 cases (3.7%), 10 of 82 cases (12.2%), and 13 of 80 cases (16.3%), respectively. MSI was 14.6% for both D3S659 and D2S123 and was 6.3% for the D3S1255 marker.

CONCLUSIONS

Loss of heterozygosity in the region of the DCC locus ranged from 9.3% to 26.7%, and MSI ranged from 12.2% to 19.5% of cases. Allelic imbalance in the region of the repair genes ranged from 6.8% to 27% in the informative cases. MSI, however, ranged from 5% to 12%. These figures are similar to those of other studies done in other parts of the world. Further, no correlation was found between the genetic results and clinicopathological parameters: i.e., tumor stage, grade and clinical parameters of age and gender. However, genetic abnormalities were more common in the younger cohort of patients, and this may translate into the earlier age of presentation. This opens the potential for genetic screening.

Allelic imbalance and microsatellite instability in chromosomes 2p, 3p, 5q, and 18q in esophageal squamous carcinoma in patients from South Africa

Microsatellite polymerase chain reaction (PCR) and fluorescent DNA technology was used to assess allelic imbalance (AI) or loss of heterozygosity (LOH) and microsatellite instability (MSI) in chromosomes 2p, 3p, 5q, and 18q in esophagectomy specimens from 39 patients who had squamous carcinoma and who lived in a high-incidence geographic location in South Africa. The squamous carcinomas were graded by conventional light microscopy and staged using the tumor-node-metastasis (TNM)-Union Internationale Contre Le Cancer (UICC) criteria. The DNA was isolated using proteinase K digestion and standard phenol-chloroform extraction procedure. Microsatellite PCR was performed using fluorescent, CY5-labeled primers for the following markers: D2S123 (2p), D3S659 (3p), D3S1255 (3p), D5S346 (5q), DCC (18q), D18S34 (18q), and D18S58 (18q). These markers were chosen because they are the most frequently used and most informative markers for these particular gene loci. Results were analyzed using software attached to an automated DNA sequencer. Molecular changes obtained were correlated with clinicopathologic parameters. Molecular analysis did not correlate with clinicopathologic features, such as tumor grade, stage, or lymph node status. No correlation with patient outcome was seen, though only limited follow-ups were obtained. Rates of MSI and LOH on 3p and 18q in these specimens are similar to the range seen in studies from other geographic areas. However, a striking point of departure is the high LOH (30% of informative cases) seen on 2p.

Relationship between loss of heterozygosity of deleted in colorectal carcinoma gene microsatellites and prognosis of colorectal adenocarcinoma

AIM: To investigate the relationship between the loss of heterozygosity (LOH) of microsatellites on the deleted in colorectal carcinoma (DCC) gene and prognosis of colorectal adenocarcinoma.

METHODS: A retrospective study of 58 colorectal adenocarcinoma cases with follow-up data and paired control normal mucosal tissues from 1983 to 1985 from files from the West China University of Medical Sciences Department of Pathology was carried out by PCR microsatellite analysis. Sixteen, 35, and seven cases had well-, moderately, and poorly differentiated tumors, respectively; 11, 30, and 17 cases were staged as Dukes’ A, B, and C, respectively.

RESULTS: LOH of DCC microsatellites was detected in 18 cases (31.0%). The 5-year survival rate between LOH-positive and LOH-negative patients was 44.4% and 77.5%, respectively (P < 0.05). The results suggest that LOH of DCC microsatellites correlate with prognosis but not with differentiation (P > 0.05) and Dukes’ stage (P > 0.05) in colorectal adenocarcinoma.

CONCLUSION: LOH of DCC microsatellites may be a marker of malignancy. Combined with the traditional prognostic indicators, LOH can predict prognosis of colorectal adenocarcinoma.

Loss of the adenomatous polyposis coli gene and human papillomavirus infection in oral carcinogenesis

Recent evidence suggests that loss of heterozygosity (LOH) of the adenomatous polyposis coli (APC) gene plays a role in colorectal tumorigenesis and other cancers. However, little is known as to whether the APC gene contributes to the pathogenesis of oral squamous cell carcinoma. To assess involvement of both the APC gene and the human papillomavirus (HPV) in the development of oral pre-malignant and malignant lesions, we analysed DNA from 14 paired oral normal and pre-malignant or malignant paraffin-embedded biopsy specimens, and DNA from cultured normal and HPV 16-immortalised oral epithelial cells for the presence of LOH of APC and for HPV infection, using PCR based techniques. LOH of APC occurred in 80% of cases of oral epithelial dysplasia, 67% of carcinoma in situ, 50% of invasive squamous cell carcinoma cases, and in the HPV 16-immortalised oral epithelial cells. HPV was detected in half of the biopsy specimens, with HPV 16 as the dominant type. More than half of the carcinoma cases were found to contain both LOH of APC and HPV infection. These results suggest that LOH of APC is an early event during oral tumorigenesis. Our findings also suggest a strong correlation between HPV infection, particularly HPV 16, and LOH of the APC gene in oral squamous cell carcinomas.

The polymerase chain reaction in histopathology

Thanks to the advent of the polymerase chain reaction (PCR) molecular genetic study of histological samples is now a relatively straightforward task and the vast histopathology archives are now open to molecular analysis. In this review we outline technical aspects of PCR analysis of histological material and evaluate its application to the diagnosis and study of genetic, infectious and neoplastic disease. In addition, we describe a number of newly developed methods for the correlation of PCR analysis with histology, which will aid the understanding of the molecular basis of pathological processes.