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Deletion analysis of the p16/CDKN2 gene in head and neck squamous cell carcinoma using quantitative polymerase chain
J D Rawnsley1, E S Srivatsan, R Chakrabarti
1Department of Surgery, University of California-Los Angeles School of Medicine, USA.
Background:
Recently, the p16/CDKN2/MTS1 gene in the 9p21-22 region has been offered as a candidate tumor suppressor gene. We examined the frequency of hemizygous and homozygous deletions of p16/CDKN2 in head and neck squamous cell carcinoma (HNSCC) using a quantitative polymerase chain reaction (PCR) method.
Design:
Twenty-one HNSCC and 12 corresponding normal DNA samples were examined for deletion of p16/ CDKN2 using PCR amplification and fluorescent quantification of DNA. All tumor and normal DNA samples were also amplified with fluorescein-labeled primers for a control DNA marker on chromosome 8p (D8S265). The ratios of the observed fluorescence of the p16/CDKN2 and 8p PCR products were compared.
Setting And Participants:
Patients with HNSCC scheduled to undergo surgical resection of their tumors were recruited. After the specimen was removed, a portion of the tissue was snap frozen for further DNA extraction.
Results:
Eight tumors (38%) had p16/CDKN2-D8S265 ratios of greater than 0.75; 8 tumors (38%), from 0.25 to 0.75; and 5 tumors (24%), of less than 0.25, the average ratio in this last group being 0.06.
Conclusions:
These ratios suggest a higher rate of homozygous deletion than previously reported and significant probable hemizygous deletion of the p16/CDKN2 gene in HNSCC.
Insights
This study investigated deletions of the p16/CDKN2 tumor suppressor gene in head and neck squamous cell carcinoma (HNSCC). Findings suggest a higher frequency of homozygous and hemizygous deletions than previously reported in HNSCC.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- The p16/CDKN2/MTS1 gene, located on chromosome 9p21-22, is a potential tumor suppressor.
- Alterations in this gene are implicated in various cancers, including head and neck squamous cell carcinoma (HNSCC).
Purpose of the Study:
- To determine the frequency of hemizygous and homozygous deletions of the p16/CDKN2 gene in HNSCC.
- To assess the role of p16/CDKN2 gene alterations in the development of HNSCC.
Main Methods:
- Quantitative polymerase chain reaction (PCR) was employed to analyze DNA samples from 21 HNSCC tumors and 12 normal tissues.
- Fluorescent quantification of PCR products for p16/CDKN2 and a control marker on chromosome 8p (D8S265) allowed for ratio comparisons.
Main Results:
- Analysis revealed varying deletion patterns: 38% of tumors showed high p16/CDKN2-D8S265 ratios (>0.75), 38% had intermediate ratios (0.25-0.75), and 24% exhibited low ratios (<0.25).
- The average ratio in the low-ratio group was 0.06, indicating substantial gene loss.
Conclusions:
- The observed deletion rates suggest a higher incidence of homozygous and probable hemizygous deletion of p16/CDKN2 in HNSCC than previously documented.
- These findings underscore the potential significance of p16/CDKN2 gene alterations in HNSCC pathogenesis.