AIMS: The differential display reverse transcription polymerase chain reaction (DDRT-PCR) technique was used to search for differences between the mRNA expression profiles of squamous cell carcinoma (SCC) cell lines established from head and neck tumours and normal keratinocytes from the mucosa of the upper aerodigestive tract. METHODS: Total RNA prepared from both cell types was reverse transcribed into cDNA then amplified in a PCR mixture. To compare the electrophoretic patterns, mRNAs were amplified by nested PCR using specific oligonucleotides. Additionally, using labelled cDNA probes, northern hybridisation was carried out on three cancer cell lines of different origin, a biopsy from a parotid gland pleomorphic adenoma, healthy mucosa, and keratinocytes. RESULTS: Comparison of the separated bands revealed a fragment with a differential expression pattern in the SCC cells. This cloned sequence of a 336 base pair mRNA fragment exhibited no significant homology with known transcripts. Additionally, after amplification and sequencing of the 3' end of the fragment no homology with a known human gene sequence was found. However, low homology with a genomic sequence of a nematode was found. Northern hybridisation confirmed the selective expression of this fragment in SCC cells versus the cancer cell lines of different origin, the biopsy of the pleomorphic adenoma, keratinocytes, and healthy mucosa. CONCLUSIONS: This is the first differentially expressed human genome transcript of squamous cell carcinoma of the head and neck identified by DDRT-PCR. It may prove useful, in the future, to characterise this tumour type.
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