Two regions of homozygosity on chromosome 3p in squamous cell carcinoma of the head and neck: Comparison with cytogenetic analysis

Background. Loss effecting the short arm of chromosome 3 occurs in nearly 60% of squamous cell carcinomas of the head and neck (SCCHN). Karyotype analysis indicated that these losses occur in two regions, 3p13- p14 and 3p21-p24. To test these findings, we examined tumor DNA from 38 SCCHN cell lines for heterozygosity and homozygosity at 6 polymorphic loci spanning this region. Methods. The polymerase chain reaction (PCR) was used to amplify polymorphic restriction sites on 3p, the amplified products were digested with the appropriate restriction enzyme, electrophoresed on agarose gels, and assessed for the presence of one or both alleles. The 38 SCCHN cell lines were established from 31 patients and included 16 that had been karyotyped. In 6 cases two or three tumor cell lines established from separate tumors in the same patients were studied. Results. The cell lines exhibited a very low frequency of heterozygosity for the regions 3p12-3p21 (D3S3, D3S30 and D3S2) and distal 3p21-3p24 (D3F15S2 and THRB), when compared with that observed in the normal population. In contrast, D3S32, located within 3p21, was heterozygous in 38% of the tumors which is close to the frequency seen in the normal population (50%). In most cases the PCR results were consistent with the cytogenetic predictions. However, in 4 cell lines 3p loss was predicted from the karyotype, but heterozygosity for D3S32 was present. Conclusions. These experiments support cytogenetic data that indicate two regions of 3p loss in SCCHN tumors. The 3p regions that show a high frequency of homozygosity may contain tumor suppressor genes involved in the development and/or progression of squamous cancer. The region surrounding D3S32 may contain an essential gene that is conserved in two copies even when much of 3p is lost.