Detailed gene expression analysis but not microsatellite marker analysis of 9p21 reveals differential defects in the INK4a gene locus in the majorityof head and neck cancers

The INK4a gene locus on chromosome 9p21 encodes two proteins, p16(INK4a) an d p14(ARF), which influence cell cycle control regulated by pRb and p53, Th e objective of this study was to use different methods for the analysis of the incidence of changes, at the INK4a locus in head and neck cancer (HNSCC ), Primary tumours were analysed for allelic imbalances (Al) with microsate llite markers for chromosome 9, by immunohistochemistry (IHC) and IHC with enhanced sensitivity by tyramide signal amplification (TSA-IHC), and by RT- PCR, No homozygous deletions at 9p21 were detected. AI at 9p21, which was f ound in approximately 60% of the tumours, completely failed to indicate the functional inactivation of the two INK4a gene products. Immunostaining of normal squamous epithelia revealed very low levels of p16(INK4a), whereas p 14(ARF) was readily detectable. In 160 tumours, IHC suggested a loss of p16 (INK4a) expression in 90%,. However, by TSA-IHC, only 53.7% showed loss of p16(INK4a) expression, and this was consistent with the RT-PCR analyses, In 100 tumours analysed for both proteins, selective loss of p16(INK4a) occur red in 37%; loss of p14(ARF) was found in only 15%, and selective loss in o nly 4%; 11% of the tumours had lost both proteins. We conclude that only IH C with high sensitivity and the combined expression analysis of mRNAs and p roteins is suitable for studying the role of INK4a in HNSCC, The INK4a gene expression defects are frequent but not universal and primarily affect p16 (INK4a) Their clinical impart is still not clear. Copyright (C) 2001 John W iley & Sons, Ltd.