Comparative application of antibody and gene array for expression profiling in human squamous cell lung carcinoma

Expression profiling by gene microarray techniques have been developed to predict malignant tissue but there are no experiences with the application of antibody arrays to identify malignancy-related proteins. Because altered protein patterns might also better interpret biological processes, we applied tumour samples from 12 patients with squamous cell lung carcinoma and individual lung tissue controls to antibody arrays spotted with 378 distinct monoclonal antibodies. Array analysis defined 20 proteins with higher and nine with lower abundance in lung tumours. Comparison with gene microarray data revealed that 31% of the differentially regulated proteins correlate with altered mRNA expression in squamous cell lung carcinomas, including PEX1, MKK7 and HDAC3 for up-regulated proteins. The histone deacetylase (HDAC) 3 was investigated in detail by immunoblot analysis showing that HDAC3 is indeed elevated in 92% of tumours ( n = 22/24; P < 0.001). Thus, antibody microarrays can be useful for detection of some target proteins related to lung cancer.