Genomic analysis has demonstrated that alternative splicing occurs in up to 60% of human genes with the majority reported to be associated with tissue-type or with normal development. Some individual gene studies have found that alternative splice variants are associated with cancer and play important roles in apoptosis, transformation, motility, and metastasis of tumors. We present an exploratory genome-wide study using Affymetrix Human Exon arrays to identify splice variant expression differences between normal lung and lung adenocarcinoma.

40 paired tumor-normal specimens from 20 patients (14 female and 6 male) with lung adenocarcinoma were used for the study. RNA from each sample was labeled and hybridized on GeneChip Human Exon 1.0 ST Arrays according to Affymetrix protocols. Analysis was focused initially on the 19,076 RefSeq genes for which there are ~285,000 probe sets on the arrays. Probe-level analysis with RMA and alternative splicing analysis with ANOVA were performed using the Partek Genomics Suite. Putative alternately spliced genes were entered into the Ingenuity Pathway Analysis software and genes reported to be associated with cancer were chosen for more detailed examination.
 >2051 genes were identified as alternately spliced between tumor and normal with p<0.0001. Function analysis indicated that the largest subset ((447 (21%)) of these genes were cancer related. Of the 447 cancer-related genes, 47 showed high frequency (≥ 10 of 20 patients) for the same alternate splicing event. For 19 genes, 2 or 3 alternative transcripts have been recorded in the RefSeq database. Alternate splicing in some these genes has been shown association with caner but that in some genes has not been reported in cancer. These genes include ERG (20/20 paired samples), EGFR4 (18/20) and CDKN1A (14/20). The remaining 28 genes may represent novel splicing events that occur at high frequency in lung tumors and include genes such as PTHR1 (20/20), RASIP1 (20/20) and ARMET (17/20). Two genes, CDKN2A and CDH3, also appear to show gender related, cancer-specific alteration. Alternative splicing of these genes in tumor vs normal occurs only in paired samples from female patients. Pathway analysis of the 47 alternately spliced genes indicates that 20 genes are associated with apoptosis, 22 with cell death, 19 with tumorigenesis, 17 with tumor growth, 12 with proliferation, and 9 with invasion.
 >We have demonstrated that alternative splicing in a high frequency occurs in lung adenocarcinomas. Two genes may also have gender-specific alternate splicing in tumors; an interesting finding given the epidemiologic and survival differences between men and women with lung adenocarcinoma. If these findings can be verified, alternate splice events could prove useful for lung cancer diagnosis and as novel targets for therapeutic development.

98th AACR Annual Meeting-- Apr 14-18, 2007; Los Angeles, CA