Identification of a novel protein isoform derived from cancer-related splicing variants using combined analysis of transcriptome and proteome

Splicing variation enhances proteome diversity and modulates cancer-associated proteins. Thus, the identification of alternative splice forms is significant for discovery of new cancer-related biomarkers. However, relatively few screening approaches of alternative splicing via proteomics have been reported. In the present study, we describe a combined analysis with proteome and transcriptome to simultaneously identify cancer-related splicing variants and splicing variant-derived protein fragments that are differentially expressed in a highly metastatic gastric cancer cell line MKN45P versus its parental cell line MKN45. We found three potential alternative-spliced genes using MS-based shotgun method and two different micro-array platforms. Among them, aldolase C, fructose-bisphosphate (ALDOC) was predicted to have novel alternative splice forms. We successfully identified and validated novel splice forms of ALDOC gene by RT-PCR and DNA sequencing analyses, the expression level of which were higher in MKN45P than in MKN45. Furthermore, the protein fragment derived from the validated splicing variant was identified using custom-built data set including sequences of ALDOC variants in MS/MS analysis. Our combined analysis will be a promising technique for screening of cancer-related splicing variants and their protein isoforms.