A computational integrative approach based on alternative splicing analysis to compare immortalized and primary cancer cells

Immortalized cell lines are widely used to study the effectiveness and toxicity of anti cancer drugs as well as to assess the phenotypic characteristics of cancer cells, such as proliferation and migration ability. Unfortunately, cell lines often show extremely different properties than tumor tissues. Also the primary cells, that are deprived of the in vivo environment, might adapt to artificial conditions, and differ from the tissue they should represent. Despite these considerations, cell lines are still one of the most used cancer models due to their availability and capability to expand without limitation, but the clinical relevance of their use is still a big issue in cancer research. Many studies tried to overcome this task, comparing cell lines and tumor samples through the definition of the genomic and transcriptomic differences. To this aim, most of them used nucleotide variation or gene expression data. Here we introduce a different strategy based on alternative splicing detection and integration of DNA and RNA sequencing data, to explore the differences between immortalized and tissue-derived cells at isoforms level. Furthermore, in order to better investigate the heterogeneity of both cell populations, we took advantage of a public available dataset obtained with a new simultaneous omics single cell sequencing methodology. The proposed pipeline allowed us to identify, through a computational and prediction approach, putative mutated and alternative spliced transcripts responsible for the dissimilarity between immortalized and primary hepato carcinoma cells.