Computational analysis of circadian splicing events in human cancer cell lines and mammalian tissues
The circadian clock regulates physiology and behavior of various organisms in synchrony with daily environmental rhythms. At the cellular level, circadian rhythmicity is driven by the interplay of clock genes and proteins that interact via negative feedback loops, thereby causing oscillations with a period of 24 h in the expression of numerous target genes. The resulting rhythms in the abundance of proteins and other biomolecules are responsible for the temporal organization of diverse biological processes. Accumulating evidence suggests that alternative splicing might be one of these clock-controlled processes. Alternative splicing describes a versatile mechanism of gene regulation that generates several distinct protein isoforms from a single gene via the differential inclusion or exclusion of alternate RNA regions. Both disruptions of the circadian clock and aberrant splicing are associated with carcinogenesis and tumor progression. This dissertation seeks to answer the question whether mammalian alternative splicing is regulated by the circadian clock, and whether the hypothesized regulation differs between cancer cells in different tumor stages. In particular, it tries to elucidate whether changes in circadian regulated splicing events could be responsible for the production of protein isoforms that contribute to the malignant development of cancer cells. The study is based on data from two human colon cancer cell lines, SW480 and SW620, that have been derived from a primary tumor and a metastasis of the same patient and thus serve as an in vitro model of colorectal tumor progression. A computational analysis was conducted to identify 24 h rhythmic genes and alternative splicing events on transcriptome-level based on the time-series data of both cell lines. As a reference, previously published time-series data of numerous healthy tissues from mouse and baboon organs were analyzed. The analysis revealed differences in the circadian phenotype of the two cell lines, with the metastasis-derived cell line SW620 exhibiting a stronger dysregulation of circadian rhythmicity. Furthermore, this work shows that splicing-related genes and putative splicing events display 24 h rhythms that differ between primary tumor- and metastasis-derived cells. Both in healthy tissues and cancer cells, rhythmic splicing was found to affect many genes that are themselves involved in splicing, suggesting a partial autoregulation of the process. Several of the spliced candidate genes encode for protein isoforms that are involved in processes promoting tumor progression, such as migration and angiogenesis. Taken together, the results presented in this dissertation point to a circadian regulation of alternative splicing that plays a role in cancer development.