MicroRNAs and their processing factors in Caenorhabditis elegans and human cancers

MicroRNAs (miRNAs) are small noncoding RNAs approximately 20-22 nucleotides (nt) long. These small RNAs (sRNAs) was initially discovered in Caenorhabditis elegans (C. elegans), but is conserved in over 50 animal species. According to miRbase, a database of miRNA sequences from various species, humans have over 2500 different miRNAs and estimated to regulate over 60% of the protein coding genes in humans. Due to their role in gene regulation, they are important for controlling key processes in the cell, and changes in miRNA expression in cell can have catastrophic consequences.

In this thesis we explore the role of miRNA and their biogenesis factor. We begin by studying the first miRNA to be identified in humans, let.7. We use the C. elegans model system with different genetic strains to describe an unknown role for this miRNA. The unravelling of this new role highlights the importance of miRNA as important regulator in cells not only for protein coding transcripts but also transcripts that do not code for proteins. The findings of this study opens up new and exciting research possibilities for miRNAs.

Because of miRNAs importance in controlling key cellular processes in cells. Changes in their expression patterns can lead to severe effect. In study II we explore one such event, development of human tumors. We characterize the miRNA profile of different types of ovarian tumors to identify biomarkers that can be used in clinics and to understand the pathology of the tumors to find an effective cure. Using only a few miRNAs we can characterize different types of ovarian tumors based on their miRNA profile. We also identify a miRNA target that could potentially be explored for therapy. The miRNA biogenesis factors are important to ensure proper production of miRNAs. Their role in the miRNA biogenesis is well characterized, but very little is known if they possess other biological function besides miRNA production. In study III we describe a new role for TARBP2, which is responsible for miRNA maturation. Hundreds of thousands RNAs are transcribed from a single cell, and each RNA molecule have different sequences or structures that are important for their function/regulation. We used computational biology to predict all the potential TARBP2-interaction sites on messenger RNAs, and found several in the 5’ untranslated region (5’UTR). The 5’UTR are just upstream of the initiation site of protein synthesis, and usually contain important regulatory sequences. We explore how the TARBP2 interaction with the 5’UTRs can affect gene expression. In particularly we found a gene that is important for regulation of a process in the cell called autophagy.

In this thesis we investigate the role of miRNAs and their processing factors in C. elegans and humans. We describe a new role for miRNA as regulator of noncoding transcript, and we explore the possibility of using them as biomarkers in ovarian tumors. Finally, we describe a new role for the miRNA biogenesis factor TARBP2 as a regulator of autophagy.

List of scientific papers

I. Zisoulis DG, Kai ZS, Chang RK, Pasquinelli AE. Autoregulation of microRNA biogenesis by let-7 and Argonaute. Nature. 486:541-4 (2012).
https://doi.org/10.1038/nature11134

II. Chang RK, Li X, Mu N, Hrydziusko O, Garcia-Majano B, Larsson C, Lui WO. MicroRNA expression profiles in non-epithelial ovarian tumors. Int J Oncol. 52:55-66 (2018).
https://doi.org/10.1002/path.4135

III. Chang RK, Gao J, Li X, Garcia-Majano B, Wiman K, Lui WO. TARBP2 regulates autophagy through post-transcriptional regulation of ATG2A expression. [Manuscript]