Investigating the Post-transcriptional Regulation of Macrophage and Prostate Cancer Transcriptome by microRNAs with focus on Tribbles-1

The TRIB1 gene has been implicated in several human pathologies, including cancer, lipid disorders and cardiovascular disease. It is well appreciated that TRIB1 is a critical regulator of macrophage polarisation, favouring the activation of an anti-inflammatory phenotype. Recent studies also pointed to a role of TRIB1 in the pathogenesis of prostate cancer, although the mechanisms behind its overexpression remain elusive.
TRIB1 protein is produced from a highly unstable mRNA, with a half-life shorter than 1 hour, suggesting it may be subject to post-transcriptional regulation. The TRIB1 transcript includes a long, conserved 3UTR, potentially enriched with putative miRNA-binding sites and polymorphisms. The latter could contribute to the regulation of TRIB1 expression, via either creating or abolishing miRNA-binding sites. However, the post-transcriptional regulation of TRIB1 by miRNAs has not been comprehensively investigated.
The work presented in this thesis explored the post-transcriptional regulation of TRIB1 by miRNAs, using a combination of bioinformatics and experimental tools, with focus on macrophage and prostate cancer biology. We identified multiple miRNAs predicted to target the 3’UTR of TRIB1 with good alignment scores and free energy values. We experimentally validated the interaction between miR-101-3p and TRIB1 in human macrophages and demonstrated that the overexpression of miR-101-3p and TRIB1 caused opposite genetic signatures, suggesting the biological importance of their interaction. Similarly, we identified 21 miRNAs targeting TRIB1, which are either downregulated or silenced in prostate cancer and could possibly account for the elevated expression of TRIB1. We focussed on the activity of the oncomiR miR-132-3p and observed that it is able to modulate the expression of TRIB1 and its downstream genes.
Additionally, a collaborative study on macrophage transcriptomes was performed using multiple RNA-seq experiments, leading to the identification of “super regulators” miRNAs and their targetome in pro-inflammatory macrophages.
Lastly, a brief preliminary research was also conducted on genetic variants affecting the 3’UTR of TRIB1: we found that TRIB1 SNPs create novel miRNA-binding sites and impairs the expression of distant genes, thus acting as potential trans-eQTLs. However, this remains to be elucidated further.