Integrative bioinformatic analysis of post-transcriptional regulation by small non-coding RNAs in osteoarthritis and heart failure models

With the progressive increase in life expectancy, chronic degenerative diseases represent an escalating social and economic burden. Among these, osteoarthritis (OA) and heart failure (HF) stand out for their complexity, characterized by profound post-transcriptional dysregulation underlying both disease onset and progression. This thesis aims to disentangle this regulatory layer by focusing on two classes of small non-coding RNAs (sncRNAs) – microRNAs (miRs) and tRNA-derived fragments (tRFs) – through an integrative bioinformatic approach. In the OA context, LPS stimulation of primary chondrocytes derived from OA patients induced a robust dysregulation of miRs, which bioinformatic analyses linked to altered protein metabolism and stress granules (SGs) assembly. Subsequent investigations in C28/I2 cells confirmed SGs formation and the redistribution of HSP70 and ubiquitinated proteins into insoluble complexes, supporting a link between RNA regulation and proteostasis imbalance. LPS also induced a marked biogenesis of tRFs, with a potential impact on gene expression through miR-like activity. Functional assays identified 3′tRFAsp(GTC) as a key regulator in OA, modulating inflammatory and matrix-degrading gene expression and influencing SG and RISC assembly. Computational analyses further suggested its interactions with RNA-binding proteins (RBPs) involved in RNA transport and translational control. To investigate sncRNAs in an in vitro model of HF, small RNA sequencing of human induced pluripotent stem cell (iPSC)-derived cardiac organoids exposed to endothelin-1 (ET-1) was performed. This analysis revealed coordinated miR and isomiR alterations driving pathology through canonical and non-canonical seed-based targeting, converging on genes involved in metabolism, cardiac development, and maladaptive remodeling. ET-1–associated tRF signatures reinforced these processes via miR-like mechanisms. Among them, 5′tRFGlu(CTC) emerged as a candidate of interest due to its significant association with hypertrophy and its predicted interactions with RBPs involved in translational control. Altogether, this work highlights sncRNAs as central regulators of OA and HF, orchestrating disease-specific stress responses through coordinated post-transcriptional mRNA regulation.