Understanding and Targeting RNA Conformational Ensemble to Develop Therapeutic Approaches for Splicing-related Diseases: A Case Study of Hutchinson-Gilford Progeria Syndrome

Diplôme Thèse Understanding and Targeting RNA Conformational Ensemble to Develop Therapeutic Approaches for Splicing-related Diseases: A Case Study of Hutchinson-Gilford Progeria Syndrome eng 2023 2023 author Sahi-Ilhan Ece 893239 director Scapozza Leonardo 600318 Section des sciences pharmaceutiques (FARMA) 216 10.13097/archive-ouverte/unige:178863 urn:nbn:ch:unige-1788630 Sc. Vie - Pharma. 262 RNA splicing is a biological process that involves the transformation of pre-mRNA into a mature mRNA. During splicing, introns are excised and exons are fused. Exons have the potential to be constitutive or alternative. Alternative splicing leads to inclusion or exclusion of specific exons in the final mRNA. The human genome has alternative exons in over 90% of the protein-coding genes, enabling the creation of several protein isoforms from one gene. Diseases can also be caused by aberrant splicing isoforms; one such example is Hutchinson-Gilford progeria syndrome (HGPS), which results from a splicing modifying mutation in the LMNA gene. The molecular mechanism of HGPS is characterised by a C to T mutation in a specific location of the LMNA gene, leading to the formation and accumulation of the protein, called progerin. Presence of progerin contributes to accelerated-aging phenotype and characteristic features seen in HGPS. As of now, progeria has no known cure and only treatments for relieving symptoms have been used. In this point, understanding the molecular mechanisms of HGPS has paved the way for research into potential therapeutic approaches targeting progerin production and its effects on cellular function. The potential of small molecules targeting RNA structural elements that regulate exon usage in treating splicing-related diseases has been demonstrated by several groups in recent times. In particular, our group has identified compounds that target the TSL2 RNA structure and modify the splicing of SMN2 transcripts, involved in Spinal Muscular Atrophy. Taken the knowledge acquired from those studies, in this PhD thesis, it was firstly aimed at understanding RNA hairpin conformation in the absence or presence of progeria mutation and secondly targeting the progeria-mutated hairpin conformation by RNA-binding small molecules as splicing modifiers to reduce progerin level in order to overcome the negative effects of the disease. Structure of Lamin A mRNA has not been well understood, and there has been insufficient research on HGPS. In the literature, effects of progeria mutation was hypothesised as a conformational change and loosening the hairpin structure. However, there is a lack of certain information concerning loop or stem interactions in hairpin structures with or without progeria mutation. Therefore, it was aimed to understand mutation effects on the conformational ensemble of cryptic splicing site, where progeria mutation occurs. Experimental outcomes showed a strong correlation and substantially supporting our hypothesis on conformation ensemble in several ways. In the second experimental part, it was successfully established binding and splicing abilities of small molecules and their effects on cellular characteristics. Intriguingly, compound 18 had been observed to ameliorate outcomes of patient-derived progeria cells as in healthy ones with no toxic effects. Besides, in vitro and in silico binding interactions with progeria mutated hairpin showed promising results. There are several of pharmaceutical treatments for progeria, but none have yielded complete recovery from the disease’s symptoms. Taken the knowledge of previous studies of HGPS and this project, where promising small molecules targeting RNA conformation are characterised, could open a new avenue for the most effective treatments as well as could instil hope for other rare diseases linked to splicing issues. Dewey 615 31 Section des sciences pharmaceutiques 17 false 979 Fabip 974 4f00e4bc-8546-4428-825e-8a592acee20f Thesis Public THESIS-Sc262-SAHI-ILHAN-Ece.pdf 15442421 application/pdf Restricted 2026-01-01 68b6f671f8a408739bbdb21aebce5c01dd956fbc8ccae6bfe652b1b722e104a6 ab167241-f9c7-405c-9099-29f6e8c3684a Imprimatur Public Imprimatur-SAHI-ILHAN-Ece.pdf 2284106 application/pdf 56dae6a7fc2f68b02e4c7145d3a33eb0db1bcb9169edf8843395e959ed19ce28 openAccess Faculté des sciences / Section des sciences pharmaceutiques

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Understanding and Targeting RNA Conformational Ensemble to Develop Therapeutic Approaches for Splicing-related Diseases: A Case Study of Hutchinson-Gilford Progeria Syndrome				2023	512	95

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