Impact of ionizable lipid source on quality and stability of siRNA-loaded lipid nanoparticles

The successful development of siRNA-lipid nanoparticle (LNP) therapeutics depends heavily on the consistent quality of excipients, particularly the ionizable lipid MC3, which is commonly used in clinically approved products such as Onpattro. MC3 plays a key role in RNA encapsulation, endosomal escape, and biocompatibility. As regulatory frameworks evolve to support the development of generic siRNA-LNPs, this work presents the first systematic comparison of how vendor-dependent variations in the purity of MC3 affect the physicochemical properties and in vitro performance of siRNA-LNPs. A multi-platform analytical workflow for impurity analysis revealed that the dienone byproduct of MC3 was the most abundant impurity across all three vendors tested and it was retained in the LNP formulation. Despite variations in purity levels (86-99%) and modest differences in particle size, polydispersity index (PDI), and distinct thermal behavior, the LNPs displayed similar critical quality attributes (CQAs), including encapsulation efficiency, surface charge, apparent pKₐ, and internal structure. In vitro studies showed that all LNPs achieved approximately 60% transthyretin (TTR) mRNA and protein knockdown in HepG2 cells at a 5 nM dose, and maintained HepG2 cell viability at 30 nM, indicating comparable efficacy and biocompatibility. Human peripheral blood mononuclear cell (PBMC) assays showed no significant cytokine induction for LNPs formulated with MC3 from any source. In stability assessments, despite no noticeable chemical changes in LNPs stored over 70 days at room temperature, changes in physicochemical properties such as particle size and PDI were observed. These changes, however, did not impact gene silencing efficiency or biocompatibility. Overall, differences in MC3 purity across the evaluated vendors influenced certain physicochemical attributes of siRNA-LNPs, while in vitro performance remained largely unaffected. Controlling lipid impurity profiles, however, is important for ensuring consistent physicochemical characteristics and supporting quality assurance. Collectively, these findings provide valuable insights for manufacturing and regulatory considerations as siRNA-LNPs progress toward generic development.