Abstract
Recent concerns about off-target immune activation following non-targeted mRNA vaccine delivery have prompted the need for rational design strategies that optimize nanoparticle formulations. Building upon our previous in silico work using the Universal Immune System Simulator to characterize immune responses to mRNA vaccines, we present a computational framework that integrates synthetic transcriptomics with artificial intelligence-driven optimization to guide the development of safer and more targeted lipid nanoparticles. We generated biologically informed, synthetic RNA-seq datasets to emulate gene expression profiles in immune-related tissues post-vaccination. Differential gene expression analysis identified compartment-specific transcriptional responses, which were then used to construct a risk index based on predicted immune activation and the number of upregulated immune markers. Parallelly, we trained a Random Forest regression model on simulated lipid nanoparticles formulations to predict immune activation values and embedded this model into a genetic algorithm to identify optimal lipid nanoparticles design parameters (size, charge, polyethylene glycol content, and targeting). The proposed framework enables early-stage, fully in silico screening of mRNA vaccine delivery strategies. Our results highlight the potential of combining mechanistic immune modeling, synthetic transcriptomic validation, and Artificial Intelligence-based design to accelerate the development of safer and more effective mRNA-based therapies. By enabling rapid, data-driven optimization of delivery systems prior to experimental validation, this approach can significantly shorten vaccine development timelines, reduce costs, and support the creation of more personalized and adaptable immunization strategies. In the long term, this paradigm shift toward computationally guided vaccine development could redefine the future of immunization, paving the way for next-generation vaccines that are safer, more targeted, and rapidly adaptable to emerging infectious threats and individual patient needs.