A multi-scale biocompatibility atlas of porous silicon nanoparticles: From whole embryo to single-cell resolution

The clinical translation of nanomedicines, such as porous silicon nanoparticles (pSiNPs), requires rigorous and multidimensional safety evaluation that extends beyond conventional in vitro assays, which often fail to capture complex in vivo interactions. Here, we establish a multi-scale assessment pipeline employing the zebrafish (Danio rerio) model, integrating whole-organism phenotyping with single-cell RNA sequencing (scRNA-seq) for high-resolution biological profiling. Zebrafish embryos demonstrated exceptional tolerance to pSiNPs, with no observable changes in survival, developmental morphology, or overall growth. Transient and mild reductions in cardiac and locomotor activity observed 2 h post-exposure were fully restored within 24 h, indicating minimal physiological perturbation. At the molecular level, unbiased scRNA-seq analyses revealed a largely quiescent transcriptomic landscape: pSiNP exposure did not disrupt cellular composition or activate gene programs related to stress, toxicity, or inflammation. This integrative, organism-to-single-cell blueprint of biocompatibility provides compelling evidence supporting the safety of pSiNPs and highlights their potential as a robust platform for next-generation drug delivery and theranostic applications.