Multi-omics approaches to decipher the interactions of nanoparticles and biological systems

Understanding how engineered nanoparticles interact with biological systems is crucial for the development and implementation of nanoparticles in clinical settings. However, investigating the complexity of these interactions at the nano–bio interface requires technologies that can accurately gather biological information at the organ, tissue, cellular and subcellular levels in a high-throughput manner. In particular, imaging and multi-omics approaches provide powerful tools to study nano–bio interactions. In this Perspective, we discuss the application of transcriptomics, epigenomics, proteomics and metabolomics technologies for the investigation of nano–bio interactions, for example, to assess the biodistribution of nanoparticles in vivo, to analyse their interactions with specific cell types, and to study cellular responses to nanoparticle uptake at subcellular levels. We also examine bioinformatics and machine learning and artificial intelligence tools to assess big multi-omics data, suggesting how these might be applied to develop and optimize nanoparticles for specific applications. Finally, we highlight how multi-omics pipelines might be incorporated in the design of new nanoparticle-based treatment strategies. The interactions of nanoparticles with the body are dynamic and complex. This Perspective examines the application of different multi-omics tools to investigate nano–bio interactions in vitro and in vivo.