Cell culture metabolomics and lipidomics

Cell cultures are one of the most useful tools in life science research and biotechnology, irreplaceable for applications as diverse as testing of drugs or toxins, development of gene and cell therapies, investigation of the function of biomolecules, production of biologics or vaccine particles. Metabolomics and lipidomics with their closest link to cell phenotype and as indicators of functional effects and changes in biological systems provide a highly valuable window into many applications of cell cultures. These omics tools can be used for the real time monitoring of cell culture growth and provide detailed, nonbiased analysis of changes within cells or in secreted media or extracellular vesicles. Metabolomics can be used to optimize cell growth for enhanced production in bioreactor applications or for monitoring cell health, for example, in cell therapy development. In this chapter, we outline some examples and methods used in metabolomics and lipidomics of cell cultures including analysis of cells, media, and extracellular vesicles. Experimental method presentation is followed by introduction to analysis and modeling tools including statistical, mechanistic, and machine learning methods with particular relevance in the applications of metabolomics and lipidomics in cell cultures.