A modular platform for measuring substrate oxidation by CO₂ production in diverse cell culture systems

Metabolism underpins cellular physiology, whereby the preference for specific substrates and catabolic pathways shapes the production of energy, anabolic substrates, and metabolite signals to address bioenergetic demands. Substrate catabolism can be directly examined by measuring metabolic endpoints. For instance, substrate oxidation can be quantified by the incorporation of carbon from labelled glucose or fatty acids into carbon dioxide, providing a sensitive and specific readout of metabolic flux. However, current platforms require relatively large culture volumes, lacking adaptability for small-scale or complex cell culture formats. Herein, we develop and validate a modular platform that can quantify substrate oxidation in a range of cell culture systems, including two- and three-dimensional cultures grown in 12- and 96-well plate formats. This platform was engineered for precise gas equilibration, minimal gas leakage, and bioinert adapters suitable for smaller-scale cultures, using inexpensive and accessible components. We demonstrate the versatility of this system by showing that: (i) dendritic cells modulate glucose catabolism in response to a tolerance-inducing biologic (anti-inflammatory protein 2), and (ii) human cardiac organoids maintain fatty acid oxidation during acute inflammatory stress. This platform can be performed in parallel with orthogonal metabolomics assays and live-cell imaging, enabling integrated analysis of metabolic and functional readouts. Together, this platform expands access to measuring substrate oxidation across a range of cellular systems.