Stable Isotopes for Tracing Mammalian-Cell Metabolism In Vivo

Abstract

Metabolism is at the cornerstone of all cellular functions and mounting evidence of its deregulation in different diseases emphasizes the importance of a comprehensive understanding of metabolic regulation at the whole-organism level. Stable-isotope measurements are a powerful tool for probing cellular metabolism and, as a result, are increasingly used to study metabolism in in vivo settings. The additional complexity of in vivo metabolic measurements requires paying special attention to experimental design and data interpretation. Here, we review recent work where in vivo stable-isotope measurements have been used to address relevant biological questions within an in vivo context, summarize different experimental and data interpretation approaches and their limitations, and discuss future opportunities in the field. Metabolism: A Central Node for Cellular Processes Metabolism can be seen as the engine of the cell, providing energy, redox cofactors, and building blocks for cell maintenance, growth, and renewal, as well as playing a key role in modulating cell signaling [1,2]. To orchestrate all these functions, metabolism consists of a complex network of genes, enzymes, and metabolites, steadily modulated in response to different stimuli [3-5]. Defining the mechanisms at the basis of this regulation and understanding their physiological role is among the most important pursuits in biological and medical research [6], particularly since the realization that many pathologies are driven by metabolic deregulations [7]. An in-depth understanding of metabolic pathways in vivo and how these are deregulated in different diseases is thus fundamental for the discovery of new therapeutic targets and clinical biomarkers, enabling the development of more robust diagnosis approaches and personalized treatments, eventually improving the overall outcome for patients [8]. In this context, stable-isotope tracers (see Glossary) have become a standard for probing cellular metabolism [9] and their increasing implementation in in vivo settings has revolutionized our current understanding of mammalian metabolism in health and disease, unraveling novel regulatory principles at both the cellular and whole-organism level [10,11]. In this review, we summarize the latest advances in in vivo metabolic measurements using stable-isotope tracers, highlighting the importance of systems-level integrative approaches and careful experimental design, pointing out open challenges and opportunities for advancing the field, and outlining strategies and potential pitfalls when interpreting these measurements (Figure 1). Tracer-Based Methods for Measuring Cellular Metabolism In Vivo Many complementary methods exist to study metabolism in vivo and, consequently, the selection of a specific approach (or set of approaches) depends largely on the biological question being addressed. Nontracer-based methods, such as assessing bioenergetics by measuring dynamic changes in oxygen consumption [12] or evaluating changes in metabolite levels via metabolomics [13],...

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