Metabolomics:
Decoding Cellular Metabolism Zeribe Nwosu, PhD Postdoctoral Fellow, Molecular & Integrative Physiology and Costas Lyssiotis, PhD Assistant Professor, Molecular & Integrative Physiology
E
very cell coordinates a complex network of enzymatic activities through which it obtains and utilizes nutrients or degrades and exports waste products. Metabolism enables cells to maintain a physiologic balance between nutrient utilization and waste removal. No cell can survive or grow without metabolism and without it, key functions such as cellular respiration, signaling and migration would grind to a halt. On the other hand, aberrant or excessive metabolic activities promote diseases such as cancer, diabetes and obesity. Understanding how cells manage nutrients and waste products is important in formulating strategies to diagnose, treat, and monitor diseases. Measuring and interpreting metabolic pathway activities, albeit fascinating, is challenging. This is because several factors influence cell metabolism and these include cell growth and metabolic rate, physicochemical properties of the metabolites, nutrient access, to name a few. For instance, most rapidly proliferating cells accelerate metabolism to sustain their growth needs and eliminate toxic waste products. Such cells complete certain metabolic reactions at extremely fast rate and maintain some metabolites at a low level. In addition, several metabolites are inherently unstable. Metabolic pathways are also intricately connected – one pathway’s waste can become another pathway’s substrate, which can make it hard to accurately measure such metabolites. These variables constitute an exciting conundrum, which metabolomics attempts to solve. In the last two decades, metabolomics has evolved as the state-of-the-art method for decoding metabolic activities in cells. Metabolomics is the study of metabolites and biochemical reactions at a holistic scale (‘high-throughput’). Typical metabolomics instrumentation includes a chromatography coupled to a mass spectrometer, which altogether improves analytical sensitivity even for extremely low metabolites. Metabolomics also enables the simultaneous measurement of hundreds to thousands of metabolites in biological specimens. This high throughput advantage enables a global insight into how cells react to various perturbations such as nutrient starvation or treatments. Two major metabolomics approaches are employed to facilitate discoveries. These are either untargeted or targeted metabolomics. In the untargeted metabolo-
20
Physiology Matters
mics, thousands of metabolites are detected without the need for a prior knowledge of the metabolite species. This enables an expansive possibility to extract metabolites in a retrospective fashion, hence extending the boundaries of novel discoveries. However, this approach is labor-intensive, time consuming, and requires expertise given the high likelihood of metabolite misidentification. On the other hand, targeted metabolomics is applied for detecting a well-curated list of metabolites of known physicochemical properties. This enables an expedited turnaround time that can prove useful in research, especially where the researcher is interested in few specific metabolites or pathways. On the downside, a targeted approach is limited in scope. Another interesting aspect of metabolomics is stable isotopes tracing. In this approach, metabolites carrying isotopically labelled carbon or nitrogen are provided to cells via culture growth media or injected into in vivo models. After a predetermined time, samples are collected, processed, and analyzed by mass spectrometry, which then elucidates the pathways through which the cell channel and use the labeled metabolites. This provides a cutting-edge approach for monitoring cellular use of a given metabolite. Computational biology and mathematical modeling approaches also offer an additional iteration of metabolomics, namely, metabolic flux
