Understanding the Basics of Cellular Metabolism and Disease

When it comes to critical processes taking place in our cells, metabolism is one of the most fundamental. Being the source of energy in the cell to ensure its survival and proper functioning, it also breaks down and provides a source of nutrients that can be used to power the cell and/or compose essential macromolecules. Removing byproducts and ensuring that cells’ metabolism is operating as it should be is also critical.

Understanding the basics of cellular metabolism, as well as when it goes wrong and the ensuing consequences, are an important foundation for any cell biologist, with links to diseases such as diabetes, obesity, and cancer. This article will look at how our growing understanding is impacting the development of new diagnostic and therapeutic approaches, and at the tools and technologies helping to drive them by revealing metabolism’s vast sphere of influence on cellular health.

An expanding landscape

“Much of our understanding of metabolic pathways (glycolysis, oxidative phosphorylation, glycogen catabolism) came from the ‘golden age’ of biochemistry in the 1920s–1960s,” says Ryan Russell, Associate Professor, Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Canada. Thankfully, our knowledge in the field has become much more sophisticated over the past couple of decades, with an influx of advanced tools and technologies.

Natalia Romero, Head of Bioassay Solutions, Cell Analysis Division, Agilent Technologies, thinks our improved understanding of cellular metabolism has highlighted the role of metabolic dysfunction as the cause of a large number of diseases. “In the last 15–20 years, the introduction of new technologies, such as highly sensitive respirometry and advances in metabolomics that allow us to detect large numbers of metabolites via mass spectrometry (MS), have enabled a much deeper understanding of the roles of cell metabolism in cellular function,” she comments. This potentially means that reprogramming cellular metabolism could be an effective therapeutic strategy. Romero also comments that cell metabolism also provides substrates for epigenetic modifications inducing long-term changes in genetic expression.

Autophagy, or the process by which our cells degrade cellular components that are either damaged or which are no longer required, has grown significantly as an area of study within cellular metabolism. In cancer research, the ability of the autophagy pathway to break down old components and produce nutrients under short periods of nutrient deprivation is thought to contribute to the survival of poorly vascularized solid tumors. “This is an area of autophagy research that we have become very interested in lately,” says Russell, whose group studies the process of autophagy and its pathways.

Paul Thompson, CSO, Mission Therapeutics, thinks that there is a spectrum of metabolic health across different individuals, with some having better or poorer metabolic health than others, and that this can often be linked to mitochondrial health. Mitochondrial health is an important aspect of metabolism, with this key cellular organelle being dubbed the powerhouse of the cell: “From acute conditions through to natal and chronic disease, the potential of improving mitochondrial health to treat human disease is vast,” he says. “Being able to target mitochondria directly is an underserved area.” Thompson thinks that companies like his could make a fundamental change to mitochondrial energetics through a therapeutic approach.

Romero agrees: “Mitochondrial diseases are a group of genetic disorders that result in a deficiency of the mitochondria to produce energy, which can affect almost every tissue, especially those with a high energetic demand such as the brain, muscles, heart, liver, and kidney. Biochemical measurements of mitochondrial activity on biopsy samples of muscle can provide diagnostic readings.”

Tools for measuring cellular metabolism

Rafael Gomez-Amaro, Scientific Advisor, High Dimensional Biology, BD Biosciences, advises that for measuring cellular metabolism numerous methods can be used including NMR, chromatography, and mass spectrometry, which allows profiling of hundreds of metabolites. Other technologies, like single-cell transcriptomics and flow cytometry have sufficient throughput and an increasing number of metabolism-focused tools and readouts.

“There are several tools available for the measurement of cellular bioenergetic metabolism, which are useful for developing and improving advanced cell-based therapies including cancer immunotherapies,” says Romero. Combining this approach with metabolomics and measuring isotopic radiotrace flux analysis by mass spec provides a significant advantage. “In the case of cell-based immunotherapies, such as CAR-T cells, products need to have the metabolic program that results in the highest support of antitumor potency,” says Romero. This means that there is also a role for measuring cellular metabolism in quality control of such cell-based therapies.

Another tool is related to a novel phosphorylation event on the autophagy protein ATG16L1, identified by Russell’s group, which is tightly linked to the level of activity of the autophagy pathway. In collaboration with Abcam, the group developed a recombinant monoclonal antibody (phospho-ATG16L1-Ser278) that can monitor autophagy levels.

Tools like untargeted LC-MS/MS are being used to compliment or inform traditional genetic testing for inherited metabolic diseases, being able to measure diverse metabolites and pathways with an untargeted approach. “The field of metabolomics—which measures many metabolites at once—has started to move into the realm of clinical diagnostics,” explains Gomez-Amaro.

Mission Therapeutics’ clinical approach is the targeting of deubiquitinating enzymes (DUBs) that control cellular ubiquitin—a small regulatory protein—by cleaving it from substrate proteins. Ubiquitin is involved in the degradation of proteins and their clearance from the cell. When DUBs remove ubiquitin, this means that proteins are no longer marked and they stay in place. It is believed that DUB-related dysregulation of ubiquitin levels can therefore have serious implications for cellular health and, more generally, health on a tissue, organ, or systemic level. Thompson emphasises: “We’re trying to help the cell to help itself, where its normal clearing pathways (i.e., autophagy) are affected, to help cells maintain optimal energetics. Considering metabolism is going to be a useful perspective from which to develop new therapeutics.”

In the lab, Thompson’s team use a variety of methods to understand the effects of DUBs and DUB inhibitors. “We treat cells with a DUB inhibitor, then measure mitochondrial ubiquitination. We also use dyes that allow visualization of membrane potential. This allows us to understand DUB inhibitor impact on mitochondrial electron transfer chain function. We use metabolomics to try to understand what changes in mitochondrial metabolism are taking place as a consequence of DUB inhibition, including corresponding changes to mitochondrial function, in an unbiased way. This includes cell-level metabolic changes through to larger tissue-level and systemic outcomes. We use a variety of model systems, being particularly careful when we translate basic cell test tube work to human metabolism, as the human body and its tissues can behave differently to cells in a dish.”

Future needs and technologies

Romero discusses some of the current needs in the field: “Technology that could provide similar measurements but in a more complex 3D model, which could identify the effect of cellular interactions in the metabolism of the different cell types, would be extremely beneficial.”

More detailed single-cell analysis could also play a role in future. “Most of what we know about cellular metabolism comes from studies looking at metabolism in bulk, averaging metabolite levels across tissues or millions of cells. We know far less about the metabolic differences between individual cells—and how that heterogeneity drives cell-type specific functions or is impacted by disease,” comments Gomez-Amaro.

In terms of better understanding disease, Russell feels that more tools are needed to monitor the autophagy pathway and its regulation in patient samples and rare cell populations. “Many of the major knowledge gaps relate to the role of autophagy in disease. The field needs specific, potent, and bio-available autophagy inhibitors to further our understanding of autophagy in normal and disease biology.”