The Metabolomic – Epigenomic Complementarity 

 The Metabolome Drives Biological Function Through the Epigenome

Why Metabolome and Metabolomics? 

The metabolome (small molecules, predominantly organic metabolites) represents that largest spectrum of chemical entities influencing biology, and the inclusion of metabolomics profiling in scientific studies comprising an essential and critical information source.  The direct impact of these small molecules on a few fundamental biological processes are highlighted below, providing insights on the critical role of metabolomics in scientific investigations.

DNA (and the genome) as the Responder, Not the Initiator of all biology  

The central dogma put forward the concept that information flow begins at the DNA; in essence, within biological systems, information starts from the DNA, moves downstream (i.e. to RNA, and proteins) to maintain biological equilibrium and survival.  The reality, however, is that biology represents a perpetual dynamic environment, requiring instant and constantenous adjustments, fine-tuning of a “push-pull” of forces (physical, chemical, and others).  The external environment of a cell represents one of the most significant of “forces” directly influencing the response required from the gene-centric signaling to establish biological equilibrium or steady state, commonly referred to as cellular homeostasis.  This implies that gene-mediated information flow is more of a “response” rather than the “initiation” following Newtonian principles that “for every action, there is an equal and opposite reaction” in its most simplistic interpretation.

Not everything driving biology is directly encoded in the DNA (genome)

The sustainability of equilibrium within biological systems requires a constant supply of energy generated close to the activity for efficient access. Glucose is the primary energy source and the most abundant organic molecule around us. Glucose is not encoded directly into our DNA; it is the product of carbon fixation, converting carbon dioxide from the atmosphere by photosynthesis to generate glucose (carbohydrates). Living systems have evolved to convert glucose (carbohydrates) into unlimited molecular variations from simple to the most complex of natural products; the interconversions (build/breakdown) and utilization (consumption) of these molecules are responsible for the observed diversities sustaining ecosystems, including humans.  Glucose (representative of monosaccharides) forms the basis for some of the largest chemical diversity in nature, including being the primary fuel source and energy producer supporting biological activities.  Many of these “essential” molecules are not directly encoded into the DNA¹.  Human biology has evolved (gene-centrically) efficient pathways for the interconversion; build, or breakdown of these essential molecules to use and/or store for energy production, growth, and continuous long-term survival. Thus, the absence of small molecule metabolite readouts results in major information gaps on significant drivers, influencers of mechanisms and outcomes in scientific investigations. The significance of this information gap due to the missingness of the small molecule in experimental biology in the context of the central dogma was appreciated nearly two decades ago by the most eminent scientists, Dr. Stuart Schreiber and Dr. James D. Watson.² This appreciation has been largely lost due to a singular focus on DNA, RNA, and protein-centric efforts due to multiple factors, including ease of detection and understanding.

Chemical diversity as an initiator of cellular response due to chemical alterations of the genome 

“We are what we eat” is a famous phrase from Ludwig Feuerbach that personifies the true impact of food and, more recently, our understanding of the microbiome’s contributions to human biology and health. The benefits of caloric restriction, intermittent fasting, ketogenic, and other diets in maintaining “healthy” biology for improved outcomes (healing) in diseases ranging from depression to cancer underscores the significant impact of chemical constituents in food and nutrition on human biology. For an individual, the components of/from the environment, food, and microbiome represent the most significant contributors to the day-to-day internal/external exposures, the “exposome”. Chemical diversity from the environment, food, and microbiome constitutes the most significant source of exposome to the cells; the gene-centric responses to the constant flux in the exposome composition directly influence growth, survival, and health status. Based on this rationale, we can state that each cell of every tissue, system, organ, and body maintains equilibrium by fine-tuning systems-wide responses to constant chemical exposure from the external environment.  This concept is, in part, the foundation for the use of clinical chemistry readout as a reasonable measure of the normal functioning of biological systems, e.g., creatinine and/or blood urea nitrogen as a measure of kidney function, where any increase or decrease outside of population reference range is indicative of organ dysfunction.

Small molecules (chemicals) drive the fundamental processes for genome to be read, copied, translated, and regulate biological function

Gene expression, the most fundamental of processes widely used as a measure of biologicals activity, requires the unpackaging of DNA.  This is tightly regulated and requires the addition or removal of chemical elements to proteins (histones, bound to DNA for packaging), DNA, and the energy (ATP) to facilitate the process.³  Most discussions on chemical modifications enabling gene expression immediately focus on the influence of enzymes responsible for the process, and very little attention is given to the chemical and the corresponding biochemical pathways generating these elements.^4,5  Furthermore, chemical modifications can occur without enzymes; the changes and their importance in influencing gene expression are appreciated but not as well understood.⁶  Because an estimated 1-2% of the genome is coded for proteins, the overall impact of chemical modifications on histones, DNA, and non-coding RNA is still unknown. Thus, the continued identification and characterization of chemical modifications and the underlying biochemical pathways regulating these modifications provide a strong argument for the incorporation of metabolomics profiling in the discovery of mechanistic and functional significance underlying the chemical modifications driving genetic expression.^7,8

Histones are the proteins that help the DNA packaging, on which chemical modifications can set the conditions for switching genes “on” or “off” for expression. The common chemical modifications on the histones include methylation, acetylation, phosphorylation ubiquitylation, and others.³ The names of the modifications identify the chemical element that is getting added and influencing gene expression, i.e., methylation refers to the addition of a methyl group.  A major methyl group donor for the methylation process regulating gene expression is S-adenosyl methionine (SAM). SAM is generated via enzyme-driven biochemical reactions involving methionine and adenosine triphosphate (ATP, the primary energy molecule in cells). SAM levels in the body and cells are, in turn, influenced by food and nutritional intake, bringing the discussion back full circle to the role of chemical exposure from the environment, food, and microbiome, the cell’s ability to modify the chemicals to forms that can influence gene expression.

Another important epigenetic modification on histone is acetylation; the acyl moiety is contributed primarily by Acetyl-CoA, a product of a core central carbon metabolic pathway that sits at the intersection of biochemical mechanisms generating metabolites for building and/or breakdown of metabolite products useful for cell function, growth, and energy production. 

Biochemical pathways are like gene-centric functional networks, wherein the generation of a specific metabolite impacting epi-transformation can be derived from and driven by the predominance of a particular metabolic pathway as a function of a shift in internal/external balance in the environment.  Thus, it is important to identify the chemical makeup of the external environment driving the intracellular biochemical pathway directly involved in enabling the epi-transformation linked to specific functions. 

Metabolome contribution to the epigenome: Cause-and-effect linkage of biological functions in health and disease 

The significance of small molecule impact on the fundamentals of biological activity supports a compelling rationale to integrate the two molecular constructs in multi-omic analysis, capturing synergy on actionable insights.  The molecular targets for chemical modification influencing gene behavior, i.e., epigenetic regulation, include DNA itself, histones, and non-coding RNAs.  The addition or removal of these chemical markings, enzymatically or non-enzymatically, turns “on” or “off” gene expression and downstream biology.⁹ Thus, at the fundamental level, the epigenome is a gene-wide compilation and characterization of chemical marking/modifications in the DNA, histones, and ncRNA, providing specific instructions on “what to do”, “where to do it” and “when to do it”.¹⁰ Thus, it is reasonable to state that metabolism is the principal regulator of the epigenome since, without the availability of the chemicals for specific functions, there is an absence of markings on the histone and DNA and significantly altered cellular function. Highly conserved biochemical networks with multiple systems level backup ensure that any deficits in a specific biochemical pathway can shift the equilibrium for chemical supply via a different, connected network.^11,12 Thus, studies of epigenomic transformations in driving disease ideally should include metabolomic profiling to identify the most significant metabolic pathways driving the epi-modification and contributing to the phenotype of interest.

References

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