ABSTRACT
Inflammatory bowel diseases (IBDs), incurable conditions characterised by recurrent episodes of immune-mediated gut inflammation and damage of unknown aetiology, are common. Current advanced therapies target key leukocyte-trafficking and cytokine-signalling hubs but are only effective in 50% of patients. With growing evidence of mitochondrial dysfunction in IBD and advances in our understanding of the role of metabolism in inflammation, we provide an overview of novel metabolic approaches to IBD therapy, challenging the current ‘therapeutic ceiling’, identifying critical pathways for intervention and re-imagining metabolic biomarkers for the 21st century.
Introduction
Antimicrobial peptides: evolutionarily conserved short-chain peptides with anti-microbial and immunomodulatory properties.
Damage-associated molecular patterns (DAMPs): small molecules released from stressed/damaged/dying cells that act as danger signals to the innate immune system, activating it in cases of sterile inflammation.
Electron transport chain (ETC): a series of protein complexes (I-IV) embedded within the inner mitochondrial membrane. Here, electrons are transported, creating a transmembrane electrochemical proton (H+) gradient. ATP synthase (complex 4) is the site of oxidative phosphorylation at which this channel allows H+ ions back across the gradient, generating ATP.
Glycolysis: the ten-step enzymatic metabolism of glucose that occurs in the cytosol of all cells and can be aerobic (leading to formation of pyruvate) or anaerobic (leading to formation of lactate). Although a quick process, it results in only a net of two ATP molecules per molecule of glucose, and so it is a relatively inefficient way for a cell to generate energy.
Hypoxia-inducible factor 1-α (HIF1A): a key transcription factor that regulates a cell's response to changes in oxygen tension and is also a master regulator of cellular metabolism.
Immunometabolism: an emerging field of immunology research that can be described as the study of immune cell metabolic processes and metabolic intermediaries in health and in stress.
Intestinal mucosa: comprising the lumen-facing epithelial cell layer, underlying lamina propria, and outer muscularis mucosa. The intact barrier allows water and nutrient uptake, promotes immune tolerance to commensals and food antigens, and prevents pathogens and toxins from accessing the systemic circulation.
Janus kinase (JAK) inhibitors: a class of drug used to treat many chronic autoimmune conditions. They act by preventing JAK (a cytoplasmic non-receptor tyrosine kinase) phosphorylating, and thus activating, STAT proteins, disrupting downstream cytokine signalling.
Metabolic re-programming: when cells alter their fundamental metabolic pathways to adapt to their environment. This is a hallmark feature of cancer cells to promote a pro-survival tumour microenvironment and is increasingly recognised in chronic inflammation.
NOD-, LRR- and pyrin domain-containing protein 3 (NLRP3): a three-protein structure found in the cytosol of immune cells. It can be activated by cell stress from a wide variety of sources – from bacterial, viral or fungal infections to sterile inflammation and environmental toxins. NLRP3 activation induces inflammasome formation, which leads to caspase activation and, in turn, secretion of active forms of IL1β, IL18 and gasdermin D.
Nuclear factor erythroid 2-related factor 2 (NRF2): a transcription factor that regulates antioxidant enzymes, e.g. superoxide dismutase, glutathione peroxidase.
Oxidative phosphorylation: collective term for the redox reactions occurring in the ETC and chemiosmosis. It occurs in the mitochondria, requires oxygen and generates the majority of cellular ATP, between 30 and 32 ATP molecules per molecule of glucose.
Pentose phosphate pathway: a ‘shunt’ from glycolysis; this cytosolic reaction generates pentose phosphates needed for DNA and RNA synthesis, but no ATP.
Sphingosine-1 phosphate (S1P) modulators: an emerging class of drugs used in some autoimmune conditions. They prevent lymphocytes from sensing S1P, limiting their migration from lymph nodes to inflamed tissues.
Stimulator of interferon gene (STING): a transmembrane protein found on the endoplasmic reticulum in cells and a key mediator of the type 1 interferon response to DNA released by dying cells, bacteria or viruses.
Toll-like receptor (TLR): transmembrane protein, of which ten subtypes have been identified in humans at the time of writing. They can be present on the cell plasma membrane of antigen-processing cells or can be intracellular. Molecules from pathogens bind to TLRs – e.g. lipopolysaccharide to TLR4 and mitochondrial DNA to TLR9 – inducing an innate immune response by initiation of a downstream signalling cascade.
Tricarboxylic acid (TCA) cycle: otherwise known as the citric acid cycle or Krebs’ cycle, a series of biochemical reactions to release the energy stored in nutrients through the oxidation of acetyl-CoA derived from carbohydrates, fats and proteins. It generates electrons, which are transferred by NAD and FADH donated to the ETC.
Xenobiotics: chemicals or toxins that are foreign to the body. They are usually metabolised hepatically, but can mount an immune response.
There have been major advances in understanding how metabolism, in particular the mitochondria, governs the immune response in homeostasis and disease states (Murphy and O'Neill, 2024) and how it drives the action of glucocorticoids, the longstanding anti-inflammatory treatment in human diseases (Auger et al., 2024). This commentary focuses on the role of immunometabolism (Box 1) as a tractable and hitherto novel therapeutic avenue in IBD.
The relevance of immunometabolism in IBD
The gastrointestinal tract is a highly metabolically active organ with an epithelial lining that is replenished every 4-6 days from intestinal stem cells (iSCs). It must balance energy-demanding physiological functions, such as nutrient absorption and gut repair, while maintaining a robust immune defence that involves the production of antimicrobial peptides (Box 1), mucus and immunoglobulins. Here also lies one of the most immune-rich tissue environments, with macrophages, dendritic cells, B cells, T cells, natural killer cells, innate lymphoid and plasma cells that provide a sophisticated and highly complex defence at the interface with trillions of gut bacteria. They function as a finely tuned biological system that senses the changes within the gut luminal environment. Tissue-resident cells, such as macrophages, are omnipresent, and there are also those that respond, differentiate or traffic to the gut in response to danger, such as monocytes, neutrophils and effector T cells, and others that maintain homeostasis, such as regulatory T cells. Thus, immune cell metabolism that is required to ‘fuel’ these dynamic needs and inflammatory potential in the gut are intricately linked. Pertinently, distinct metabolic changes in the gut can profoundly influence the tissue's immune response in a primary manner (Buck et al., 2017).
The regulation of metabolism is dependent on intertwined biological networks including nutrient and energy sensor pathways, such as mechanistic target of rapamycin (mTOR) and AMP-activated protein kinase (AMPK) (Saxton and Sabatini, 2017). In broad terms, this metabolic system can be actively switched to anti- or pro-inflammatory functions depending on the biological need. In vitro work has demonstrated that both innate and adaptive immune cells upregulate glycolysis (Box 1) in the presence of pro-inflammatory stimuli to accommodate rapid generation of ATP, and downregulate oxidative phosphorylation (Box 1), which is associated with an anti-inflammatory immune cell phenotype and function. Accompanying metabolic changes in immune cells during inflammation include an increase in substrate flux through the pentose phosphate pathway (Box 1) and ‘breaks’ in the tricarboxylic acid (TCA) cycle (Box 1), leading to the accumulation of metabolites that are known to have immunoregulatory functions – succinate and citrate. These are termed ‘immuno-metabolites’ and have been shown to act as co-factors for metabolic enzyme reactions, mediate post-translational modifications, signal between cells as cytokines would (metabokines), and even drive immune cell phenotype and function (Murphy and O'Neill, 2018). The gut is also a source of molecules that arise from the metabolism of host microbiota, such as short-chain fatty acids, that are essential metabolic fuel sources and have major local and systemic immunomodulatory properties (Mann et al., 2024).
The mitochondrion provides the intracellular platform for many key metabolic functions (Monzel et al., 2023). Of interest, mitochondria can remodel their shape by fission and fusion to become active controllers of cellular metabolism during health and disease (Nunnari and Suomalainen, 2012). Within the gut, mitochondria are uniquely exposed to high levels of potentially harmful bacteria, immune-active ligands, toxins and xenobiotics (Box 1). Hence, there is more mitochondrial stress and potential for damage in the gut than in other tissues and organs.
Genome-wide association studies indicate that ∼5% of IBD susceptibility genes have important roles in regulating mitochondrial function
Mitochondrial dysfunction in IBD and its consequences
There is growing evidence of mitochondrial dysfunction in IBD. Genome-wide association studies indicate that ∼5% of IBD susceptibility genes have important roles in regulating mitochondrial function (Ho and Theiss, 2022). This is strongly supported by transcriptomic data pointing towards a downregulation of mitochondrial- and nuclear-encoded mitochondrial genes in the IBD gut (Haberman et al., 2019), and mitochondrial gene polymorphisms associated with energy deficiency (Dankowski et al., 2016). Mitochondria can also be directly damaged in the IBD gut (Mottawea et al., 2016), which is further amplified by loss of the protective mechanisms for the mitochondria in IBD (Ho et al., 2018). Consequentially, this can result in the accumulation of damaged mitochondria and the generation of pro-inflammatory mitochondrial reactive oxygen species (mROS). Although excessive reactive oxygen species (ROS) generation has a pro-inflammatory effect, a baseline level of ROS is generated from oxidative phosphorylation and is required for epithelial differentiation (Rodriguez-Coleman et al., 2017) and activation of antigen-specific T cells (Sena et al., 2013). Moreover, ROS deficiency can lead to epithelial barrier disruption and increase susceptibility to colitis (Aviello et al., 2019; Hsu et al., 2023). Nevertheless, failed clearance or repair of damaged mitochondria and excessive mROS can lead to their accumulation and the release of mitochondrial constituents (DNA, formylated peptides), which serve as damage-associated molecular patterns (DAMPs; Box 1) that can further perpetuate gut inflammation (Boyapati et al., 2018).
Bioenergetic failure due to mitochondrial dysfunction renders the epithelial lining more susceptible to damage and poor healing (Bar et al., 2013). Furthermore, mitochondrial damage in iSCs can be propagated and imprinted in the gut epithelial phenotype, thus influencing how the epithelium metabolises, regenerates and repairs (Smith et al., 2020). Finally, mitochondrial damage and metabolic reprogramming of adaptive and innate immune cells are intimately linked (see next section for more detail). These lines of evidence point to mitochondrial dysfunction as a pro-inflammatory factor that can perpetuate chronic inflammation and become a major barrier for mucosal healing even when immunosuppressive drugs are used.
The current ‘therapeutic ceiling’ of 50% of patients responding to advanced immune therapies suggests that there remains a major unmet need and that the direct targeting of the inflammatory pathways alone is insufficient
Immunometabolism opens new therapeutic avenues for IBD
The current ‘therapeutic ceiling’ of 50% of patients responding to advanced immune therapies suggests that there remains a major unmet need and that the direct targeting of the inflammatory pathways alone is insufficient (Ho et al., 2022). Here, the nascent field of immunometabolism will be highly relevant, with many potential ‘druggable’ pathways and perhaps the option of repurposing existing therapeutics. These therapeutic approaches are based on the concept of beneficial modulation of the complex inflammatory IBD gut that promotes pro-resolution and repair functions of relevant immune cells (macrophage and T cells), in addition to improving the fitness of the epithelial cells during mucosal healing. Therefore, there are several translational scientific opportunities, as described below.
Modulating mitochondrial function and metabolism
Many pre-clinical studies relevant to autoimmune diseases show that inhibiting mitochondrial ROS can be beneficial in inflammatory states, as exogenously inducing mROS worsened acute colitis in a mouse model, whereas inhibition of mROS attenuated disease (Lood et al., 2016; Jackson et al., 2020; Ho et al., 2018). The necessary translational step is now to explore whether such a simple approach can be efficacious in human inflammatory disease. In this context, the MARVEL study (www.marvelstudy.uk; NCT04276740) in the UK is currently investigating the use of mitochondrial antioxidant MitoQ as an adjunct to steroid therapy for UC (Gwyer-Findlay et al., 2021).
Nod-like receptor-1 (NLRX1) is a negative regulator of inflammation (Leber et al., 2018) and is found on the outer mitochondrial membrane of most cells, including epithelial and immune cells. Its deficiency in mouse models of colitis correlates with more severe disease and a pro-inflammatory, pro-glycolytic T-cell phenotype (Leber et al., 2017). NX-13, an oral agonist of NLRX1, showed promising results in ameliorating disease in pre-clinical models (Leber et al., 2019) and is currently being studied in phase 2 trials for UC (NEXUS trial, NCT05785715).
Targeting mitochondrial dynamics is a further avenue, whereby inhibiting mitochondrial fission through the administration of P110, a compound that prevents the binding of two key mitochondrial fission proteins, has been shown to improve chemically induced mouse colitis (Mancini et al., 2020).
Targeting immunometabolites
The immunometabolite succinate is of particular interest, as levels of both it and its receptor SUCNR1 are increased in IBD (Fremder et al., 2021; Macias-Ceja et al., 2019). Furthermore, pro-inflammatory macrophages have high levels of succinate (Diskin et al., 2021). In vitro, succinate has been shown to be released from macrophages and then signal via SUCNR1 present on dendritic cells and macrophages, acting as a pro-inflammatory mediator (de Goede et al., 2019). Succinate also inhibits the enzymes responsible for degrading hypoxia-inducible factor 1-α (HIF1A; Box 1), leading to its stabilisation even in normoxia. This can lead to increased IL1β production and reversal of the role of the electron transport chain (ETC; Box 1) from ATP generation to ROS production (Tannahill et al., 2013). Countering the effects of HIF1A and succinate, aconitate decarboxylase 1 (ACOD1) acts as a regulator of the inflammatory response to infection and other inflammatory stimuli. ACOD1 is the obligate source of the metabolite itaconate, which stabilises nuclear factor erythroid 2-related factor 2 (NRF2; also known as NFE2L2; Box 1). NRF2 attenuates NOD-, LRR- and pyrin-domain containing protein 3 (NLRP3; Box 1)-driven inflammation and stimulator of interferon gene (STING; also known as STING1; Box 1)-modulated IFN responses, promoting anti-inflammatory and anti-oxidant effects (Michelucci et al., 2013; Naujoks et al., 2016; Lampropoulou et al., 2016). During healthy conditions, itaconate is present in negligible quantities. Its expression can be induced by a suite of factors, including Toll-like receptor (TLR; Box 1)4 ligands, type I and II IFN, bacteria and viruses, although much of this evidence is derived from in vitro studies of stimulated murine blood leukocytes (Lampropoulou et al., 2016; Michelucci et al., 2013; Naujoks et al., 2016). Thus, emerging evidence places itaconate as a major anti-inflammatory metabolite, with 4-octyl itaconate (4-OI), an analogue of itaconate, being explored currently in phase 1 trials for IBD (https://www.sitryx.com/pipeline#pipeline).
Improving metabolic fitness in IBD gut repair
With data implicating mitochondrial dysfunction in iSCs (Parikh et al., 2019; Smillie et al., 2019), future pro-repair approaches have been explored in intestinal organoids, including strategies to repair metabolic defects at the mitochondrial level, particularly for the purpose of treating severe IBD (Rutherford and Ho, 2023). Of interest, the ketone body β-hydroxybutyrate has been shown to promote an anti-inflammatory macrophage phenotype and proliferation of intestinal epithelial cells, which improved experimental colitis in a mouse model (Cheng et al., 2019; Huang et al., 2022).
Clinical approaches to immunometabolism in IBD – ‘low-hanging fruits’
There are now many IBD randomised clinical trials (phases II-IV), but it will be very difficult to envisage future novel approaches being more successful than advanced immune therapies, such as anti-TNF and JAK inhibitors, in the clinical trial setting. Our view is that immunometabolic therapies will be used as an adjunct rather than primary treatment, with future clinical trials designed in this context. ‘Multidrug resistant’ IBD patients that rapidly cycle through different immune therapies or those that cannot achieve satisfactory gut mucosal healing are good initial clinical cohorts to investigate and define immunometabolic profiles. In CD, there is a wealth of evidence implicating macrophage dysfunction in disease aetiology, including defective bacterial killing, monocyte–macrophage differentiation and mucosal healing. Here, macrophage-targeted drugs may be the ‘low-hanging fruit’ for immunometabolic therapies (Hegarty et al., 2023) (Box 2). The paradigm of anti- versus pro-inflammatory metabolism similarly applies to T-cell function, with a wealth of data demonstrating its importance in infection and cancer (reviewed in detail in Reina-Campos et al., 2021), and, more specifically, in CD4+ T cells (Baixauli et al., 2022) and T-helper (Th)17 responses (Johnson et al., 2018) that are highly relevant to IBD. It is beyond the scope of our commentary to provide an in-depth review of this; however, clinically available IL23–Th17-targeted therapies for IBD, such as ustekinumab and risankizumab, provide an opportunity to carry out human experimental studies and provide more mechanistic insights into the impact of these therapies on gut T cells. For example, future studies could interrogate how immunometabolism changes in gut T cells before and after therapy in patients.
Macrophages are the most abundant immune cell in the intestinal mucosa and are largely continuously replenished by circulating classical monocytes. In health, these monocytes differentiate into macrophages with an anti-inflammatory, pro-homeostatic phenotype, and play key roles in immune tolerance to food antigens and commensal organisms. In IBD, loss of barrier function and subsequent translocation of pro-inflammatory stimuli result in the recruitment of monocytes that differentiate into aggressively pro-inflammatory macrophages that persist in the IBD gut and shape the pathogenic T-effector responses. These macrophages and many of their products, such as TNF, IL1β and oncostatin M, activate and perpetuate gut inflammation in IBD, including the recruitment of other immune cells such as neutrophils. Current treatments such as anti-TNF, anti-α4β7 and anti-IL23 therapies target pro-inflammatory pathways in innate and adaptive immune cells (Hegarty et al., 2023).
It is clear that altered metabolism in macrophages plays a role in IBD pathogenesis, but there are key questions outstanding for effective immunometabolic interventions that target these cells:
- (1)
Is the pro-inflammatory macrophage function amenable to specific pharmacologic modulation?
- (2)
Will this increase the likelihood of complete mucosal healing in IBD?
- (3)
Can we stratify immunometabolic therapy based on functional phenotyping of IBD macrophages?
Left: macrophages in the human gut shown in brown (CD68–DAB). Right: the presence of granuloma in the human IBD gut; red dotted lines outline aggregates of macrophages in Crohn's disease.
Metabolic biomarkers to stratify future therapy in IBD
Given the heterogeneity of IBD and mucosal inflammatory milieu – with so many factors that can affect mitochondria function and metabolism – finding metabolic biomarkers that can stratify patients to the relevant immunometabolic therapies is crucial. Experimental approaches to study immunometabolism are now increasingly advanced, from using functional metabolomic and flow-cytometry panels, such as single-cell energetic metabolism by profiling translation inhibition (SCENITH) (Arguello et al., 2020) and metabolism by flow cytometry (MetFlow) (Ahl et al., 2020), to single-cell analyses (Voss et al., 2021). However, they need more realistic consideration of how to apply them in larger-scale populations and how closely patient samples used for the analyses recapitulate in vivo situations, especially in the unique hypoxic and metabolic environment of the gut. High levels of mitochondrial DNA in the blood – often seen in the context of extensive tissue damage, such as trauma or sepsis, and in immune-mediated conditions, such as systemic lupus erythematosus – have also been observed in active IBD (Lood et al., 2016; Zhang et al., 2010; Boyapati et al., 2018). Measuring circulating mitochondrial DNA (and other DAMPs) is currently being investigated as a surrogate for mitochondria dysfunction (www.musicstudy.uk; NCT04760964). Simple high-throughput screening of TCA metabolites is now also needed, especially with the advent of itaconate mimetics. The addition of metabolic read-outs is increasingly considered in large multi-omic studies in IBD.
Immunometabolism is a rapidly advancing field. In IBD, this is a translational area of significant interest with the potential to break the ‘therapeutic ceiling’ in treating IBD gut inflammation.
Conclusion
Immunometabolism is a rapidly advancing field. In IBD, this is a translational area of significant interest with the potential to break the ‘therapeutic ceiling’ in treating IBD gut inflammation. Beyond this, there is also significant potential for other vital patient-centred outcomes, such as fatigue, and more widely for other immune-mediated conditions, such as rheumatoid arthritis, where such a novel approach will be highly relevant (Schett et al., 2021).
Footnotes
Funding
C.E.A. (510601/Z/21/Z) and G.R.J. (220725/Z/20/Z) are funded by the Wellcome Trust; D.G.R. is supported by Chief Scientist Office, Scottish Government Health and Social Care Directorate (CAF/21/13); and G.H. is supported by Leona M. and Harry B. Helmsley Charitable Trust (G-1911-03343).
References
Competing interests
The authors declare no competing or financial interests.