Aromatic Amino Acid Metabolism in Multiple Sclerosis: A Multi-Omic Perspective

Multiple sclerosis (MS) is a chronic inflammatory and neurodegenerative disorder of the central nervous system in which immune-mediated injury contributes to demyelination, axonal damage, and progressive neurological disability. Although genetic susceptibility and environmental exposures are both known to influence MS, the biological mechanisms connecting these factors remain incompletely understood. In the study “Multi-omic evaluation of metabolic alterations in multiple sclerosis identifies shifts in aromatic amino acid metabolism,” Fitzgerald and colleagues investigated whether circulating metabolites could provide a molecular link between environmental influences, gut microbial activity, immune regulation, and disease severity. Metabolomics is particularly valuable for this purpose because the metabolome reflects the combined influence of diet, host genetics, cellular activity, medication exposure, and microbial metabolism. The investigators therefore examined whether people with MS exhibit a characteristic metabolic signature and, more importantly, whether specific metabolic disturbances are associated with neurological disability. Their findings identify aromatic amino acid metabolism as a prominent biochemical pathway altered in MS and suggest that the balance between potentially immunoregulatory and potentially harmful microbial metabolites may be biologically relevant to disease progression.

A Large-Scale Multi-Omic Study Design
The study analyzed 954 metabolomic profiles derived from 756 individuals, including 514 people with MS and 241 healthy controls, making it substantially larger than many earlier metabolomic investigations of MS. Following rigorous quality-control procedures, 269 reliably measured metabolites were included in the principal analyses. Participants were recruited from several clinical centers, including Johns Hopkins University, the University of California San Francisco, and Henry Ford Hospital-associated cohorts, thereby increasing the diversity of the study population and reducing dependence on a single clinical site. Mass spectrometry-based metabolomic profiling was used to compare the circulating concentrations of individual metabolites, while pathway-based and network-based statistical methods were applied to identify coordinated biochemical changes. The investigators also developed a “metabolomic dysfunction” score to quantify how strongly an individual's overall metabolic profile differed from that of healthy controls. To move beyond simple biomarker discovery, the researchers integrated publicly available single-cell RNA sequencing data from blood and cerebrospinal fluid and subsequently performed laboratory experiments with human monocytes. This multi-omic strategy was particularly important because it allowed associations observed in the circulation to be evaluated alongside cellular gene-expression changes and experimentally tested immune-cell functions.

Aromatic Amino Acid Metabolism Emerges as a Major Abnormality
One of the most striking observations was a broad disturbance in the metabolism of aromatic amino acids, particularly phenylalanine, tyrosine, and tryptophan. The researchers found substantial reductions in several aromatic amino acid-derived lactate metabolites, including phenyllactate, 3-(4-hydroxyphenyl)lactate, and indolelactate, with false discovery rate-adjusted statistical values indicating highly robust differences between participants with MS and healthy controls. These compounds are important because many are produced through reductive metabolic pathways involving the intestinal microbiota and may exert immunomodulatory effects. Indolelactate, for example, can interact with the aryl hydrocarbon receptor, a signaling pathway involved in regulating immune and glial-cell activity, while related lactate metabolites can activate hydroxycarboxylic acid receptor 3, which is expressed by innate immune cells. At the same time, the study identified relative increases in several metabolites produced through oxidative aromatic amino acid metabolism, including p-cresol sulfate, p-cresol glucuronide, indole acetate, and phenylacetylglutamine. Several of these molecules have previously been described as “metabotoxins” because elevated circulating concentrations have been associated with inflammatory or cardiovascular effects. The overall pattern therefore suggested not simply a generalized metabolic disruption, but a directional shift away from the production of potentially protective metabolites and toward compounds with potentially pro-inflammatory or toxic biological properties. The graphical abstract on page 1 summarizes this proposed imbalance between reductive and oxidative aromatic amino acid metabolism and its possible immunological consequences.

Metabolic Imbalance Is Associated With Disease Severity
A particularly important aspect of the study was the relationship between altered metabolism and clinical disability. Higher overall metabolomic dysfunction scores were observed among individuals with greater neurological impairment, including participants who required a cane for ambulation. Lower concentrations of several aromatic amino acid metabolites were associated with higher Expanded Disability Status Scale (EDSS) scores, a widely used measure of disability in MS. Reduced 3-(4-hydroxyphenyl)lactate showed a statistically significant association with greater disability, while lower indolelactate, phenyllactate, tryptophan, phenylalanine, kynurenine, and kynurenate also demonstrated relevant trends. In contrast, higher levels of oxidative pathway products such as p-cresol sulfate, p-cresol glucuronide, and phenylacetylglutamine were associated with greater disability. The investigators strengthened this observation by calculating ratios between oxidative and reductive metabolites. Increased oxidative-to-reductive ratios for phenylalanine, tyrosine, and tryptophan metabolism were consistently associated with higher EDSS scores. Similar associations were observed using retinal optical coherence tomography, where selected metabolites and metabolic ratios correlated with thinning of the ganglion cell and inner plexiform layers, a marker related to neurodegeneration in MS. Figure 2 of the article visually illustrates these relationships, showing that the metabolic shift is more pronounced in individuals with greater disability. These findings raise the possibility that aromatic amino acid metabolism may provide not only biomarkers of disease state but also biochemical indicators of disease severity.

Single-Cell Transcriptomics Links Metabolism to Immune-Cell Biology
To determine whether the metabolic abnormalities observed in plasma and serum were reflected at the cellular level, the investigators analyzed single-cell RNA sequencing data from immune cells isolated from blood and cerebrospinal fluid. The analysis focused particularly on pathways involved in aromatic amino acid metabolism. Significant differences were detected in monocyte populations, including monocyte-like cells enriched in both peripheral blood and cerebrospinal fluid, with people with MS generally demonstrating lower pathway activity than healthy controls. The study also examined gene networks associated with the aryl hydrocarbon receptor and hydroxycarboxylic acid receptor 3 because metabolites reduced in MS can activate these receptors. Expression of genes associated with the aryl hydrocarbon receptor network was significantly lower in monocytes from participants with MS, supporting the hypothesis that changes in circulating metabolites may coincide with altered immune signaling. Figure 3 on page 12 demonstrates these cell-type-specific differences across blood and cerebrospinal fluid compartments. The convergence of metabolomic and transcriptomic observations is scientifically important: rather than identifying isolated changes in blood chemistry, the results suggest that altered amino acid metabolism may be integrated with changes in immune-cell physiology. In particular, monocytes and related myeloid cells appear to represent a plausible cellular interface through which metabolite disturbances could influence inflammatory processes within and outside the central nervous system.

Laboratory Experiments Demonstrate Functional Effects on Monocytes
The investigators further strengthened their conclusions by testing selected metabolites directly on human immune cells. Peripheral blood mononuclear cells and purified CD14-positive monocytes from healthy donors were exposed to metabolites identified in the clinical analyses. Treatment with indole acetate, an oxidative tryptophan-derived metabolite associated with greater disability, increased tumor necrosis factor-alpha production in CD14-high monocytes in a dose-dependent manner. In a subset of experiments, indole acetate and phenylacetylglutamine also increased interleukin-6 production, supporting a potential pro-inflammatory role for oxidative aromatic amino acid metabolites. In contrast, indolelactate, which was reduced in participants with MS, demonstrated effects consistent with a more regulatory phenotype. Exposure to indolelactate increased monocyte endocytosis and reduced the production of the pro-inflammatory cytokines interleukin-6 and interleukin-1β. Figure 4 on page 13 illustrates these experiments and the associated changes in cytokine production and endocytic activity. These functional findings provide an important mechanistic dimension to the observational results: a metabolic shift toward higher concentrations of oxidative products and lower concentrations of reductive metabolites could theoretically favor a more inflammatory monocyte phenotype. Because cytokines such as tumor necrosis factor-alpha, interleukin-6, and interleukin-1β have established roles in neuroinflammatory processes, these experiments suggest a plausible biological pathway through which metabolic alterations might influence MS activity or severity.

Scientific Significance, Limitations, and Future Directions
The study provides evidence for a potentially important connection among gut microbial metabolism, circulating metabolites, immune-cell function, and neurological disability in MS. Its principal strength lies in the integration of large-scale metabolomics, clinical disability measurements, retinal imaging, single-cell transcriptomics, and functional immune-cell experiments. The findings collectively support a model in which aromatic amino acid metabolism is shifted toward oxidative pathways that generate potentially harmful metabolites, while the production of potentially immunoregulatory reductive metabolites is diminished. Nevertheless, the results should not be interpreted as demonstrating that these metabolic changes cause MS progression. The study was largely cross-sectional, meaning that it cannot establish whether metabolic alterations precede worsening disease or develop as a consequence of inflammation, disability, medication exposure, dietary changes, or other factors. Comprehensive dietary information, gut microbiome sequencing, and meal-timing data were also unavailable for many participants, limiting the researchers' ability to determine the precise origin of the observed metabolites. Future longitudinal studies integrating metagenomics, metabolomics, immune profiling, dietary assessment, and repeated measures of neurological function will therefore be essential. Such work could determine whether specific aromatic amino acid metabolites can serve as prognostic biomarkers or therapeutic targets. More broadly, this investigation demonstrates how multi-omic approaches can reveal disease mechanisms that would remain difficult to detect through conventional clinical measurements alone, offering a more integrated view of MS as a disorder involving not only the nervous and immune systems but also systemic and microbial metabolism.

Disclaimer: This blog post is based on the provided research article and is intended for informational purposes only. It is not intended to provide medical advice. Please consult with a healthcare professional for any health concerns.

References:
Zhang, Y., Zhou, Y., van der Mei, I. A. F., Simpson, S., Ponsonby, A. L., Lucas, R. M., Tettey, P., Charlesworth, J., Kostner, K., Taylor, B. V., & Ausimmune/AusLong Investigators Group (2019). Lipid-related genetic polymorphisms significantly modulate the association between lipids and disability progression in multiple sclerosis. Journal of neurology, neurosurgery, and psychiatry, 90(6), 636–641. https://doi.org/10.1136/jnnp-2018-319870