Gut Microbiome Diversity Linked to Treatment Response to Methotrexate

A study published in Arthritis and Rheumatology¹ has found rheumatoid arthritis patients with a less diverse gut microbiome do not respond as well to methotrexate, suggesting that the gut microbiome may have a direct effect on metabolism of methotrexate and treatment outcomes.

Although methotrexate is well tolerated and has a significantly lower cost compared with newer biologic therapies, only around one in two patients achieve an adequate clinical response to methotrexate monotherapy. The reason behind this is not clearly understood.

Studies in rodents have demonstrated that the gut microbiome is capable of metabolizing methotrexate into its inactive metabolite 2,4- diamino- N10- methylpteroic acid (DAMPA) and have shown that although methotrexate metabolites can be excreted in the feces of conventionally reared animals, DAMPA is not detected in germ-free or antibiotics-treated mice. These findings suggest that the gut microbiome is necessary for this biotransformation. There is also evidence that several other drugs, ranging from digoxin and L-dopa to cancer immunotherapies, can be either metabolized by the human gut microbiome or are dependent on it for their efficacy.

“Based on this evidence, we hypothesized that perhaps the intestinal microbiome of some patients may have the functional capability to metabolize oral methotrexate and, as a consequence, alter the future treatment response,” said Carles Ubeda of the Centro Superior de Investigación en Salud Pública, FISABIO in Valencia and CIBER en Epidemiología y Salud Pública in Madrid, Spain.

To test this hypothesis, the researchers performed 16S rRNA gene and shotgun metagenomic sequencing on the gut microbiomes of 26 drug-naïve, new-onset RA (NORA). At four months, 39% were classed as methotrexate responders based on improvement in DAS28 score of at least 1.8 points. They found significant associations between the abundance of gut bacterial taxa and their genes with future clinical response, including orthologs related to purine and methotrexate metabolism.

Ex vivo experiments were used to evaluate the association between microbiome-driven methotrexate depletion and clinical response. These showed that

methotrexate levels remaining after incubation with distal gut samples significantly correlated with the magnitude of future clinical response.

“The microbiome could be influencing the bioavailability of methotrexate thought direct metabolism of the drug,” explained Ubeda. “We have found significant differences in the abundance of gene orthologs encoded by the microbiome of naïve rheumatoid arthritis patients depending on their capacity to clinically respond to methotrexate. Importantly, some of these gene orthologs are related to methotrexate metabolism. In addition, supporting a direct role of the microbiome in the response to methotrexate, we found that methotrexate levels remaining after ex vivo incubation with distal gut samples from pre-treatment rheumatoid arthritis patients significantly correlated with the magnitude of future clinical response.”

Another possibility, he added, is that the microbiome may be influencing response to methotrexate by modulating the immune system.

The researchers applied machine learning techniques to the metagenomic data to develop a microbiome-based model that was able to predict lack of response to methotrexate in an independent group of 21 patients.

“The most important take home message for rheumatologists is that we can predict lack of response to methotrexate by analyzing the fecal microbiome of patients before the initiation of the treatment,” said Dr Jose Scher, MD, rheumatologist from the Department of Medicine, Mount Sinai School of Medicine, New York. “Another important message is that we show for the first time that the human microbiome can metabolize methotrexate.”

Jose Scher, MD

The findings suggest that in the future it may be possible to develop of biomarkers of methotrexate response, either by high-throughput sequencing or through simplified (e.g., PCR-based) precision medicine approaches. Dr Scher explains, “Further, our results open the possibility to rationally design microbiome-modulating strategies to improve oral absorption of methotrexate and its downstream immune effects, inform clinical-decision making or both.”

However, he cautioned: “We should be careful about proposing microbiome-modulation strategies, since they could have detrimental effects on other diseases related to microbiome changes. Thus, other alternative options, such as the synthesis of drugs that cannot be metabolized by the microbiome, may have less undesired secondary effects.”

Reference

Artacho A, Isaac S, Nayak R, et al. The Pre-treatment Gut Microbiome is Associated with Lack of Response to Methotrexate in New Onset Rheumatoid Arthritis [published online ahead of print, 2020 Dec 13]. Arthritis Rheumatol. 2020;10.1002/art.41622. doi:10.1002/art.41622