Identifying and targeting gut microbial mechanisms that contribute to methotrexate response in rheumatoid arthritis

Low-dose methotrexate (MTX) is first-line therapy for millions of patients with inflammatory arthritis or skin disease, but as many as 50-70% of patients do not adequately respond to MTX. A study of the Veterans Affairs Rheumatoid Arthritis registry demonstrated that the mortality rate among veterans with RA is more than double the rate of those without RA, which highlights the need for adequate treatment in this population. Modifying factors that limit MTX response would enable more patients to benefit from this anchor drug that synergistically increases the efficacy of other immunomodulatory medications. We recently showed that the gut microbiome of rheumatoid arthritis (RA) patients predicts MTX responsiveness, raising the possibility that gut microbiota contributes to MTX response. Unexpectedly, we found that MTX, originally designed to inhibit human folate enzymes, exerts growth-inhibitory effects on gut microbiota, and transplantation of MTX-exposed microbiotas into gnotobiotic mice led to decreased immune activation. Our findings suggest that one mechanism by which MTX exerts its anti-inflammatory effects is via modulation of the gut microbiota. Thus, the gut microbiome may be a modifiable factor that can be targeted to enable more patients to benefit from MTX. There is, therefore, a critical need to identify microbial genes responsible for sensitivity to MTX and mechanisms by which MTX affects the microbiota to shape host immunity to determine how to enhance MTX response in the host. This information can enable us to potentially modify the microbiota and better target MTX therapy to advance precision medicine for RA patients. The long-term goal of our lab is to identify the molecular mechanisms by which the human gut microbiome impacts the treatment of rheumatic and autoimmune diseases and determine how modulation of the microbiome can enhance therapeutic responses. The overall objectives of this application are to (i) identify microbial genes that determine the sensitivity of microbiota to MTX and (ii) and evaluate the mechanisms by which MTX acts on microbes to affect host immunity. We will test the hypothesis that targeting bacterial pathways involved in antibiotic resistance and folate metabolism can increase bacterial sensitivity to MTX, leading to increased extracellular adenosine and reduced inflammation in the host. The rationale is that identifying these mechanistic links is critical to determine a scientific framework for development of microbiota-targeted therapies to improve patient response to MTX. Using an innovative combination of microbial genetics and genomics, bacterially targeted drug therapies, gnotobiotic mouse models, and studies of patient-derived microbiotas, we first aim to (1) identify genetic determinants of MTX sensitivity in bacteria, and (2) decipher mechanisms of immunomodulation by MTX-altered bacteria. This project is significant because MTX non-response affects a majority of those tried on MTX. This project is innovative because it systematically probes drug-microbiota interactions to determine contributions to MTX response in the host. The results from these studies are critical to lay the foundation for the development of microbially-directed therapies to improve MTX response, potentially enabling a greater number of patients to benefit from an anchor drug in rheumatology.