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      Antimetabolite Drugs Exhibit Distinctive Immunomodulatory Mechanisms and Effects on the Intestinal Microbiota in Experimental Autoimmune Uveitis

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          Abstract

          Purpose

          The purpose of this study was to investigate the effect of antimetabolite drugs on T-cell responses and intestinal microbial composition in autoimmune uveitis.

          Methods

          Experimental autoimmune uveitis (EAU) was induced in C57BL/6J mice treated with 0.00625 mg/mL methotrexate (MTX) or 0.625 mg/mL mycophenolate mofetil (MMF) in drinking water for 4 weeks prior to immunization and 2 weeks thereafter. The effector T cell (Teff) and regulatory T cell (Treg) populations were identified using flow cytometry. The 16S rRNA gene sequencing was applied for gut microbiome characterization. DESeq2 analysis was used to discriminate relative abundances of taxa and PLS-DA to integrate cytometric and microbiome data between groups.

          Results

          Both MTX and MMF abrogated uveitis in EAU without clinical signs of toxicity as compared to water-fed controls. MTX reduced Teff and Treg expansion in peripheral tissues and eyes. MTX decreased alpha diversity, increased Akkermansia, and reduced Lachnoclostridium abundances. Conversely, MMF enhanced Tregs in the mesenteric lymph node and the eyes. In parallel, MMF increased the gut alpha diversity, including an increased abundance of Lachnospiraceae NK4A136 group and a decreased abundance of Lachnospiraceae UCG-001. A significant congruent correlation among intestinal microbial changes, T-cell responses, and clinical scores was observed for both antimetabolites.

          Conclusions

          Although MTX and MMF both abrogated uveitis in EAU, they showed different effects on T-cell subsets and the intestinal bacterial composition. This work indicates unique immunomodulation by each drug and is the first to demonstrate potential microbiota-related mechanisms.

          Resumen

          Objetivo

          Investigar el efecto de los fármacos antimetabolitos sobre las respuestas de células T y la composición microbiana intestinal en la uveítis autoinmune.

          Métodos

          Se indujo uveítis autoinmune experimental (UAE) en ratones C57BL/6J tratados con 0.00625 mg/ml de metotrexato (MTX) o 0.625 mg/ml de micofenolato mofetilo (MFM) en agua de bebida durante 4 semanas antes de la inmunización y 2 semanas después. Las poblaciones de células T efectoras (Tef) y reguladoras (Treg) se identificaron por citometría de flujo. La caracterización del microbioma intestinal se realizó mediante secuenciación del gen 16S ARNr. El análisis discriminante de abundancias relativas en los taxones se llevó a cabo por DESeq2 y se usó un análisis PLS-DA para integrar los datos microbianos y citométricos entre grupos.

          Resultados

          MTX y MFM inhibieron la UAE sin signos clínicos de toxicidad comparado con los controles. MTX disminuyó la expansión de Tef y Treg en los tejidos periféricos y oculares. MTX redujo la alfa diversidad, incrementando la abundancia de Akkermansia, y reduciendo la de Lachnoclostridium. En cambio, MFM aumentó los Tregs en el ganglio mesentérico y en los ojos. Paralelamente, MFM aumentó la alfa diversidad, incluyendo un aumento de la abundancia del grupo Lachnospiraceae NK4A136 y un descenso de la de Lachnospiraceae UCG-001. Se observó una correlación congruente significativa, para ambos fármacos, entre los cambios en el microbioma, las respuestas de células T y los grados clínicos de uveítis.

          Conclusiones

          Aunque ambos, MTX y MFM, suprimieron la UAE, mostraron efectos diferentes sobre los subtipos de células T y sobre la composición del microbioma. Este estudio indica un efecto inmunomodulador único para cada fármaco y es el primero en demostrar potenciales mecanismos relacionados con el microbioma.

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          Most cited references45

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            DADA2: High resolution sample inference from Illumina amplicon data

            We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
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              phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

              Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. Conclusions The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.
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                Author and article information

                Journal
                Invest Ophthalmol Vis Sci
                Invest Ophthalmol Vis Sci
                IOVS
                Investigative Ophthalmology & Visual Science
                The Association for Research in Vision and Ophthalmology
                0146-0404
                1552-5783
                31 March 2022
                March 2022
                : 63
                : 3
                : 30
                Affiliations
                [1 ]Clínic Institute of Ophthalmology (ICOF), Clínic Hospital of Barcelona, Barcelona, Spain
                [2 ]Biomedical Research Institute August Pi i Sunyer (IDIBAPS), Clínic Hospital of Barcelona, Barcelona, Spain
                [3 ]Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
                Author notes
                [* ]Correspondence: Victor Llorenç, Clínic Institute of Ophthalmology, Clínic Hospital of Barcelona, Sabino de Arana str., 1, 2nd floor, PC 08028-Barcelona, Spain; llorens.victor@ 123456gmail.com .
                Article
                IOVS-21-33680
                10.1167/iovs.63.3.30
                8976920
                35357394
                12807246-925a-4c9c-839c-8b194f301083
                Copyright 2022 The Authors

                This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

                History
                : 08 March 2022
                : 26 August 2021
                Page count
                Pages: 13
                Categories
                Immunology and Microbiology
                Immunology and Microbiology

                antimetabolites,experimental autoimmune uveitis,methotrexate,intestinal microbiome,mycophenolate mofetil,uveitis

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