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The synovial and blood monocyte DNA methylomes mirror prognosis, evolution, and treatment in early arthritis
Carlos de la Calle-Fabregat, … , Juan D. Cañete, Esteban Ballestar
Carlos de la Calle-Fabregat, … , Juan D. Cañete, Esteban Ballestar
Published March 24, 2022
Citation Information: JCI Insight. 2022;7(9):e158783. https://doi.org/10.1172/jci.insight.158783.
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Research Article Inflammation

The synovial and blood monocyte DNA methylomes mirror prognosis, evolution, and treatment in early arthritis

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Abstract

Identifying predictive biomarkers at early stages of inflammatory arthritis is crucial for starting appropriate therapies to avoid poor outcomes. Monocytes (MOs) and macrophages, largely associated with arthritis, are contributors and sensors of inflammation through epigenetic modifications. In this study, we investigated associations between clinical features and DNA methylation in blood and synovial fluid (SF) MOs in a prospective cohort of patients with early inflammatory arthritis. DNA methylation profiles of undifferentiated arthritis (UA) blood MOs exhibited marked alterations in comparison with those from healthy donors. We identified additional differences both in blood and SF MOs after comparing patients with UA grouped by their future outcomes, i.e., good versus poor. Patient profiles in subsequent visits revealed a reversion toward a healthy level in both groups, those requiring disease-modifying antirheumatic drugs and those who remitted spontaneously. Changes in disease activity between visits also affected DNA methylation, which was partially concomitant in the SF of UA and in blood MOs of patients with rheumatoid arthritis. Epigenetic similarities between arthritis types allow a common prediction of disease activity. Our results constitute a resource of DNA methylation–based biomarkers of poor prognosis, disease activity, and treatment efficacy for the personalized clinical management of early inflammatory arthritis.

Authors

Carlos de la Calle-Fabregat, Javier Rodríguez-Ubreva, Laura Ciudad, Julio Ramírez, Raquel Celis, Ana Belén Azuaga, Andrea Cuervo, Eduard Graell, Carolina Pérez-García, César Díaz-Torné, Georgina Salvador, José A. Gómez-Puerta, Isabel Haro, Raimon Sanmartí, Juan D. Cañete, Esteban Ballestar

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Figure 4

Evolution of DNA methylation profiles in subsequent visits.

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Evolution of DNA methylation profiles in subsequent visits.
(A) Box plot...
(A) Box plots showing z-scored β values of DMPs between the first and fourth visits, by GP and PP, paired by patient and using DAS28 as a covariate (FDR < 0.05). (B) Heatmap of the DMPs in the hypomethylated cluster. Group, DAS28, and treatment are shown for every patient at the top, and the respective legend scales are shown to the right of the heatmap. Blue and red indicate lower and higher methylation, respectively. (C) IFNAR locus with PCHi-C interaction public data. (D) DNA methylation of cg09277541 (left panel) and gene expression of IFNAR1 and IFNAR2 (right panel) in visits 1–4, by prognosis group. DMP and interacting HindIII fragments are shown below a genome browser annotation of transcripts and MO ChromHMM tracks (see Methods). DNA methylation and gene expression from D were analyzed by bisulfite pyrosequencing and qRT-PCR, respectively. RPL38 was used as the HKG. The number of samples analyzed for each group in every time point is indicated in Supplemental Figure 1A. In A and D, each box represents the 25th to 75th percentiles. The lines inside the boxes represent the median. The lines outside the boxes represent the 25th percentile minus 1.5 times the IQR and the 75th percentile plus 1.5 times the IQR. Pairwise group differences were evaluated by 2-tailed Wilcoxon’s tests. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.

Copyright © 2022 American Society for Clinical Investigation
ISSN 2379-3708

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