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The synovial and blood monocyte DNA methylomes mirror prognosis, evolution, and treatment in early arthritis
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
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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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 5

Correlation of DNA methylation and DAS28 in blood and SF of UA.

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Correlation of DNA methylation and DAS28 in blood and SF of UA.
(A) Viol...
(A) Violin plots showing z-scored β values of DAS28-correlated CpGs (P < 0.001, ρ ≥ 0.7), by activity category, in blood MOs. (B) Violin plots showing z-scored β values of DAS28-correlated CpGs in blood, by activity category, in SF MOs. Color in A and B indicates mean DAS28 score of each group. The number of samples in every activity category is noted in parentheses. (C) Scatter plots showing the correlation between the Δ of DAS28 and the Δ of z-scored β values between the first and fourth visits, in blood. Color indicates changes in activity categories. (D) Linear regression prediction of DAS28 from DNA methylation. First-visit blood samples were used to train the model, and prediction was performed on fourth-visit blood samples and first-visit SF samples. (E) Linear regression prediction of DAS28 on public data of MO samples from patients with RA, at first and second visits, after follow-up. In D and E, correlation coefficients (R2) and P values were calculated by Pearson’s correlation. Activity categories are defined as follows by the DAS28 value: remission (<2.6), low activity (2.6–3.2), moderate activity (3.2–5.1), and high activity (>5.1). In A and B, violin plots show density curves, and circles and vertical lines show the median and the 25th to 75th percentiles. The number of samples in D and E is indicated in Supplemental Figure 3G. In D and E, gray shades indicate the 95% CI of the value distributions.

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