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Original article
Protein and DNA methylation-based scores as surrogate markers for interferon system activation in patients with primary Sjögren’s syndrome
  1. Albin Björk1,
  2. Elina Richardsdotter Andersson1,
  3. Juliana Imgenberg-Kreuz2,
  4. Gudny Ella Thorlacius1,
  5. Johannes Mofors1,
  6. Ann-Christine Syvänen3,
  7. Marika Kvarnström1,
  8. Gunnel Nordmark2 and
  9. Marie Wahren-Herlenius1
  1. 1 Division of Rheumatology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
  2. 2 Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
  3. 3 Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
  1. Correspondence to Professor Marie Wahren-Herlenius; marie.wahren{at}ki.se

Abstract

Objective Standard assessment of interferon (IFN) system activity in systemic rheumatic diseases depends on the availability of RNA samples. In this study, we describe and evaluate alternative methods using plasma, serum and DNA samples, exemplified in the IFN-driven disease primary Sjögren’s syndrome (pSS).

Methods Patients with pSS seropositive or negative for anti-SSA/SSB and controls were included. Protein-based IFN (pIFN) scores were calculated from levels of PD-1, CXCL9 and CXCL10. DNA methylation-based (DNAm) IFN scores were calculated from DNAm levels at RSAD2, IFIT1 and IFI44L . Scores were compared with mRNA-based IFN scores measured by quantitative PCR (qPCR), Nanostring or RNA sequencing (RNAseq).

Results mRNA-based IFN scores displayed strong correlations between B cells and monocytes (r=0.93 and 0.95, p<0.0001) and between qPCR and Nanostring measurements (r=0.92 and 0.92, p<0.0001). The pIFN score in plasma and serum was higher in patients compared with controls (p<0.0001) and correlated well with mRNA-based IFN scores (r=0.62–0.79, p<0.0001), as well as with each other (r=0.94, p<0.0001). Concordance of classification as ‘high’ or ‘low’ IFN signature between the pIFN score and mRNA-based IFN scores ranged from 79.5% to 88.6%, and the pIFN score was effective at classifying patients and controls (area under the curve, AUC=0.89–0.93, p<0.0001). The DNAm IFN score showed strong correlation to the RNAseq IFN score (r=0.84, p<0.0001) and performed well in classifying patients and controls (AUC=0.96, p<0.0001).

Conclusions We describe novel methods of assessing IFN system activity in plasma, serum or DNA samples, which may prove particularly valuable in studies where RNA samples are not available.

  • Sjögren’s syndrome
  • interferon
  • IFN
  • Nanostring
  • DNA methylation
http://creativecommons.org/licenses/by-nc/4.0/

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Footnotes

  • Contributors MW-H, AB, ERA, JI-K, GET, JM and GN conceived the study. MK, GN and AB recruited the patients. AB, ERA and JI-K performed the experiments. AB, JI-K, ERA, GET, JM and MW-H analysed the data. A-CS oversaw the RNA sequencing and DNA methylation analyses. AB and MW-H wrote the manuscript. All authors critically evaluated the manuscript and participated in the editing until its final version.

  • Funding The study was supported by grants from the Swedish Research Council, the Stockholm County Council, the Karolinska Institute, the Swedish Rheumatism association and the King Gustaf the V:th 80-year foundation and a Merck Research Collaboration grant.

  • Competing interests None declared.

  • Patient consent for publication Not required.

  • Ethics approval The study was approved by the Regional Ethics Board in Uppsala and the Regional Ethics Committee in Stockholm.

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Data availability statement Data are available on reasonable request.

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