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Identification and evaluation of serum protein biomarkers which differentiate psoriatic from rheumatoid arthritis

Citation

Mc Ardle, Angela (2021), Identification and evaluation of serum protein biomarkers which differentiate psoriatic from rheumatoid arthritis, Dryad, Dataset, https://doi.org/10.5061/dryad.9zw3r22df

Abstract

Objectives

To identify serum protein biomarkers which might separate early inflammatory arthritis (EIA) patients with psoriatic arthritis (PsA) from those with rheumatoid arthritis (RA) and may be used to support appropriate early intervention.

Methods

The serum proteome of patients with PsA and RA was interrogated using liquid chromatography mass spectrometry (LC-MS/MS) (n=64 patients), a multiplexed antibody assay (Luminex) for 48 proteins (n=64 patients) and an aptamer-based assay (SOMAscan) targeting 1,129 proteins (n=36 patients). Multiple reaction monitoring assays were developed to evaluate the performance of putative markers in the discovery cohort (n=60) as well as an independent cohort of PsA and RA patients (n=167).

Results

Multivariate analysis of the protein discovery data revealed that it was possible to discriminate PsA from RA patients with an area under the curve (AUC) of 0.94 for nLCMS/MS, 0.69 for Luminex based measurements; 0.73 for SOMAscan analysis. Random forest models confirmed that a subset of protein measured by MRM could differentiate PsA and RA patients with an AUC of 0.79 and 0.85 during separate evaluation and verification studies.

Conclusion

We report a serum protein biomarker panel which can separate EIA patients with PsA from those with RA. We suggest that the routine use of such a panel in EIA patients will improve clinical decision making. With continued evaluation and refinement on additional and larger patient cohorts including those with other arthropathies we suggest the panel identified here will contribute toward improved clinical decision making.

Usage Notes

Supplementary tables associated with the paper entitled: Identification and Evaluation of Serum Protein Biomarkers Which Differentiate Psoriatic from Rheumatoid Arthritis

Suppl Table 1. Lists 66 proteins were significantly differentially expressed between PsA and RA patients. This table reports a list of 66 proteins that were found to discriminate between patients with PsA (n=30) from those with RA (n=30) during nLC-MS/MS analysis of individual patient serum samples (FDR 0.01, p < 0.01).

Supp Table 2: Lists top 50 ‘nLC-MS/MS’ proteins that discriminate PsA patients from those with RA. Multivariate analysis (RF model) of nLC-MS/MS data revealed a list of serum proteins that could be used to discriminate between patients with PsA and RA (AUC 0.94). The top 50 most discriminatory proteins are reported here. Proteins are listed based on their contribution to the AUC (from high to low).

Supp Table 3. Lists 175 proteins found to be significantly differentially expressed between individuals with psoriatic (PsA) and rheumatoid arthritis (RA). Proteins were identified using an aptamer based assay which supported the analysis of 36 patients with PsA (n=18) and RA (n=18).

Supp Table 4. List the top most discrimantory proteins identied during two round of MRM analysis. Proteins are listed alphabetically were rerpresented by proteotypic peptides when measured by MRM (A) Of the 34 listed, 25 were measured in both MRM phase I and phase II assays. (B) Of those 25 proteins, 8 proteins were top contributers to the AUC in generated during phase I (AUC 0.79) and phase II (AUC 0.85). (C) Of the 8 protiens in (B), 6 were significantly urpegualted in RA (un-pairded T test, see Suppl Fig 4). *Coagulation factor X1 and thrombospndin did not reach statstical signficance during phase I analysis  (Suppl Fig 4) Of the 34 proteins listed in (D), 9 proteins providing AUC 0.85 were exclusively present in the MRM phase II assay. 

Suppl Table 5. Lists functional roles of discriminatory proteins included in MRM analysis. Table was generated based of results from STRING software.