RA-MAP, molecular immunological landscapes in early rheumatoid arthritis and healthy vaccine recipients

Abstract

Rheumatoid arthritis (RA) is a chronic inflammatory disorder with poorly defined aetiology characterised by synovial inflammation with variable disease severity and drug responsiveness. To investigate the peripheral blood immune cell landscape of early, drug naive RA, we performed comprehensive clinical and molecular profiling of 267 RA patients and 52 healthy vaccine recipients for up to 18 months to establish a high quality sample biobank including plasma, serum, peripheral blood cells, urine, genomic DNA, RNA from whole blood, lymphocyte and monocyte subsets. We have performed extensive multi-omic immune phenotyping, including genomic, metabolomic, proteomic, transcriptomic and autoantibody profiling. We anticipate that these detailed clinical and molecular data will serve as a fundamental resource offering insights into immune-mediated disease pathogenesis, progression and therapeutic response, ultimately contributing to the development and application of targeted therapies for RA.

Fig. 1

Overview of the RA-MAP project. a multi-omic bio-resource to facilitate the study of immune response in rheumatoid arthritis (RA) patients and healthy vaccine recipients (VC).

Fig. 2

Summary of sample-platform overlap in (a) The TACERA cohort, (b) The Vaccine Cohort. Vaccine V1-V8 relates to visits 1, 2, 4, 6 & 8 at day -7, 0, 3, 56, 63.

Fig. 3

Principal component analysis (PCA) across multiple omic platforms at baseline and 6-months in whole blood and cell subsets in (a) the TACERA early RA cohort and (b) across 6 visits (day −7, 0, 3, 56 and 63) in the vaccine cohort. Similar separation by cell type is evident in both RA and vaccine cohorts. Some evidence of separation by time is seen in the RA cohort, but this is less evident in the Vaccine cohort. Multi-omic PCA comparison at baseline and 6-months in early RA across (c) whole blood mRNA, (d) micro RNA (serum), (e) proteome (plasma), (f) autoantibodies (serum), (g) metabolome (serum) and (h) metabolome (urine). Clear separation with time is seen in Whole Blood and cell subset mRNA, Serum miRNA, Serum Autoantibodies and Urine metabolome.

Fig. 4

Unsupervised PCA Driver analysis of multi-omic compartments across TACERA early RA patients and Hepatitis B vaccine recipients, showing clinical features and their degree of association with Principal Components (PC) 1–5, percentage indicating variation accounted for by the PC and with coloring indicating the –log q-value of the association (scaled to maximum range of PC1 across all compartments, off scale associations are indicated in grey with –log q written). Significant drivers with an FDR threshold of 5% are indicated by outline. Specific drivers of variation in expression in analysed samples are indicated in TACERA patients in (a) Whole Blood mRNA, (b) PBMC mRNA, (c) CD4 mRNA, (d) CD8 mRNA, (e) CD14 mRNA, (f) Whole Blood micro RNA, (g) Plasma proteomics, (h) Serum autoantibodies, (i) Serum metabolome, (j) Urine metabolome. In VACCINE recipients in (k) Whole Blood mRNA, (l) PBMC mRNA, (m) CD4 mRNA, (n) CD8 mRNA, (o) CD14 mRNA. Clinical features include XRAY (quantitative measure of bone erosion at sample timepoint (0 or 6 m)), TIME (sample annotation at baseline or 6-months), SYMP_DUR (Symptom duration at diagnosis), SMOKER (smoking status Y, N, Previous), SEX (M/F), RF (Rheumatoid factor positive Y/N), PAIN (quantitative measure of pain at sample timepoint (0 or 6 m)), FATIGUE (quantitative measure of fatigue at sample timepoint (0 or 6 m)), ETHNICITY (Ethnic origin), DAS28 (disease activity score in 28 joints at sample timepoint (0 or 6 m)), CRP (quantitative measure of C-reactive protein at sample timepoint (0 or 6 m)), BMI (Body Mass Index at baseline), ALCOHOL (Y/N), AGE (Age at baseline), ACPA (anti-citrullinated protein antibody positive Y/N), SEROLOGY (Hepatitis B serology at week 9). In the TACERA cohort in 3a-j the first two PCs are closely associated with DAS28 scores in Whole Blood, PBMC mRNA, CD4 mRNA, and CD14 mRNA; and rather less closely associated with the other platforms. In 3k-o, in contrast to the highly dysregulated immune system seen in RA patients, the biological perturbation following a vaccine-related immune challenge in the healthy volunteers appears negligible.