Novel expression signatures identified by transcriptional analysis of separated leucocyte subsets in systemic lupus erythematosus and vasculitis.
OBJECTIVE
To optimise a strategy for identifying gene expression signatures differentiating systemic lupus erythematosus (SLE) and antineutrophil cytoplasmic antibody-associated vasculitis that provide insight into disease pathogenesis and identify biomarkers.


METHODS
44 vasculitis patients, 13 SLE patients and 25 age and sex-matched controls were enrolled. CD4 and CD8 T cells, B cells, monocytes and neutrophils were isolated from each patient and, together with unseparated peripheral blood mononuclear cells (PBMC), were hybridised to spotted oligonucleotide microarrays.


RESULTS
Using expression data obtained from purified cells a substantial number of differentially expressed genes were identified that were not detectable in the analysis of PBMC. Analysis of purified T cells identified a SLE-associated, CD4 T-cell signature consistent with type 1 interferon signalling driving the generation and survival of tissue homing T cells and thereby contributing to disease pathogenesis. Moreover, hierarchical clustering using expression data from purified monocytes provided significantly improved discrimination between the patient groups than that obtained using PBMC data, presumably because the differentially expressed genes reflect genuine differences in processes underlying disease pathogenesis.


CONCLUSIONS
Analysis of leucocyte subsets enabled the identification of gene signatures of both pathogenic relevance and with better disease discrimination than those identified in PBMC. This approach thus provides substantial advantages in the search for diagnostic and prognostic biomarkers in autoimmune disease.
Lyons
Paul A
PA
Department of Medicine, Cambridge Institute for Medical Research, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0XY, UK. pal34@cam.ac.uk
McKinney
Eoin F
EF
Rayner
Tim F
TF
Hatton
Alexander
A
Woffendin
Hayley B
HB
Koukoulaki
Maria
M
Freeman
Thomas C
TC
Jayne
David R W
DR
Chaudhry
Afzal N
AN
Smith
Kenneth G C
KG
D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D056648:Anti-Neutrophil Cytoplasmic Antibody-Associated Vasculitis / Q000175:diagnosis* / Q000235:genetics / Q000276:immunology; D015496:CD4-Positive T-Lymphocytes / Q000276:immunology; D003937:Diagnosis, Differential; D005260:Female; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods; D006801:Humans; D007962:Leukocytes / Q000276:immunology*; D008180:Lupus Erythematosus, Systemic / Q000175:diagnosis* / Q000235:genetics / Q000276:immunology; D008213:Lymphocyte Activation / Q000276:immunology; D008297:Male; D008875:Middle Aged; D009000:Monocytes / Q000276:immunology; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D011379:Prognosis; D012720:Severity of Illness Index; D016176:T-Lymphocyte Subsets / Q000276:immunology; D014158:Transcription, Genetic; D055815:Young Adult