I have been using a custom spotted oligo microarray platform to investigate gene expression signatures in autoimmune diseases, specifically ANCA-associated systemic vasculitis and SLE. The highly heterogeneous clinical phenotypes seen in these syndromes make classification and diagnosis problematic and potentially confound attempts to further investigate underlying pathogenesis.
I am using a cell separation step in RNA extraction from whole blood to derive labelled cDNA from 5 cell subsets (CD4,8,14,16 and 19) as well as unseparated PBMC. Samples are collected during active disease and subsequently after 3 and 12 months of therapy, during which time patients undergo close clinical monitoring. This allows correlation of derived expression signatures with extensive clinical data and mining for novel disease biomarkers with both diagnostic and prognostic value.
co-stimulation ; B cells ; microarrays ; co-stimulatory molecules ; statistical analysis ; regulatory T cells ; T cell receptor (TCR) ; cytokines ; cross-sectional and cohort studies ; autoimmunity ; genetics ; adhesion ; inflammation ; Fc receptors ; cytotoxic T cells (CTL) ; apoptosis ; activation ; T cells ; human studies ; antibody responses ; immune complexes ; randomised control trials ; pattern recognition receptors ; inflammatory mediators ; computational modelling ; cell development ; clinical immunology ; FACS
Richard AC, Lyons PA, Peters JE, Biasci D, Flint SM, Lee JC, McKinney EF, Siegel RM, Smith KG. Comparison of gene expression microarray data with count-based RNA measurements informs microarray interpretation. BMC Genomics. 2014 Aug 4;15(1):649.
McKinney EF, Willcocks LC, Broecker V, Smith KG. The immunopathology of ANCA-associated vasculitis. Semin Immunopathol. 2014 Jul;36(4):461-78.
Toshner M, Dunmore BJ, McKinney EF, Southwood M, Caruso P, Upton PD, Waters JP, Ormiston ML, Skepper JN, Nash G, Rana AA, Morrell NW. Transcript analysis reveals a specific HOX signature associated with positional identity of human endothelial cells.
PLoS One. 2014 Mar 20;9(3):e91334. d
Ferreira RC, Guo H, Coulson RM, Smyth DJ, Pekalski ML, Burren OS, Cutler AJ, Doecke JD, Flint S, McKinney EF, Lyons PA, Smith KG, Achenbach P,Beyerlein A, Dunger DB, Wicker LS, Todd JA, Bonifacio E, Wallace C, Ziegler AG. A type I interferon transcriptional signature precedes autoimmunity in children genetically at-risk of type 1 diabetes. Diabetes. 2014 Jul;63(7):2538-50.
Abdul V, Aziz N, Lim YT, Ng Ai Poh A, Jin Hui Chan S, Ho Xin Pei E, Lew FC, Shui G, Jenner AM, Bowen L, McKinney EF, Lyons PA, Kemeny MD, Smith KG, Wenk MR, Macary PA. Lipid anti-lipid antibody responses correlate with disease activity in systemic lupus erythematosus. PLoS One. 2013;8(2):e55639. doi: 10.1371/journal.pone.0055639.
Kain R, Tadema H, McKinney EF, Benharkou A, Brandes R, Peschel A, Hubert V, Feenstra T, Sengölge G, Stegeman C, Heeringa P, Lyons PA, Smith KG, Kallenberg C, Rees AJ. High prevalence of autoantibodies to hLAMP-2 in anti-neutrophil cytoplasmic antibody-associated vasculitis. J Am Soc Nephrol. 2012 Mar;23(3):556-66.
Lee JC, Lyons PA, McKinney EF, Sowerby JM, Carr EJ, Bredin F, Rickman HM, Ratlamwala H, Hatton A, Rayner TF, Parkes M, Smith KG. Gene expression profiling of CD8+ T cells predicts prognosis in patients with Crohn disease and ulcerative colitis. J Clin Invest. 2011 Oct;121(10):4170-9.
McKinney EF, Lyons PA, Carr EJ, Hollis JL, Jayne DR, Willcocks LC, Koukoulaki M, Brazma A, Jovanovic V, Kemeny DM, Pollard AJ, Macary PA, Chaudhry AN, Smith KG. A CD8+ T cell transcription signature predicts prognosis in autoimmune disease. Nat Med. 2010 May;16(5):586-591
Lyons PA, McKinney EF, Rayner TF, Hatton A, Woffendin HB, Koukoulaki M, Freeman TC, Jayne DR, Chaudhry AN, Smith KG. Novel expression signatures identified by transcriptional analysis of separated leucocyte subsets in systemic lupus erythematosus and vasculitis. Ann Rheum Dis. 2010 Jun;69(6):1208-13.
Arnott ID, Nimmo ER, Drummond HE, Fennell J, Smith BR, McKinney EF, Morecroft J, Anderson J, Kelleher D, Satsangi J NOD-2/CARD15, TLR4 and CD14 mutations in Scottish and Irish Crohns disease patients: evidence for genetic heterogeneity within Europe? Genes Immun 2004 Aug;5(5):417–25