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.
McKinney EF & Smith KGC. Metabolic exhaustion in cancer, infection and autoimmunity. Nature Immunology 2018. DOI: 10.1038/s41590-018-0045-y
McKinney EF & Smith KGC. T cell exhaustion and immune-mediated disease – the potential for therapeutic exhaustion. Current Opinion in Immunology 2016. DOI: 10.1016/j.coi.2016.09.005
McKinney EF & Smith KGC. T cell exhaustion: understanding the interface of chronic viral and autoinflammatory diseases. Immunology & Cell Biology 2016. DOI: 10.1038/icb.2016.81
McKinney EF, Lee JC … Smith KG; T cell exhaustion, costimulation and clinical outcome in autoimmunity and infection. Nature 2015. DOI: 10.1038/nature14468