Genomics and Proteomics as Tools for Gene Discovery in Lupus
Recently evolving technologies have made possible the large-scale measurement of gene and protein expression levels from human samples. These genomic and proteomic platforms provide a means for identification of gene and protein signatures that are linked to human disease. Such signatures have the potential to serve as clinically useful biomarkers that could improve the monitoring and management of patients, and could provide novel therapeutic targets. These researchers are interested in identifying signatures of the autoimmune disease systemic lupus erythematosus (SLE). Using whole-genome gene expression microarray profiling of peripheral blood cells, they have identified several gene signatures that distinguish SLE patients from healthy controls. Additional signatures are correlated with clinical features of SLE. They have also demonstrated that levels of certain proteins are elevated in the serum of SLE patients and correlate with disease activity. Based on these preliminary data, they proceeded to generate gene expression data on an additional ~300 patient visits. they have also obtained serum proteomic data on all longitudinal visits of 300 patients (~1500 samples). In addition to identifying clinically useful biomarkers, these experiments are designed to help us identify genes that predispose to autoimmunity. The researchers have also obtained whole-genome single nucleotide polymorphism (SNP) chips on 372 SLE patients, all of whom also have gene expression microarray data, and approximately half of these patients also have serum protein data. They recently resequenced a genomic region in 309 of the SLE patients that was identified in their SNP-gene expression association studies using nextgen sequencing methodology. The researchers expect that the data generated by their gene expression, DNA resequencing, and proteomic studies will assist them in interpreting this massive dataset.
A bibliography of this group’s publications is attached.
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