Meta-Analysis Derived (MAD) Transcriptome of Psoriasis Defines the “Core” Pathogenesis of Disease

• Published in: PloS one Vol. 7; no. 9; p. e44274
• Main Authors: Tian, Suyan, Krueger, James G., Li, Katherine, Jabbari, Ali, Brodmerkel, Carrie, Lowes, Michelle A., Suárez-Fariñas, Mayte
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 05.09.2012; Public Library of Science (PLoS)
• Subjects: Algorithms; Analysis; Arteriosclerosis; Atherosclerosis; Biology; Biomarkers; Cardiovascular diseases; Computational Biology - methods; Data processing; Dermatology; Development; DNA methylation; DNA microarrays; Fatty acids; Gene expression; Gene Expression Profiling - methods; Genes; Genetic aspects; Genomes; Genomics; Humans; Immunology; Inflammation; Inflammatory diseases; Laboratories; Lipid Metabolism; Mathematics; Medicine; Meta-analysis; Metabolic disorders; Metabolic syndrome; Metabolism; Methods; Methylation; Models, Genetic; Models, Statistical; Oligonucleotide Array Sequence Analysis - methods; Pathogenesis; Psoriasis; Psoriasis - genetics; Psoriasis - metabolism; Psoriasis - physiopathology; R&D; Regularization; Research & development; Reviews; Rheumatoid arthritis; Signal Transduction; Signaling; Skin; Skin - metabolism; Skin diseases; Stem cells; Studies; Tissues; Transcription Factors - metabolism; Transcriptome; New York; United States > US; Pennsylvania
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0044274

The cause of psoriasis, a common chronic inflammatory skin disease, is not fully understood. Microarray experiments have been widely used in recent years to identify genes associated with psoriasis pathology, by comparing expression levels of lesional (LS) with adjacent non-lesional (NL) skin. It is commonly observed that the differentially expressed genes (DEGs) differ greatly across experiments, due to variations introduced in the microarray experiment pipeline. Therefore, a statistically based meta-analytic approach, which combines the results of individual studies, is warranted. In this study, a meta-analysis was conducted on 5 microarray data sets, including 193 LS and NL pairs. We termed this the Meta-Analysis Derived (MAD) transcriptome. In "MAD-5" transcriptome, 677 genes were up-regulated and 443 were down-regulated in LS skin compared to NL skin. This represents a much larger set than the intersection of DEGs of these 5 studies, which consisted of 100 DEGs. We also analyzed 3 of the studies conducted on the Affymetrix hgu133plus2 chips and found a greater number of DEGs (1084 up- and 748 down-regulated). Top canonical pathways over-represented in the MAD transcriptome include Atherosclerosis Signaling and Fatty Acid Metabolism, while several "new" genes identified are involved in Cardiovascular Development and Lipid Metabolism. These findings highlight the relationship between psoriasis and systemic manifestations such as the metabolic syndrome and cardiovascular disease. Then, the Meta Threshold Gradient Descent Regularization (MTGDR) algorithm was used to select potential markers distinguishing LS and NL skin. The resulting set (20 genes) contained many genes that were part of the residual disease genomic profile (RDGP) or "molecular scar" after successful treatment, and also genes subject to differential methylation in LS tissues. To conclude, this MAD transcriptome yielded a reference list of reliable psoriasis DEGs, and represents a robust pool of candidates for further discovery of pathogenesis and treatment evaluation.