Global gene expression analysis reveals evidence for decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin

Abstract

Psoriasis is a genetically determined inflammatory skin disease. Although the transition from uninvolved into lesional skin is accompanied by changes in the expression of multiple genes, much less is known about the difference between uninvolved skin from psoriatic patients as opposed to skin from normal individuals. Multiple biochemical and morphological changes were reported decades ago in uninvolved psoriatic skin but remain poorly understood. Here, we show dysregulation of 223 transcripts representing 179 unique genes in uninvolved psoriatic skin, 178 of which were not previously known to be altered in their expression. The proteins encoded by these transcripts are involved in lipid metabolism, antimicrobial defenses, epidermal differentiation, and control of cutaneous vasculature. Cluster analysis of transcripts with significantly altered expression identified a group of genes involved in lipid metabolism with highly correlated gene expression. Promoter analysis showed enrichment for binding sites of three transcription factors; peroxisome proliferator-activator receptor alpha (PPARA), sterol regulatory element-binding protein (SREBF), and estrogen receptor 2 (ESR2), suggesting that the coordinate regulation of lipid metabolic genes may be related to the action of these factors. Taken together, our results identify a "pre-psoriatic" gene expression signature, suggesting decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin.

Figure 1. Principal component analysis

The first and second principal components are shown. Two uninvolved samples (2/58) overlapped minimally with the lesional samples whereas large overlap was observed between the control and uninvolved samples.

Figure 2. Progressive gene changes in NN vs. PN vs. PP skin

To analyze genes that show progressive change through all three sample groups we used a threshold of equal or greater than 1.3-fold change and a nominal p-value of less than 0.05 between NN and PN samples, whereas 2-fold change was used comparing lesional versus uninvolved and control skin with an FDR corrected p-value of less than 0.05. The blue color indicates low expression whereas the red color indicates high expression.

Figure 3. QRT-PCR analysis of selected transcripts in NN vs. PN vs. PP skin

QRT-PCR was performed as described in Materials and Methods. Error bars indicate SEM (n=25 in control, uninvolved and lesional groups). P values for various comparisons are indicated above the horizontal bars. On average, C10orf99 was up-regulated by approximately 1.7-fold in uninvolved samples, whereas ALOX15B was down-regulated by 2.0 fold, galanin (GAL) by 1.9-fold and ELOVL3 2.4-fold. C10orf99 was 30-fold up-regulated in lesional skin.

Figure 4. Correlated expression of genes involved lipid metabolism

Genes shown fall under the GO term “lipid metabolic process”, the term subsuming the largest number of down-regulated transcripts in our sample. We observed a strong correlation between all the genes within this GO category except for CYP1B1 and CD74. CD74 is the invariant polypeptide associated with MHC Class II molecules and has been shown to have a role in enhancing lipid antigen presentation on CD1d. CYP1B1 is a member of the cytochrome P450 family which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipid. It has been implicated in arachidonic acid metabolism in the cornea (Schwartzman et al., 1987). The most likely reason that these two genes do not show the same correlation as the rest of the group, is that these are only marginally associated with lipid metabolic processes.

Figure 5. Bioinformatic analysis of promoter binding sites

The transcription factors: PPARA, ESR2, and SREBF were found to have increased number of promoter binding sites in the lipid metabolism group compared to three control groups consisting of genes with low, medium and high expression in our dataset.

Figure 6. Pathway analysis of lipid metabolic process genes

To interrogate known interactions amongst the 25 lipid metabolic process genes that are co-regulated in PN and NN skin and the three transcription factors that show enriched numbers of binding sites in the promoters of these genes, we utilized Genomatix BiblioSphere to build gene interaction networks. Two of the enriched transcription factors, PPARA and ESR, connected most (17/25) of the genes in an extended network.