LC-MS/MS analysis of lesional and normally looking psoriatic skin reveals significant changes in protein metabolism and RNA processing

Abstract

Background: Plaque psoriasis is a chronic autoimmune disorder characterized by the development of red scaly plaques. To date psoriasis lesional skin transcriptome has been extensively studied, whereas only few proteomic studies of psoriatic skin are available.

Aim: The aim of this study was to compare protein expression patterns of lesional and normally looking skin of psoriasis patients with skin of the healthy volunteers, reveal differentially expressed proteins and identify changes in cell metabolism caused by the disease.

Methods: Skin samples of normally looking and lesional skin donated by psoriasis patients (n = 5) and samples of healthy skin donated by volunteers (n = 5) were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). After protein identification and data processing, the set of differentially expressed proteins was subjected to protein ontology analysis to characterize changes in biological processes, cell components and molecular functions in the patients' skin compared to skin of the healthy volunteers. The expression of selected differentially expressed proteins was validated by ELISA and immunohistochemistry.

Results: The performed analysis identified 405 and 59 differentially expressed proteins in lesional and normally looking psoriatic skin compared to healthy control. In normally looking skin of the patients, we discovered decreased expression of KNG1, APOE, HRG, THBS1 and PLG. Presumably, these changes were needed to protect the epidermis from spontaneous activation of kallikrein-kinin system and delay the following development of inflammatory response. In lesional skin, we identified several large groups of proteins with coordinated expression. Mainly, these proteins were involved in different aspects of protein and RNA metabolism, namely ATP synthesis and consumption; intracellular trafficking of membrane-bound vesicles, pre-RNA processing, translation, chaperoning and degradation in proteasomes/immunoproteasomes.

Conclusion: Our findings explain the molecular basis of metabolic changes caused by disease in skin lesions, such as faster cell turnover and higher metabolic rate. They also indicate on downregulation of kallikrein-kinin system in normally looking skin of the patients that would be needed to delay exacerbation of the disease. Data are available via ProteomeXchange with identifier PXD021673.

Fig 1. Venn diagram comparing DEPs in skin samples obtained from lesional and normally looking skin of the same psoriasis patients (n = 5) andskin of the healthy volunteers (n = 5) as assessed by LC/MS-MS analysis.

The numbers indicated in the diagram are the numbers of DEPs in compared groups of samples (FDR < 0.05, fold change >1.5).

Fig 2. Heat map representing three clusters of DEPs involved in mRNA translation, according to the average quantitative expression levels in two groups of samples.

a) Ribosome proteins; b) Aminoacyl-tRNA synthetases; c) Translation initiation elongation and termination factors; From left to right column–the results of comparative analysis for normally looking skin of the patients vs. skin of the healthy volunteers, lesional vs. normally looking skin of the patients, and lesional skin of the patients vs. skin of the healthy volunteers. Red color indicates low expression levels whereas green color indicates high expression levels. The DEPs uniprot ID, official gene symbols of the encoding genes, fold changes and Benjamini corrected P-values are shown in S2 Table in S1 File.

Fig 3. Heat map representation of the differentially expressed subunits of proteasome and immunoproteasome, according to the average quantitative expression levels in two groups of samples.

From left to right column–the results of comparative analysis for normally looking skin of the patients vs. skin of the healthy volunteers, lesional vs. normally looking skin of the patients, and lesional skin of the patients vs. skin of the healthy volunteers. Red color indicates low expression levels whereas green color indicates high expression levels. The DEPs uniprot ID, official gene symbols of the encoding genes, fold changes and Benjamini corrected P-values are shown in S2 Table in S1 File.

Fig 4. Heat map showing mean expression profiles of the DEPs associated with membrane-bound vesicles, according to the average quantitative expression levels in two groups of samples.

From left to right column–the results of comparative analysis for normally looking skin of the patients vs. skin of the healthy volunteers, lesional vs. normally looking skin of the patients, and lesional skin of the patients vs. skin of the healthy volunteers. Red color indicates low expression levels whereas green color indicates high expression levels. The DEPs uniprot ID, official gene symbols of the encoding genes, fold changes and Benjamini corrected P-values are shown in S2 Table in S1 File.

Fig 5. Heat map for the expression levels of the DEPs that function as chaperones in the cell.

From left to right column–the results of comparative analysis for normally looking skin of the patients vs. skin of the healthy volunteers, lesional vs. normally looking skin of the patients, and lesional skin of the patients vs. skin of the healthy volunteers. Red color indicates low expression levels whereas green color indicates high expression levels. The DEPs uniprot ID, official gene symbols of the encoding genes, fold changes and Benjamini corrected P-values are shown in S2 Table in S1 File.

Fig 6. Heat map for the expression levels of DEPs capable of ATP binding.

A–proteins constituting ATP synthase and ATPases. B.–RNA helicases. From left to right column–the results of comparative analysis for normally looking skin of the patients vs. skin of the healthy volunteers, lesional vs. normally looking skin of the patients, and lesional skin of the patients vs. skin of the healthy volunteers. Red color indicates low expression levels whereas green color indicates high expression levels. The DEPs uniprot ID, official gene symbols of the encoding genes, fold changes and Benjamini corrected P-values are shown in S2 Table in S1 File.