RPL6: A Key Molecule Regulating Zinc- and Magnesium-Bound Metalloproteins of Parkinson's Disease

Abstract

Parkinson's disease (PD) is a progressive neurodegenerative disease with no definite molecular markers for diagnosis. Metal exposure may alter cellular proteins that contribute to PD. Exploring the cross-talk between metal and its binding proteins in PD could reveal a new strategy for PD diagnosis. We performed a meta-analysis from different PD tissue microarray datasets to identify differentially expressed genes (DEGs) common to the blood and brain. Among common DEGs, we extracted 280 metalloprotein-encoding genes to construct protein networks describing the regulation of metalloproteins in the PD blood and brain. From the metalloprotein network, we identified three important functional hubs. Further analysis shows 60S ribosomal protein L6 (RPL6), a novel intermediary molecule connecting the three hubs of the metalloproteins network. Quantitative real-time PCR analysis showed that RPL6 was downregulated in PD peripheral blood mononuclear cell (PBMC) samples. Simultaneously, trace element analysis revealed altered serum zinc and magnesium concentrations in PD samples. The Pearson's correlation analysis shows that serum zinc and magnesium regulate the RPL6 gene expression in PBMC. Thus, metal-regulating RPL6 acts as an intermediary molecule connecting the three hubs that are functionally associated with PD. Overall our study explores the understanding of metal-mediated pathogenesis in PD, which provides a serum metal environment regulating the cellular gene expression that may light toward metal and gene expression-based biomarkers for PD diagnosis.

Keywords: Parkinson’s disease; gene expression; meta-analysis; metalloprotein network; serum metals.

FIGURE 1

Study design: Systematic workflow describing the major steps adopted in this study: (1) collection, curation, and meta-analysis of datasets; (2) identification of differential genes and selecting the genes that encode metalloproteins; (3) genes that encode metalloproteins showing a common trend in the blood and brain were selected and subjected to metalloprotein network; (4) identification of the linker protein that connects the hubs extracted from the metalloprotein network; (5) recruitment of research participants to determine the gene expression linker protein in peripheral blood mononuclear cell (PBMC) and the serum metal concentration of proteins in the hubs.

FIGURE 2

Metalloprotein network representing the interaction between metalloproteins that are commonly upregulated and downregulated in both the brain and blood of Parkinson’s disease patients.

FIGURE 3

Highly interactive metalloprotein hubs: Three highly interconnected protein hubs (A–C) extracted from the metalloprotein network. Colored circular nodes represent metalloproteins connecting to the core protein (blue rectangular box). The edges (colored line) between the proteins and their cofactor metals (violet rhombus). Black rhombus representing the cofactors that bound with more metalloproteins in the hubs.

FIGURE 4

Pathway enrichment of hubs: The common pathway (red rhombus) shared by three protein hubs (yellow rectangle) extracted from the metalloprotein network.

FIGURE 5

Network connectivity of hub proteins: The network showing the proteins (green nodes) with their connected interaction (dotted violet edges). The 60S ribosomal protein L6 (RPL6) (yellow node) with violet edges that connects core proteins (orange hexagon) of the hubs. The protein (gray node) connects a maximum of two core proteins (orange hexagon) in the network.

FIGURE 6

Relative expression: Gene expression analysis of 60S ribosomal protein L6 (RPL6) in peripheral blood mononuclear cells (PBMCs) of control (black) and PD (gray). The columns represent the average gene expression with standard deviation error bar, and asterisk denotes statistical significance with p-value ≤ 0.05.