Preservation Analysis of Macrophage Gene Coexpression Between Human and Mouse Identifies PARK2 as a Genetically Controlled Master Regulator of Oxidative Phosphorylation in Humans

• Published in: G3 : genes - genomes - genetics Vol. 6; no. 10; pp. 3361 - 3371
• Main Authors: Codoni, Veronica, Blum, Yuna, Civelek, Mete, Proust, Carole, Franzén, Oscar, Björkegren, Johan L M, Le Goff, Wilfried, Cambien, Francois, Lusis, Aldons J, Trégouët, David-Alexandre
• Format: Journal Article
• Language: English
• Published: United States Oxford University Press 01.10.2016; Genetics Society of America
• Subjects: Animals; Biochemistry, Molecular Biology; Computational Biology - methods; cross-species comparison; eQTL analysis; Evolution, Molecular; Gene expression; gene expression network analysis; Gene Expression Profiling; Gene Expression Regulation; Gene Expression Regulation, Enzymologic; Gene Regulatory Networks; Genome-Wide Association Study; Genomics; Genotype; High-Throughput Nucleotide Sequencing; Humans; Investigations; Life Sciences; macrophages; Macrophages - metabolism; Mice; Oxidative Phosphorylation; Phosphorylation; Quantitative Trait Loci; Species Specificity; trans genetic effects; Transcriptome; Ubiquitin-Protein Ligases - genetics; Ubiquitin-Protein Ligases - metabolism; Workflow; macrophages; gene expression network analysis; genetic effects; cross-species comparison; eQTL analysis; trans genetic effects
• ISSN: 2160-1836; 2160-1836
• DOI: 10.1534/g3.116.033894

Abstract Macrophages are key players involved in numerous pathophysiological pathways and an in-depth characterization of their gene regulatory networks can help in better understanding how their dysfunction may impact on human diseases. We here conducted a cross-species network analysis of macrophage gene expression data between human and mouse to identify conserved networks across both species, and assessed whether such networks could reveal new disease-associated regulatory mechanisms. From a sample of 684 individuals processed for genome-wide macrophage gene expression profiling, we identified 27 groups of coexpressed genes (modules). Six modules were found preserved (P < 10−4) in macrophages from 86 mice of the Hybrid Mouse Diversity Panel. One of these modules was significantly [false discovery rate (FDR) = 8.9 × 10−11] enriched for genes belonging to the oxidative phosphorylation (OXPHOS) pathway. This pathway was also found significantly (FDR < 10−4) enriched in susceptibility genes for Alzheimer, Parkinson, and Huntington diseases. We further conducted an expression quantitative trait loci analysis to identify SNP that could regulate macrophage OXPHOS gene expression in humans. This analysis identified the PARK2 rs192804963 as a trans-acting variant influencing (minimal P-value = 4.3 × 10−8) the expression of most OXPHOS genes in humans. Further experimental work demonstrated that PARK2 knockdown expression was associated with increased OXPHOS gene expression in THP1 human macrophages. This work provided strong new evidence that PARK2 participates to the regulatory networks associated with oxidative phosphorylation and suggested that PARK2 genetic variations could act as a trans regulator of OXPHOS gene macrophage expression in humans.