Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

Abstract

Evolutionary change in gene expression is generally considered to be a major driver of phenotypic differences between species. We investigated innate immune diversification by analyzing interspecies differences in the transcriptional responses of primary human and mouse macrophages to the Toll-like receptor (TLR)–4 agonist lipopolysaccharide (LPS). By using a custom platform permitting cross-species interrogation coupled with deep sequencing of mRNA 5′ ends, we identified extensive divergence in LPS-regulated orthologous gene expression between humans and mice (24% of orthologues were identified as “divergently regulated”). We further demonstrate concordant regulation of human-specific LPS target genes in primary pig macrophages. Divergently regulated orthologues were enriched for genes encoding cellular “inputs” such as cell surface receptors (e.g., TLR6, IL-7Rα) and functional “outputs” such as inflammatory cytokines/chemokines (e.g., CCL20, CXCL13). Conversely, intracellular signaling components linking inputs to outputs were typically concordantly regulated. Functional consequences of divergent gene regulation were confirmed by showing LPS pretreatment boosts subsequent TLR6 responses in mouse but not human macrophages, in keeping with mouse-specific TLR6 induction. Divergently regulated genes were associated with a large dynamic range of gene expression, and specific promoter architectural features (TATA box enrichment, CpG island depletion). Surprisingly, regulatory divergence was also associated with enhanced interspecies promoter conservation. Thus, the genes controlled by complex, highly conserved promoters that facilitate dynamic regulation are also the most susceptible to evolutionary change.

Immune-responsive gene 1 protein links metabolism to immunity by catalyzing itaconic acid production

“…A major difference between mouse and human is the elevated production of NO in mouse macrophages under inflammatory conditions (24). It is well known that NO inhibits aconitase, the A B enzyme producing the itaconic acid precursor cis-aconitate (25)(26)(27).…”

Inflammatory Responses Induced by Lipopolysaccharide Are Amplified in Primary Human Monocytes but Suppressed in Macrophages by Complement Protein C5a

“…Some interpretations of human disease mechanisms have been made based on extrapolating from observations of mouse studies. However, there are important differences in LPS-induced TLR4 signaling between humans and mice (20)(21)(22), necessitating careful assessment of C5aR/TLR4 crosstalk in human cells.…”

Comparative Analysis of Monocyte Subsets in the Pig

“…Whereas there are major differences between humans and mice in terms of the patterns of pathogen-induced gene expression in macrophages, pigs share a much greater proportion of inducible genes with humans, corresponding to greater promoter sequence conservation (2,3). The precursors of macrophages in the blood, the blood monocytes, are heterogeneous in terms of surface markers and gene expression.…”