Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee

Abstract

Humans experience higher rates of age-associated diseases than our closest living evolutionary relatives, chimpanzees. Environmental factors can explain many of these increases in disease risk, but species-specific genetic changes can also play a role. Alleles that confer increased disease susceptibility later in life can persist in a population in the absence of selective pressure if those changes confer positive adaptation early in life. One age-associated disease that disproportionately affects humans compared with chimpanzees is epithelial cancer. Here, we explored genetic differences between humans and chimpanzees in a well-defined experimental assay that mimics gene expression changes that happen during cancer progression: A fibroblast serum challenge. We used this assay with fibroblasts isolated from humans and chimpanzees to explore species-specific differences in gene expression and chromatin state with RNA-Seq and DNase-Seq. Our data reveal that human fibroblasts increase expression of genes associated with wound healing and cancer pathways; in contrast, chimpanzee gene expression changes are not concentrated around particular functional categories. Chromatin accessibility dramatically increases in human fibroblasts, yet decreases in chimpanzee cells during the serum response. Many regions of opening and closing chromatin are in close proximity to genes encoding transcription factors or genes involved in wound healing processes, further supporting the link between changes in activity of regulatory elements and changes in gene expression. Together, these expression and open chromatin data show that humans and chimpanzees have dramatically different responses to the same physiological stressor, and how a core physiological process can evolve quickly over relatively short evolutionary time scales.

Fig. 1.

—Characterization of the serum response in human and chimpanzee fibroblasts. (A) Overview of experimental procedure. (B) Log₂ fold-change in gene expression versus P-value of CSR genes between T0 and T12. Positive log₂ fold-change indicates higher level of gene expression at T12. Solid blue line indicates P-value 0.1. Points are CSR downregulated (red) and upregulated (blue) genes. (C) Plots of enrichment scores and distribution of a priori gene sets within the expression set, rank-ordered by differential expression between T0 and T12. Red bars below plots indicate clusters of downregulated CSR genes at the bottom of the ranked list. Inset values are normalized enrichment score (black), and false discovery rate (red).

Fig. 2.

—Common GO terms across time points. GO BP categories significantly higher in human and chimpanzee at all time points. Bars represent mean values across 4 time points for ln P-value (below axis) and fold-enrichment (above axis). Colors group similar biological processes and vertical lines represent 1 standard deviation from the mean.

Fig. 3.

—Differential chromatin accessibility in human and chimpanzee fibroblasts. (A) Differential chromatin DNaseI hypersensitivity was determined using a 5% FDR from a likelihood ratio test. (B) and (C) Active DHS sites are locations in which a DNaseI signal with a P-value of at least 1e-5 is present in at least one replicate. Red lines with filled markers represent activity of human-specific DHS sites. Blue lines with filled markers represent activity of chimpanzee-specific DHS sites. Red lines with empty markers represent activity of shared DHS sites in human fibroblasts. Blue lines with empty markers represent activity of shared DHS sites in chimpanzee fibroblasts.

Fig. 4.

—Fuzzy clustering and ontology enrichments. Clusters represent either an (A) increase or (B) decrease in chromatin accessibility following serum replacement. (C) and (D) Common GO terms generated from genes nearest DHS sites belonging to clusters that indicate (C) increasing or (D) decreasing chromatin accessibility.