Gene expression and genetic variation in response to endoplasmic reticulum stress in human cells

Abstract

The accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) results in the condition called "ER stress," which induces the unfolded protein response (UPR), a complex cellular process that includes changes in expression of many genes. Failure to restore homeostasis in the ER is associated with human diseases. To identify the underlying changes in gene expression in response to ER stress, we induced ER stress in human B cells and then measured gene expression at ten time points. We followed up those results by studying cells from 60 unrelated people. We rediscovered genes that were known to play a role in the ER-stress response and uncovered several thousand genes that are not known to be involved. Two of these are VLDLR and INHBE, which showed significant increase in expression after ER stress in B cells and in primary fibroblasts. To study the links between UPR and disease susceptibility, we identified ER-stress-responsive genes that are associated with human diseases and assessed individual differences in the ER-stress response. Many of the UPR genes are associated with Mendelian disorders, such as Wolfram syndrome, and complex diseases, including amyotrophic lateral sclerosis and diabetes. Data from two independent samples showed extensive individual variability in ER-stress response. Additional analyses with monozygotic twins revealed significant correlations within twin pairs in their responses to ER stress, thus showing evidence for heritable variation among individuals. These results have implications for basic understanding of ER function and its role in disease susceptibility.

Figure 1

XBP1 Splicing in Cells Treated with Thapsigargin and Tunicamycin Cells from two individuals with (T) and without (U) treatment with thapsigargin and tunicamycin. In treated cells, XBP1 splicing, a hallmark of ER stress, was observed.

Figure 2

Temporal Gene Expression Pattern of Classic UPR Genes in Cells at Baseline and Nine Time Points after Exposure to Tunicamycin and Thapsigargin Hierarchical clustering based on pairwise correlations for 57 classic UPR genes. Analyses were carried out with the use of GenePattern software.

Figure 3

Examples of ER-Stress-Responsive Genes that Showed Similar Expression Patterns in Response to Tunicamycin and Thapsigargin

Figure 4

Examples of Genes that Showed Significant Changes in Response to ER Stress among 60 Unrelated Individuals Shown are two genes (PARL and LRRC47) that showed significant but modest fold change after ER stress. In addition, two genes (INHBE and VLDLR) that were not known to play a role in ER stress showed significant and large fold change after exposure to tunicamycin.

Figure 5

Extensive Individual Variation in Gene Expression Response to ER Stress Fold changes for ten genes in B cells from 60 unrelated individuals at 8 hr after exposure to tunicamycin are shown. Eight of the genes are highly variable, and two (EIF3B and SOS2) showed less variability.

Figure 6

Gene Expression Response of PSPHL to ER Stress of Members of MZ Twin Pairs ER stress was induced in B cells from 14 pairs of twins of European descent. A vertical line connects the members of a single MZ pair. Similar results were found for African American twins (European descent ICC = 0.8, p = 9 x10⁻⁵; African American ICC = 0.69, p = 3.3 × 10⁻³).