Glucocorticoid exposure during hippocampal neurogenesis primes future stress response by inducing changes in DNA methylation

Abstract

Prenatal stress exposure is associated with risk for psychiatric disorders later in life. This may be mediated in part via enhanced exposure to glucocorticoids (GCs), which are known to impact neurogenesis. We aimed to identify molecular mediators of these effects, focusing on long-lasting epigenetic changes. In a human hippocampal progenitor cell (HPC) line, we assessed the short- and long-term effects of GC exposure during neurogenesis on messenger RNA (mRNA) expression and DNA methylation (DNAm) profiles. GC exposure induced changes in DNAm at 27,812 CpG dinucleotides and in the expression of 3,857 transcripts (false discovery rate [FDR] ≤ 0.1 and absolute fold change [FC] expression ≥ 1.15). HPC expression and GC-affected DNAm profiles were enriched for changes observed during human fetal brain development. Differentially methylated sites (DMSs) with GC exposure clustered into 4 trajectories over HPC differentiation, with transient as well as long-lasting DNAm changes. Lasting DMSs mapped to distinct functional pathways and were selectively enriched for poised and bivalent enhancer marks. Lasting DMSs had little correlation with lasting expression changes but were associated with a significantly enhanced transcriptional response to a second acute GC challenge. A significant subset of lasting DMSs was also responsive to an acute GC challenge in peripheral blood. These tissue-overlapping DMSs were used to compute a polyepigenetic score that predicted exposure to conditions associated with altered prenatal GCs in newborn’s cord blood DNA. Overall, our data suggest that early exposure to GCs can change the set point of future transcriptional responses to stress by inducing lasting DNAm changes. Such altered set points may relate to differential vulnerability to stress exposure later in life.

Cell-type specific impact of glucocorticoid receptor activation on the developing brain

“…This result could only be identified in a complex multi-cellular system like organoids, which contain progressively maturing celltypes from early neuroepithelia to dorsal neurons. While it confirms some previous results from cell and animal models showing glucocorticoids' involvement in neurogenesis by increasing proliferation while decreasing differentiation 23,24,50 , our study is the first to support that aberrant GR-activation could lead to neuronal maturation and differentiation delay in a complex human developing brain model.…”

“…When breaking down this effect by individual time-point (D30, D60, D90), all genes were consistently downregulated (significant when q-value≤0.05) in Neurons, while in Progenitors this was only true for ENO2 and HES6. Together with an enrichment of common GO terms in DE transcripts from both Progenitors and Neurons which included cell differentiation, head development, neurogenesis, neuron differentiation and nervous system development ( Table S9, Supplementary Results), these findings suggest that sustained GR-activation during neurodevelopment may interfere with neuronal differentiation and maturation in the long term, confirming previous data from 2-dimensional cell systems 24 .…”

“…Since glucocorticoid-response has previously been established by our group and others in different tissue types like peripheral blood cells 75 as well as more recently neuronal cell types like hippocampal progenitors 24 , we wanted to test the overlap of these previous findings with our results from GC-exposure in organoids. We tested whether the effects we observed following glucocorticoid exposure was dependent on expression of the glucocorticoid receptor (NR3C1 gene).…”

“…To investigate dependence of the Dex response on expression of the GR, we fitted the MAST model as described above for each of the three coarser cell classes and obtained log2foldchanges between cells that do or do not express the gene NR3C1 (GR). As a next step, we intersected the full gene list with genes previously identified to be differentially responsive to Dex in hippocampal progenitors 24 . We then used the Wilcoxon signed-ranks test to ask if there was a significant difference in the response between NR3C1-positive and -negative cells in each of the three cell-type groups.…”

“…In addition, animal models do not allow mapping of human-specific GREs and their possible interaction with human genetic variation, given that such enhancers are poorly conserved across species. A second interesting model system consists of primary human neuronal progenitor cell lines 23,24 . While these allow investigation of human-specific genomic effects, they do not recapitulate the complex architecture and cell types seen in the multi-cellular human brain.…”