A Meta-Analysis of the Effects of Early Life Stress on the Prefrontal Cortex Transcriptome Reveals Long-Term Downregulation of Myelin-Related Gene Expression

Abstract

Background: Early life stress (ELS) refers to exposure to negative childhood experiences, such as neglect, disaster, and physical, mental, or emotional abuse. ELS can permanently alter the brain, leading to cognitive impairment, increased sensitivity to future stressors, and mental health risks. The prefrontal cortex (PFC) is a key brain region implicated in the effects of ELS.

Methods: To better understand the effects of ELS on the PFC, we ran a meta-analysis of publicly available transcriptional profiling datasets. We identified five datasets (GSE89692, GSE116416, GSE14720, GSE153043, and GSE124387) that characterized the long-term effects of multiday postnatal ELS paradigms (maternal separation, limited nesting/bedding) in male and female laboratory rodents (rats, mice). The outcome variable was gene expression in the PFC later in adulthood as measured by microarray or RNA-Seq. To conduct the meta-analysis, preprocessed gene expression data were extracted from the Gemma database. Following quality control, the final sample size was n = 89(n = 42 controls and n = 47 ELS: GSE116416, n = 23 (no outliers); GSE116416, n = 44 (two outliers); GSE14720, n = 7 (no outliers); GSE153043, n = 9 (one outlier); and GSE124387, n = 6 (no outliers)). Differential expression was calculated using the limma pipeline followed by an empirical Bayes correction. For each gene, a random-effects meta-analysis model was then fit to the ELS versus control effect sizes (Log2 Fold Changes) from each study.

Results: Our meta-analysis yielded stable estimates for 11,885 genes, identifying five genes with differential expression following ELS (false discovery rate < 0.05) - transforming growth factor alpha (Tgfa), IQ motif containing GTPase activating protein 3 (Iqgap3), collagen, type XI, alpha 1 (Col11a1), claudin 11 (Cldn11), and myelin-associated glycoprotein (Mag) - all of which were downregulated. Broadly, gene sets associated with oligodendrocyte differentiation, myelination, and brain development were downregulated following ELS. In contrast, genes previously shown to be upregulated in major depressive disorder patients were upregulated following ELS.

Conclusion: These findings suggest that ELS during critical periods of development may produce long-term effects on the efficiency of transmission in the PFC and drive changes in gene expression similar to those underlying depression.

Keywords: RNA‐Seq; early life stress; meta‐analysis; microarray.

FIGURE 1

Diagram overviewing dataset search and selection. We identified transcriptional profiling datasets examining ELS models in laboratory rodents within the Gemma database using prespecified keywords. Our initial search encompassed tissue from three brain regions implicated in the effects of ELS: the hippocampus, anterior cingulate, and prefrontal cortex (PFC). The focus of our meta‐analysis was later narrowed to the PFC based on the availability of datasets. The titles, abstracts, and metadata for the datasets were initially scanned and filtered using prespecified inclusion/exclusion criteria, including indications that the dataset was not derived from a bulk dissection of brain tissue or that the content was unrelated to the research question (ELS). The secondary screening step included a detailed review of the metadata on Gemma and published methodology, followed by a final specification of the region of interest (ROI: PFC). Datasets were excluded in the secondary dataset filtering if they did not include an ELS manipulation during the preweaning period, the publication was not publicly available, tissue was collected during development (instead of adulthood), or transcriptional profiling was not performed for the ROI. n, number of datasets.

FIGURE 2

Genes within a network focused on oligodendrocyte differentiation are differentially expressed in early life stress models. (A–C) Forest plots for two differentially expressed genes from the meta‐analysis (FDR < 0.05: Cldn11 and Mag) and a third gene that shows a trend toward differential expression (FDR < 0.10: Mal) that are all part of a network related to oligodendrocyte differentiation. Rows illustrate ELS Log2FC (squares) with 95% confidence intervals (whiskers) for each of the datasets and the meta‐analysis random effects model (RE Model). Forest plots allow for visual inspection of the consistency and magnitude of effects across the five studies. (A) A forest plot showing the downregulation of claudin 11 (Cldn11) in ELS models. (B) A forest plot showing the downregulation of myelin‐associated glycoprotein (Mag) in ELS models. (C) A forest plot showing the trend toward a downregulation of mal, T cell differentiation protein (Mal) in early life stress models. (D) Multiple top differentially expressed genes are found in the same predicted protein–protein interaction (PPI) network enriched for genes associated with oligodendrocyte differentiation. To create the PPI network, top genes from the meta‐analysis (p < 0.001: 40 genes) were entered into the StringDB database. The only identifiable network (cluster) of eight genes included six genes with either significant differential expression in ELS models (FDR < 0.05: Mag and Cldn11) or a nonsignificant trend toward differential expression in ELS models (FDR < 0.10: Mal, Fa2h, Klk6, and Ugcg). The nodes represent proteins and are labeled with mouse gene symbol annotation. The lines represent predicted protein–protein associations. The associations are meant to be specific and meaningful (proteins jointly contribute to a shared function), but this does not necessarily mean they are physically binding to each other. The shaded nodes (gray) were identified as being part of a gene set involved in oligodendrocyte differentiation (GO:0048709) that was enriched with differential expression. Other genes within the network are part of a gene set involved in central nervous system myelination (GO:0022010) that was also enriched with differential expression (including Klk6) or have also been previously associated with oligodendrocyte function and myelination (Cldn11).