Comparative transcriptomic rhythms in the mouse and human prefrontal cortex

Abstract

Introduction: Alterations in multiple subregions of the human prefrontal cortex (PFC) have been heavily implicated in psychiatric diseases. Moreover, emerging evidence suggests that circadian rhythms in gene expression are present across the brain, including in the PFC, and that these rhythms are altered in disease. However, investigation into the potential circadian mechanisms underlying these diseases in animal models must contend with the fact that the human PFC is highly evolved and specialized relative to that of rodents.

Methods: Here, we use RNA sequencing to lay the groundwork for translational studies of molecular rhythms through a sex-specific, cross species comparison of transcriptomic rhythms between the mouse medial PFC (mPFC) and two subregions of the human PFC, the anterior cingulate cortex (ACC) and the dorsolateral PFC (DLPFC).

Results: We find that while circadian rhythm signaling is conserved across species and subregions, there is a phase shift in the expression of core clock genes between the mouse mPFC and human PFC subregions that differs by sex. Furthermore, we find that the identity of rhythmic transcripts is largely unique between the mouse mPFC and human PFC subregions, with the most overlap (20%, 236 transcripts) between the mouse mPFC and the human ACC in females. Nevertheless, we find that basic biological processes are enriched for rhythmic transcripts across species, with key differences between regions and sexes.

Discussion: Together, this work highlights both the evolutionary conservation of transcriptomic rhythms and the advancement of the human PFC, underscoring the importance of considering cross-species differences when using animal models.

Keywords: circadian rhythms; human post mortem tissue; mouse; prefrontal cortex; transcriptomics.

Figure 1

Rhythms in the mouse mPFC transcriptome. (A) The number (and percentage) of rhythmic transcripts detected in the mouse mPFC at different significance cutoffs. At a cutoff of p < 0.05, 12% of transcripts in the mPFC are rhythmic. (B) The top 10 rhythmic transcripts in the mouse mPFC, as determined by p-value. Top rhythmic transcripts include known circadian genes including the core molecular clock component Arntl. (C) Scatterplots depicting rhythmic expression across 24 h of the top two rhythmic transcripts. Time of death is depicted on the X-axis while expression is depicted on the Y-axis. Each point represents one subject. n = 9-10/timepoint. mPFC = medial prefrontal cortex, ZT = zeitgeber time.

Figure 2

Rhythms in canonical circadian transcripts are conserved across species. Scatterplots depicting the expression of canonical circadian transcripts PER1, PER2, and NR1D1 in the mouse mPFC and both human PFC subregions, separated by sex. Time of death is depicted on the X-axis while expression is depicted on the Y-axis. Each point represents one subject. mPFC = medial prefrontal cortex, DLPFC = dorsolateral prefrontal cortex, ACC = anterior cingulate cortex, ZT = zeitgeber time.

Figure 3

Greatest overlap in rhythmic transcripts between the mPFC and ACC in females. (A) Venn diagrams depicting the overlap in rhythmic transcripts (p < 0.05) between the mouse mPFC and human PFC subregions, separated by sex. Twenty percent of rhythmic transcripts in the mouse mPFC are also rhythmic in the human ACC in females. All other comparisons across species share ~5–10% of rhythmic transcripts. (B) Rank-rank hypergeometric overlap plots visualizing the overlap in rhythmic transcripts between the mouse mPFC and human PFC subregions. This threshold-free approach indicates that there is the most overlap in rhythmic transcripts between the mouse mPFC and the human ACC in females. (C) Ingenuity Pathway Analysis (IPA) was used to determine the top 10 pathways enriched for rhythmic transcripts (p < 0.05) and their overlap between the mouse mPFC and human PFC subregions in males. (D) The top 10 pathways enriched for rhythmic transcripts (p < 0.05), determined by IPA, and their overlap between the mouse mPFC and human PFC subregions in females. While the overlap in biological processes associated with rhythmic transcripts differs by region and sex, circadian rhythm signaling is among the top 10 pathways in the mouse mPFC and the human PFC subregions of both sexes. mPFC = medial prefrontal cortex, DLPFC = dorsolateral prefrontal cortex, ACC = anterior cingulate cortex.

Figure 4

Temporal patterns of rhythmic expression vary by region, sex, and species. (A,B) The peak time of rhythmic transcripts (p < 0.05), plotted as the percentage of total rhythmic transcripts peaking in each 2-h bin across 24 h (ZT) in (A) males and (B) females. In males, rhythmic transcripts largely peak in the opposite phase between the mouse mPFC and human PFC subregions. In females, over half of rhythmic transcripts peak in the active phase (light) in humans, whereas about half of transcripts peak in each phase in the mouse mPFC. mPFC = medial prefrontal cortex, DLPFC = dorsolateral prefrontal cortex, ACC = anterior cingulate cortex, ZT = zeitgeber time.