Hippocampal Subregion Transcriptomic Profiles Reflect Strategy Selection during Cognitive Aging

Abstract

Age-related cognitive impairments are associated with differentially expressed genes (DEGs) linked to defined neural systems; however, studies examining multiple regions of the hippocampus fail to find links between behavior and transcription in the dentate gyrus (DG). We hypothesized that use of a task requiring intact DG function would emphasize molecular signals in the DG associated with a decline in performance. We used a water maze beacon discrimination task to characterize young and middle-age male F344 rats, followed by a spatial reference memory probe trial test. Middle-age rats showed increased variability in discriminating two identical beacons. Use of an allocentric strategy and formation of a spatial reference memory were not different between age groups; however, older animals compensated for impaired beacon discrimination through greater reliance on spatial reference memory. mRNA sequencing of hippocampal subregions indicated DEGs in the DG of middle-age rats, linked to synaptic function and neurogenesis, correlated with beacon discrimination performance, suggesting that senescence of the DG underlies the impairment. Few genes correlated with spatial memory across age groups, with a greater number in region CA1. Age-related CA1 DEGs, correlated with spatial memory, were linked to regulation of neural activity. These results indicate that the beacon task is sensitive to impairment in middle age, and distinct gene profiles are observed in neural circuits that underlie beacon discrimination performance and allocentric memory. The use of different strategies in older animals and associated transcriptional profiles could provide an animal model for examining cognitive reserve and neural compensation of aging.SIGNIFICANCE STATEMENT Hippocampal subregions are thought to differentially contribute to memory. We took advantage of age-related variability in performance on a water maze beacon task and next-generation sequencing to test the hypothesis that aging of the dentate gyrus is linked to impaired beacon discrimination and compensatory use of allocentric memory. The dentate gyrus expressed synaptic function and neurogenesis genes correlated with beacon discrimination in middle-age animals. Spatial reference memory was associated with CA1 transcriptional correlates linked to regulation of neural activity and use of an allocentric strategy. This is the first study examining transcriptomes of multiple hippocampal subregions to link age-related impairments associated with discrimination of feature overlap and alternate response strategies to gene expression in specific hippocampal subregions.

Keywords: aging; hippocampus; pattern separation; reference memory; spatial discrimination; transcription.

Figure 1.

Spatial discrimination water maze beacon task experimental setup. A, Experimental timeline. B, For beacon discrimination testing, animals were placed at one of six starting positions: two located near the platform beacon (S⁺, red arrows), two located equidistant between the decoy and platform beacons (Equid, black arrows), and two located near the decoy beacon (S^–, blue arrows). Spatial cues, platform positions, and beacon positions were unchanged through all days of beacon discrimination testing.

Figure 2.

Middle-age animals are impaired relative to young in beacon discrimination, but not spatial reference memory. A, Young (blue symbols) and middle-age animals (red symbols) showed improvement in escape swim distance during cue training, despite impaired performance of middle-age animals compared with young. B, Average number of errors made per trial (Average Errors) across all days of testing and all trial start positions. Average errors decreased with training, with increased separation (circles represent 45 cm; diamonds represent 73 cm), and for young relative to middle-age animals. C, Average errors were influenced by start location such that errors increased as the distance from the start location and goal increased (S^– > equidistant > S⁺) and was higher in animals tested at 45 cm beacon separation compared with 73 cm for trials beginning at the equidistant or S^– start positions. D, DI scores were higher for animals trained at 73 cm beacon separation compared with 45 cm separation, and no age difference in DI score was observed for either the 45 or 73 cm separation group. E, Relationship of beacon discrimination performance (average errors from the equidistant starting position for the 45 cm separation) and spatial reference memory (DI score). Within middle-age animals, a significant correlation was noted between DI score and average number of errors made in the beacon discrimination task with trials beginning at the equidistant start point (Pearson's r = 0.72, p = 0.002). Better reference memory was thus associated with worse beacon discrimination ability. Dotted lines indicate the threshold for chance-level performance. Error bars indicate SEM. *p < 0.05. **p < 0.01. ***p < 0.001.

Figure 3.

Age is associated with differential regulation of genes within the DG, CA1, and CA3. A, By middle-age, the DG was found to show the greatest number of DEGs relative to young rats. B, The number of DEGs in common among different brain regions. Arrowheads indicate the direction of differential gene expression. All gene counts represent genes that passed our statistical filter for age and were indexed in DAVID.

Figure 4.

Functional annotation clustering shows substantial differential gene expression by middle-age compared with young animals in the DG (A), CA1 (B), and CA3 (C). Graphs represent the top GO and KEGG terms of the DEGs of middle-age rats relative to young. The complete list of significant GO and KEGG terms for each tissue is provided in Extended data Figure 4-3. Gene categories showing common differential regulation in all hippocampal subregions with age are provided in Extended data Figure 4-2.

Figure 5.

Beacon discrimination performance is correlated with differential regulation of genes primarily within the DG. A, Among all hippocampal subregions tested, the DG showed the greatest number of genes correlating with beacon discrimination performance on the 45 cm beacon separation task within middle-age animals. B, The DG showed the greatest number of gene clusters correlating with beacon discrimination performance, including downregulation of genes related to the synapse (GO:0044456) and neurogenesis (GO:0022008) with worse beacon discrimination performance. C, CA3 featured downregulation of genes relating to the myelin sheath (GO:0043209) with worse beacon discrimination performance. All values represent genes, found to pass our statistical filters for age and correlation with beacon discrimination performance within middle-age rats tested at 45 cm beacon separation only, which were also indexed in DAVID.

Figure 6.

Examples of DG genes that are differentially expressed with age and significantly correlated with equidistant average errors in middle-age animals. Each gene depicted shows decreased expression in animals with worse beacon discrimination performance. For plots of age differences, data in the y axes reflect the z distributions of normalized gene counts within both young and middle-age animals. For plots depicting correlations for middle-age animals, the y axes reflect the z distributions of normalized gene counts for middle-age animals only. In correlation figures, the x axes represent the z distributions of average equidistant errors within middle-age animals only. Each gene depicted shows decreased expression in animals with worse beacon discrimination performance. A, B, Genes from the synapse part (GO:0044456). C–F, Genes associated with neurogenesis (GO:0022008).

Figure 7.

Examples of CA1 genes that are differentially expressed with age and significantly correlated with DI score in middle-age animals. For plots of age differences, data in the y axes reflect the z distributions of normalized gene counts within both young and middle-age animals. For plots depicting correlations for middle-age animals, the y axes reflect the z distributions of normalized gene counts for middle-age animals only. In correlation figures, the x axes represent the z distributions of DI scores within middle-age animals only. Animals with better reference memory performance, reflected by greater DI score, showed increased expression of Syt6 (A), Mr1 (B), and Cyb5d2 (C); and decreased expression of Fos (D), Hcn4 (E), and Kcnj14 (F). A full list of genes showing a significant correlation to DI score is provided in Extended data Figure 7-1.