A comprehensive study of the adult mouse brain transcriptome: analysis of inter-individual differences in cognitive aging and cell-type specific changes in the hippocampus upon voluntary exercise
by Aditi Methi
Date of Examination:2023-09-22
Date of issue:2023-12-19
Advisor:Prof. Dr. André Fischer
Referee:Prof. Dr. André Fischer
Referee:Prof. Dr. Tiago Fleming Outeiro
Persistent Address:
http://dx.doi.org/10.53846/goediss-10259
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Abstract
English
The hippocampus (HPC) is a brain region crucial for learning and memory processes, and this link between the HPC and cognition has been extensively studied in recent decades. Previous research has demonstrated that external factors like environmental enrichment and physical exercise can increase neuronal plasticity, improve memory and cognition and enhance protection against neurodegeneration. However, there are still gaps in our knowledge of the specific cellular and molecular mechanisms underlying these beneficial effects. We addressed this in the first manuscript by conducting an in-depth analysis of the mouse hippocampal transcriptome at the single-cell level after four weeks of voluntary wheel-running, using single nucleus RNA sequencing (snRNA-seq). We found that exercise impacts adult neurogenesis by promoting faster maturation of a subpopulation of GABAergic neurons characterized by high expression of the Prdm16 gene, which was observed as a stark decrease in the proportion of these Prdm16-high neurons in nuclei from the exercise samples. This was supported by a post-exercise increase in nuclei number for an excitatory cluster that represented newborn excitatory neurons which were found to eventually integrate with the mature granule cell network in the dentate gyrus (DG), further indicating enhanced neurogenesis linked to exercise. Our findings also revealed a complex interplay of vital signaling pathways, such as Notch, Wnt/β-catenin and retinoic acid (RA) signaling, in a specific cluster of excitatory neurons within the Cornu Ammonis (CA) region of the HPC. These pathways include NF-κB, Wnt/β-catenin, Notch, and retinoic acid (RA). Exercise led to differential expression and regulation of genes associated with these pathways, indicating their involvement in the response of the HPC to physical activity and their potential contribution to enhanced synaptic plasticity and cognitive functions. In summary, our first study provides a valuable resource dataset for investigating how 4 weeks of exercise influence the transcriptome of distinct cell-types in the adult mouse hippocampus. We propose that downregulating the activity of Prdm16 in maturing hippocampal neurons might serve as a significant control mechanism through which exercise enhances adult neurogenesis, raising the possibility of exploring methods that target Prdm16 activity in the hippocampus as a therapeutic avenue for enhancing cognitive function. While our findings are currently based on interpretations from bioinformatics analyses and a single dataset obtained through snRNA-seq, we believe they encourage further research that delves into the functional interpretation and validation of these results. The data also indicate that using snRNA-seq analysis following exercise could be a suitable method for identifying distinct molecular stages of adult neurogenesis, and corroborate existing research in demonstrating that physical exercise, which is accessible to most individuals, holds significant potential as a preventive and even therapeutic approach for mitigating cognitive decline, addressing genetic or sporadic neurological disorders, and tackling the increasing burden of age-related neurodegeneration. In the second manuscript, we focused on unraveling the adaptive and compensatory molecular processes that give rise to inter-individual differences resulting in varying cognitive aging outcomes among similarly aged healthy individuals. We employed the Morris water maze (MWM) test as a standard task paradigm for evaluating spatial learning and memory in two cohorts of aged wild-type mice. We introduced a new spatial learning index called the 'cognitive score, ' which was able to quantify the cognitive ability of a mouse into a single, numeric value based on search strategies that were automatically classified using metrics extracted from the MWM performance of a mouse, implemented with a custom pipeline. The mice were ranked from best to worst performers (learners) within behavioral groups based on their individual cognitive scores. We then delved into the molecular level by analyzing both coding and non-coding RNA (ncRNA) expression data from the hippocampus of selected mice categorized as either 'good' or 'bad' learners in the MWM test, in order to link changes in the RNAome to the cognitive scores of the mice. The findings from this indicate that the differences observed in cognitive aging are accompanied by subtle alterations in the expression of specific genes and ncRNAs, including miRNAs. Notably, the long non-coding RNA (lncRNA) Mir124a-1hg emerged as a promising candidate whose downregulation could be associated with healthy cognitive aging in mice. As life expectancy increases globally, there's a growing urgency to unravel the precise mechanisms behind the variable cognitive decline seen in aging individuals. Understanding the connection between gene and ncRNA expression patterns and successful cognitive aging holds potential for developing treatments that could counter cognitive deterioration and enhance the quality of life in old age. In conclusion, our study provides an innovative approach to quantifying performance in a water maze using the cognitive score and highlights the neuron-specific lincRNA Mir124a-1hg as a compelling candidate that could be explored further with experimental validation to shed light on its potential function in regulating healthy cognitive aging.
Keywords: hippocampus, learning and memory, aerobic exercise, gene-expression, single cell RNAseq, bulk RNA-seq, mouse model; spatial memory; cognition; non-coding RNA; interindividual differences, cognitive aging
