Ketogenic diet dampens excitatory neurotransmission by shrinking synaptic vesicle pools
Data files
Nov 19, 2025 version files 1.31 MB
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12wOld-4wKD_FDR_genes.xlsx
748.83 KB
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4wOld-3wKD_FDR_genes.xlsx
558.05 KB
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README.md
3.89 KB
Abstract
The ketogenic diet (KD) is a common dietary intervention for treating seizures in intractable childhood epilepsies and has been proposed to improve disease outcome in neurodegenerative disorders. Despite its clinical applications, we know little about how this diet impacts brain circuitry and neuronal function to elicit its protective effects. Here, we examined the impact of the KD on hippocampal function through integrative analysis of gene expression, epigenetics, and neurotransmission. We found that KD induces profound transcriptional reprogramming of the hippocampus, including dampened expression of numerous synaptic genes. Through proteomic analysis of histone variants and post-translational modifications, we uncovered significant changes in activating and repressive histone marks in the hippocampus of KD mice. To determine how transcriptional rewiring of the hippocampus under KD impacts neurotransmission, we performed electrophysiological recordings of neurotransmission and synaptic dynamics at excitatory CA3-CA1 synapses. We found that KD diminishes synaptic gain and dampens short-term plasticity at excitatory synapses, resulting in reduced integration of synaptic inputs at the circuit level. Combining electrophysiology and electron microscopy, we determined that effects of KD in excitatory synapses are caused by a reduction in size of the readily releasable pool of synaptic vesicles, as well as the total vesicle pool. Our findings show that the ketogenic diet triggers synaptic remodeling in the hippocampus, driven by broad transcriptional and epigenetic changes that reduce synaptic vesicle pools and short-term plasticity at excitatory synapses ultimately dampening excitatory synaptic gain and integration at the circuit level. These synaptic adaptations may represent a major mechanism underlying the anti-epileptic effects of this diet.
Dataset DOI: 10.5061/dryad.rv15dv4m0
Description of the data and file structure
C57bl6/NJ male mice were fed a ketogenic diet (KD) or chow diet (control). Total hippocampi were harvested for bulk RNA sequencing. Following RNA extraction, samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.2. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.0.
Files and variables
File: 12wOld-4wKD_FDR_genes.xlsx
Description: 12 week-old mice were fed a ketogenic diet or a chow-diet for 4 weeks followed by a 4-hour fast. Whole hippocampi were then harvested for bulk RNA sequencing as described above.
Variables
- In both files, the first tab represents the total modulated genes based on logFC (column H) of the average of 5 KD-fed mice (sample.kd; columns Q-U) as compared to 5 chow diet-fed mice (sample.ctrl; columns V-Z);
- Each column represents: Gene ID, gene code, gene name, gene biotype, external gene source, transcript count and description of the gene; average expression, p-value and adjusted p-value, and linearFC (fold change).
- CI.L (column I) and CI.R (column J) represents the left and right boundaries of each confidence intervals;
- t (column L) represents the statistical significance of the gene expression difference between chow and KD groups.
- B (column O) represents the probability of the gene being differentially expressed
- Each row represent a differentially modulated gene in KD mice as compared to chow-diet mice.
- The 2nd tab represents significantly differentially expressed genes in KD mice as compared to chow-diet mice, with adj p-value<0.05 (column N).
- Missing values are indicated as "NA".
File: 4wOld-3wKD_FDR_genes.xlsx
Description: 4 week-old mice were fed a ketogenic diet or a chow-diet for 3 weeks. Whole hippocampi were then harvested for bulk RNA sequencing as described above.
Variables
- In both files, the first tab represents the total modulated genes based on logFC (column H) of the average of 5 KD-fed mice (sample.kd; columns Q-U) as compared to 5 chow diet-fed mice (sample.ctrl; columns V-Z);
- Each column represents: Gene ID, gene code, gene name, gene biotype, external gene source, transcript count and description of the gene; average expression, p-value and adjusted p-value, and linearFC (fold change).
- CI.L (column I) and CI.R (column J) represents the left and right boundaries of each confidence intervals;
- t (column L) represents the statistical significance of the gene expression difference between chow and KD groups.
- B (column O) represents the probability of the gene being differentially expressed
- Each row represent a differentially modulated gene in KD mice as compared to chow-diet mice.
- The 2nd tab represents significantly differentially expressed genes in KD mice as compared to chow-diet mice, with adj p-value<0.05 (column N).
- Missing values are indicated as "NA".
Code/software
Microsoft Excel