DOI: 10.5061/dryad.rv15dv4m0
title: Ketogenic diet dampens excitatory neurotransmission by shrinking synaptic vesicle pools

description: 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.
description: # Ketogenic diet dampens excitatory neurotransmission by shrinking
 synaptic vesicle pools Dataset DOI:
 [10.5061/dryad.rv15dv4m0](https://doi.org/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 2^nd^ tab represents significantly differentially expressed genes in
 KD mice as compared to chow-diet mice, with adj p-value&lt;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 2^nd^ tab represents
 significantly differentially expressed genes in KD mice as compared to
 chow-diet mice, with adj p-value&lt;0.05 (column N). * Missing values are
 indicated as "NA". ## Code/software Microsoft Excel