Significance Intellectual disability is a common clinical entity with few therapeutic options. Kabuki syndrome is a genetically determined cause of intellectual disability resulting from mutations in either of two components of the histone machinery, both of which play a role in chromatin opening. Previously, in a mouse model, we showed that agents that favor chromatin opening, such as the histone deacetylase inhibitors (HDACis), can rescue aspects of the phenotype. Here we demonstrate rescue of hippocampal memory defects and deficiency of adult neurogenesis in a mouse model of Kabuki syndrome by imposing a ketogenic diet, a strategy that raises the level of the ketone beta-hydroxybutyrate, an endogenous HDACi. This work suggests that dietary manipulation may be a feasible treatment for Kabuki syndrome.

Abstract Kabuki syndrome is a Mendelian intellectual disability syndrome caused by mutations in either of two genes (KMT2D and KDM6A) involved in chromatin accessibility. We previously showed that an agent that promotes chromatin opening, the histone deacetylase inhibitor (HDACi) AR-42, ameliorates the deficiency of adult neurogenesis in the granule cell layer of the dentate gyrus and rescues hippocampal memory defects in a mouse model of Kabuki syndrome (Kmt2d+/βGeo). Unlike a drug, a dietary intervention could be quickly transitioned to the clinic. Therefore, we have explored whether treatment with a ketogenic diet could lead to a similar rescue through increased amounts of beta-hydroxybutyrate, an endogenous HDACi. Here, we report that a ketogenic diet in Kmt2d+/βGeo mice modulates H3ac and H3K4me3 in the granule cell layer, with concomitant rescue of both the neurogenesis defect and hippocampal memory abnormalities seen in Kmt2d+/βGeo mice; similar effects on neurogenesis were observed on exogenous administration of beta-hydroxybutyrate. These data suggest that dietary modulation of epigenetic modifications through elevation of beta-hydroxybutyrate may provide a feasible strategy to treat the intellectual disability seen in Kabuki syndrome and related disorders.

Kabuki syndrome [KS; Mendelian Inheritance in Man (MIM) 147920, 300867] is a monogenic disorder, the manifestations of which include intellectual disability, postnatal growth retardation, immunological dysfunction, and characteristic facial features. Mutations in either lysine (K)-specific methyltransferase 2D (KMT2D) or lysine (K)-specific demethylase 6A (KDM6A) are known to lead to KS (1⇓–3). Interestingly, each of these genes plays an independent role in chromatin opening, a process essential for transcription, as KMT2D encodes a lysine methyltransferase that adds a mark associated with open chromatin (histone 3, lysine 4 trimethylation; H3K4me3), whereas KDM6A encodes a histone demethylase that removes a mark associated with closed chromatin (histone 3, lysine 27 trimethylation; H3K27me3). If a deficiency of chromatin opening plays a role in KS pathogenesis, agents that promote open chromatin states, such as histone deacetylase inhibitors (HDACis), could ameliorate ongoing disease progression (4).

Previously, in a mouse model of KS (Kmt2d+/βGeo), we observed a deficiency of adult neurogenesis, a dynamic process during adult life (5), in association with hippocampal memory deficits (6). After 2 wk of treatment with the HDACi AR-42, an antineoplastic agent, we observed normalization of these phenotypes (6) (Fig. S1). However, transitioning an antineoplastic drug to patients with a nonlethal intellectual disability disorder may prove problematic. Recently, beta-hydroxybutyrate (BHB), a ketone body that is the natural end product of hepatic fatty acid beta oxidation, has been shown to have HDACi activity (7). Because BHB is actively transported into the central nervous system during ketosis (8), and furthermore has been shown to directly enter the hippocampus (9), it should be readily available to modulate histone modifications in relevant cells (neurons); this would be expected to ameliorate the deficiency of adult neurogenesis in Kmt2d+/βGeo mice (6). A dietary intervention could be quickly transitioned to the clinic and is unlikely to have major adverse effects.

Fig. S1. Schematic summary of prior findings. Kmt2d+/βGeo mice on a mixed C57BL/6J and 129SvEv background demonstrated a global deficiency of the open chromatin mark H3K4me3 in association with decreased neurogenesis in the GCL of the DG (Middle) compared with littermate Kmt2d+/+ mice (Left). These defects were rescued with AR-42 (Right) (6), a class 1 and 2 histone deacetylase inhibitor (24), which has recently been shown to inhibit HDAC5 in liver cells (49).

Here, we demonstrate that treatment with a ketogenic diet (KD) for 2 wk normalizes the global histone modification state and corrects the deficiency of neurogenesis seen in the granule cell layer (GCL) of the dentate gyrus (DG). This dietary change also rescues the hippocampal memory defects in Kmt2d+/βGeo mice. Furthermore, administration of exogenous BHB also rescues the neurogenesis defect in Kmt2d+/βGeo mice, suggesting that the increased levels of BHB play a major role in the observed therapeutic effect of the KD. Our data show that some of the neurological effects of a debilitating germline mutation can be offset by dietary modification of the epigenome and suggest a mechanistic basis of the KD, a widely used therapeutic strategy in clinical medicine.

Discussion Although BHB has previously been shown to have HDACi activity (7, 21), the potential for therapeutic application remains speculative. Here, we show that therapeutically relevant levels of BHB are achieved with a KD modeled on protocols that are used and sustainable in humans (22, 23). In addition, we demonstrate a therapeutic rescue of disease markers in a genetic disorder by taking advantage of the BHB elevation that accompanies the KD. Our findings that exogenous BHB treatment lead to similar effects on neurogenesis as the KD support the hypothesis that BHB contributes significantly to the therapeutic effect. In our previous study (6), the HDACi AR-42 led to improved performance in the probe trial of the MWM for both Kmt2d+/βGeo and Kmt2d+/+ mice (genotype-independent improvement). In contrast, KD treatment only led to improvement in Kmt2d+/βGeo mice (genotype-dependent improvement). This discrepancy may relate to the fact that AR-42 acts as an HDACi but also affects the expression of histone demethylases (24), resulting in increased potency but less specificity. Alternatively, because the levels of BHB appear to be higher in Kmt2d+/βGeo mice on the KD, the physiological levels of BHB might be unable to reach levels in Kmt2d+/+ mice high enough to make drastic changes on chromatin. Although we cannot exclude a contribution from other biochemical actions of BHB such as direct butyrylation of histone tails (25) or the effects of BHB on mitochondrial respiration, synaptic physiology (26), or cellular oxidative stress (7), the concordance of therapeutic effects with those observed on administration of an HDACi (6) provides strong, albeit correlative, evidence that the BHB acts, at least in part, through modulation of histone marks. The global epigenetic abnormalities seen in Kmt2d+/βGeo mice occur in association with altered expression of genes, some of which (such as Glp1r) lead to overlapping neurodevelopmental abnormalities when targeted in mice (17). Interestingly, Glp1r and several of the genes most highly differentially expressed demonstrate normalization on the KD. As with other disorders associated with primary perturbation of epigenetic factors, it is not possible to attribute specific aspects of the disease phenotype to specific genes or pathways; rather, it is likely that phenotypic consequences integrate the combined action of many genes that are dysregulated on attenuation of KMT2D function. In addition to the effects seen on hippocampal function and morphology, we also uncovered a metabolic phenotype in Kmt2d+/βGeo mice, which leads to both increased BHB/AcAc and lactate/pyruvate ratios during ketosis; an increased NADH/NAD+ ratio could explain both observations. This increased NADH/NAD+ ratio may relate to a previously described propensity of Kmt2d+/βGeo mice toward biochemical processes predicted to produce NADH, including beta-oxidation, and a resistance to high-fat-diet–induced obesity (27). If this exaggerated BHB elevation holds true in patients with KS, the KD may be a particularly effective treatment strategy for this patient population; however, this remains to be demonstrated. Alterations of the NADH/NAD+ ratio could also affect chromatin structure through the action of sirtuins, a class of HDACs that are known to be NAD+ dependent (28). Advocates of individualized medicine have predicted therapeutic benefit of targeted dietary interventions, although currently there are few robust examples (29⇓–31). This work serves as a proof-of-principle that dietary manipulation may be a feasible strategy for KS and suggests a possible mechanism of action of the previously observed therapeutic benefits of the KD for intractable seizure disorder (22, 23).

Materials and Methods Study Design. The purpose of this study was to test the hypothesis that the KD could be used as a therapeutic strategy in a mouse model of KS. At least four biological replicates were used for each biochemical analysis. Data collection was performed for a predetermined period, as dictated by literature-based or core facility-based standards, and no exclusion criteria were applied. All analyses were performed by examiners blinded to genotype and/or treatment group. For drug treatments, mice were randomly assigned to treatment groups with approximately equivalent numbers in each group. In box and whisker plots, whiskers extend 1.5 times the interquartile range, as is the default in the R programming language; circles indicate data points outside this range. All data points were used in statistical analysis. Mice and Dietary Manipulations. Our mouse model, Kmt2d+/βGeo, also known as Mll2Gt(RRt024)Byg, was generated by BayGenomics through the insertion of a gene trap vector. The KD [4:1 (fat:protein) ratio, F6689 Rodent Diet, Ketogenic, Fat:Paste] paste was acquired from Bio-Serv. Mice were given 2 wk free (ad libitum) access to KD paste as a sole food source. Paste was replaced several times per week. During MWM testing, given the length of testing (more than a week), we treated for 3 wk. Crebbp+/−, also known as Crebbptm1Dli (13), mice were acquired from the Jackson laboratories. All mice used in these studies were between 1 and 2 mo of age unless otherwise noted. All experiments were performed on mice fully backcrossed to C57BL/6J background unless otherwise noted. All mouse experiments were performed in accordance with the NIH Guide for the Care and Use of Laboratory Animals and were approved by the Animal Care and Use Committee of Johns Hopkins University. Serum and Brain BHB Analysis. Serum and homogenized brain tissue from Kmt2d+/βGeo and Kmt2d+/+ mice that had been treated with both standard diet and a KD for 2 wk was assayed for BHB levels using a BHB assay kit (MAK041; Sigma). Serum Creatinine and Blood Urea Nitrogen Analysis. Serum creatinine and blood urea nitrogen are commonly used markers of kidney function. Both creatinine and blood urea nitrogen levels were measured from serum from Kmt2d+/βGeo and Kmt2d+/+ mice, using standard clinical assays run at the Johns Hopkins comparative medicine analysis core. BHB Injection and Urine Assay. Either 5 mM/kg (R)-(−)-3-hydroxybutyric acid sodium salt (32⇓–34) (Santa Cruz Biotechnology) or saline was injected (100 µL) intraperitoneally once or three times a day. (R)-(−)-3-Hydroxybutyric acid sodium salt becomes (R)-(−)-3-hydroxybutyric acid in the blood and can interconvert into BHB, the form measured by ketone assays. Therefore, in text and legends, we used BHB as the label for simplicity. Urine BHB was quantified by the β-hydroxybutyrate (Ketone Body) Colorimetric Assay Kit (Cayman Chemical Company). Urine from injected mice was collected ∼1.5–2 h after injection. Urine from mice on the KD was taken in the early afternoon unless otherwise stated in the text. Osmotic Pumps. An Alzet (Durect Co.) microosmotic pump (model 1002) made to allow for 14 d of diffusion was filled (84-µL reservoir) with either 2.5 mg/mL (R)-(−)-3-hydroxybutyric acid sodium salt (Santa Cruz Biotechnology) in saline vehicle or saline vehicle alone. Mice were anesthetized, after which a small incision was made on the skin of the lower back and the pump was placed directly under the skin. Reporter Alleles. HEK 293 cells were transfected with lipofectamine LTX (Thermo Fisher) with either our H3K4me3 or H4ac reporter alleles that have been previously described (6). We selected for and maintained stably transfected cells through positive selection with blasticidin at a dose of 10 mg/mL (Life Technologies). Blasticidin selection was stopped 24 h before exposure to BHB. For BHB treatment, (R)-(−)-3-hydroxybutyric acid sodium salt (Santa Cruz Biotechnology) was added to the medium 24 h before FACSVerse flow sorting (BD Sciences). Data were analyzed using FlowJo (Tree Star Inc.). Serum Lactate and Pyruvate Analysis. Serum was extracted from whole blood by centrifugation at 3,500 × g for 10 min after 1 h incubation at room temperature. Subsequently, the supernatant was removed and stored at −20 °C. Serum samples were then assayed for levels of lactate and pyruvate with the Lactate Assay Kit (Sigma Aldrich) and Pyruvate Assay Kit (Sigma Aldrich). Mass Spectrometry for AcAc and BHB. AcAc and BHB were prepared via acid extraction and BSTFA [N,O-bis(trimethylsilyl)trifluoroacetamide)] derivatization, and detected via gas chromatography–mass spectrometry. The mass spectrometer was set in SCAN mode to detect all mass fragments in a range of m/z 50–600. Compounds were identified on the basis of their characteristic retention time and ion peaks. Results were reported as a ratio of AcAc to BHB. Microarray Experiment. Microarray results are based on a joint analysis of two different experiments. Hippocampi were dissected from wild-type and Kmt2d+/βGeo mice on a standard diet. In the first experiment, four wild-type and three Kmt2d+/βGeo mice were profiled, and in the second experiment, three wild-type and three Kmt2d+/βGeo mice were profiled. RNA was extracted from whole hippocampi, using the Qiagen RNeasy kit or TRIzol reagents (Ambion Life Technologies), followed with DNase I treatment (Qiagen). For microarray, cDNA was synthesized by the JHMI High Throughput Biology Center, using the SuperScript II RT assay (Thermo Fisher) following recommended conditions, and hybridized to Affymetrix Mouse Gene 1.0 microarrays. Analysis of Microarray Data. The microarray data were preprocessed using the robust multi-array analysis method (35⇓–37), as implemented in the oligo package (38) from Bioconductor (39, 40). Unwanted noise was removed using surrogate variable analysis (41⇓–43) with five surrogate variables. Only probe-sets of the “core” category were analyzed. After surrogate variable analysis, data were analyzed using the limma package (44) with an empirical Bayes variance estimator method (45), and P values were corrected for multiple testing, using the Benjamini-Hochberg procedure (46). RT-qPCR Validation. For RT-qPCR validation cDNA was synthesized using the Applied Biosciences High-Capacity cDNA Reverse Transcription Kit. RT-qPCR was done on RNA from the same mice used for microarray (n = 3–4 per group), as well as an additional second cohort treated in an identical fashion with a KD (n = 5–7 per group). The Taqman probes (Life Technologies) used were Pld5, Mm00620912_m1, Fam, S; Glp1r, Mm00445292_m1, Fam, S; Ankfn1: Mm03039417-m1, Fam, S; Kmt2d, Mm01717064-g1, Fam, S, with Pgk1 and Gapdh as controls (Mm99999915_g1, Vic; Mm00435617_m1, Vic, S). For Zic5, the available Taqman probe did not yield any data, so we designed and used a Sybr green assay (Zic5-F: 5′-GAGGCGCTTCCTAGTACTCC-′3; Zic5-R: 5′-GCTGCTATTGGCAAACTTCCTA-′3 with control gene Tfrc (Tfrc-F: 5′-GAGGCGCTTCCTAGTACTCC-′3; Tfrc-R: 5′-CTTGCCGAGCAAGGCTAAAC-′3). The two experimental groups were run and normalized to untreated wild-type and then combined for analysis. Perfusion, Sectioning, and Staining. Perfusion, cryosectioning, and immunofluorescence staining were performed as previously described (6). EdU (Life Technologies) in PBS/6% (vol/vol) DMSO (10 mg/mL) injections (50 µg/g/d), were delivered either for 7 consecutive days, followed by immediate perfusion (proliferation), or 7 consecutive days of injection and then perfusion on the 30th day after the first injection (survival). For staining, every sixth brain section was used, and blocking was done with 5% (mass/vol) BSA. EdU was labeled with Click-iT EdU Alexa Fluor 488 Imaging Kit (Thermo Fisher), as well as DAPI mounting with Vectamount (Vector Laboratories). EdU quantification was performed blinded to genotype and treatment. Labeled cells were counted in every sixth slice in the GCL of the DG, and average number per slice was calculated for each brain. Immunofluorescence was performed with the following primary antibodies: DCX (Santa Cruz Biotechnology; 1:200 goat), trimethylated H3K4 (Cell Signaling; 1:500 rabbit), acetylated H3K9, and H3K14 (Cell Signaling; 1:5,000 rabbit). Incubations were performed overnight at 4 °C in blocking buffer. Previous experiments performed on normal serum from which the antibodies were derived showed no nonspecific immunoreactivity (6). Confocal Microscopy. Z-stack images were taken at either 10×, using Zeiss Axiovert 200 (Carl Zeiss), or 25×, using Zeiss AxioExaminer multiphoton (Carl Zeiss), with genotypes and treatment blinded to the researcher. Fluorescence intensity of the highlighted GCL layer at the midpoint of the z-stack was measured at 10× magnification, using the Zen software (Carl Zeiss). Fluorescence intensity of either the H3K4me3 or H3ac antibody was divided by the DAPI fluorescence intensity to normalize for cell numbers. For ease of interpretation, values were normalized to Kmt2d+/+ levels. Group comparisons were done using a Student's t test, with significance set at P < 0.05. DCX Area Measurement. The DCX positive fraction of the GCL was measured by taking 4× pictures and using the Bezier tool on NS elements 2.0 software (Nikon) to measure the area of DCX+ cells that expressed DCX, as well as the entire area of the GCL. The researcher was blinded to mouse genotype and treatment. The fraction of the GCL that showed DCX+ cells was then calculated, and group differences were analyzed using a Student's t test with significance value set at P < 0.05. Behavioral Testing. Behavioral testing was conducted on mice between 1 and 2 mo of age and performed and analyzed blinded to genotype and treatment, with all experiments performed in the late morning or early afternoon. Each particular behavioral test was performed at a consistent time of day. For open-field testing, Kmt2d+/+ and Kmt2d+/βGeo mice were placed individually in an open-field chamber (San Diego Instruments) for ten 180-s intervals. These intervals were combined to give an average activity level, and treatment and genotype groups were compared using a Student's t test with significance value set at P < 0.05. For grip strength, mice were allowed to grab onto the grip strength meter (Columbus Instruments) and were lightly pulled by the tail with increasing force until releasing their grip. This was repeated five times for each mouse, with the highest and lowest value being discarded. The remaining three values were then averaged. Average grip strength for treatment and genotype groups were compared with a Student’s t test with significance value set at P < 0.05. For the MWM, all testing was performed in a standard 1.1-m diameter tank filled with room temperature water stained with white tempera paint (Crayola). The tank had a small platform submerged 2 cm below the water level in the middle of one of the four tank quadrants. For the first 3 d, the platform had a visible flag on top (flag training), and each mouse was placed in the tank for four consecutive 60-s trials in which they were trained to reach the visible platform. During each trial, the platform was moved to a different quadrant, but the mouse was always entered into the tank in the same location. Latency for each trial for each mouse was recorded, and if the mouse could not reach the platform in 60 s, they were placed on the platform. After flag training, the visible flag was removed, and for 5 d, mice were trained to reach the now hidden platform (hidden platform training), with four consecutive trials per mouse per day, with a maximum allotment of 60 s per trial. The platform was never moved, but each trial, the mouse was entered into a different quadrant, with the order of these quadrants randomly assigned for each day. On the final day (probe trial), the platform was removed, the mice were allowed to swim for 90 s, and the number of crossings over the previous location of the platform was measured. For training and probe tests, data were recorded both manually and electronically, with ANY-maze software (San Diego Instruments). The four genotype and treatment groups were analyzed for differences, using a Student's t test during the probe trial and with repeated-measures ANOVA within-subjects test for the latencies.

Acknowledgments We thank Dr. H. Dietz, Dr. B. Migeon, Dr. A. Chakravarti, Dr. P. Cole, and Dr. D. Valle for their many helpful suggestions. We thank Catherine Kiefe for her assistance with creating and editing Figs. S1 and S4. We also thank H. S. Cho for his work in the early stages of this project and Dr. J. A. Fahrner for her work on the latter stages of this project. Finally, we thank M. F. Kemper, R. J. Pawlosky, and R. L. Veech for advice regarding how to best measure BHB in brain. This work was supported by a National Institute of Health grant (to H.T.B.; Director’s Early Independence Award, DP5OD017877) and a gift from the Benjamin family (no relation to the first author).