A ketogenic diet rescues hippocampal memory defects in a mouse model of Kabuki syndrome.
Journal: 2017/July - Proceedings of the National Academy of Sciences of the United States of America
ISSN: 1091-6490
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.
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Proc Natl Acad Sci U S A 114(1): 125-130

A ketogenic diet rescues hippocampal memory defects in a mouse model of Kabuki syndrome

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205;
Predoctoral Training Program in Human Genetics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205;
Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205;
Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205;
Department of Pediatrics at the Johns Hopkins University School of Medicine, Baltimore, MD, 21205;
Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, 21205;
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205;
Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik 101, Iceland.
To whom correspondence should be addressed. Email: ude.imhj@1snrojbh.
Edited by Stephen T. Warren, Emory University School of Medicine, Atlanta, GA, and approved November 20, 2016 (received for review August 4, 2016)

Author contributions: J.S.B. and H.T.B. designed research; J.S.B., G.O.P., G.A.C., L.Z., D.L.H., and H.J.V. performed research; J.S.B., G.O.P., L.Z., L.A.G., H.J.V., K.D.H., and H.T.B. analyzed data; and J.S.B. and H.T.B. wrote the paper.

Deceased January 27, 2016.
Edited by Stephen T. Warren, Emory University School of Medicine, Atlanta, GA, and approved November 20, 2016 (received for review August 4, 2016)

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.

Keywords: epigenetics, histone machinery, adult neurogenesis, intellectual disability, ketone bodies
Significance

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). 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 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 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.

Abstract

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 (13). 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), 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 mice (6). A dietary intervention could be quickly transitioned to the clinic and is unlikely to have major adverse effects.

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Schematic summary of prior findings. Kmt2d 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 mice. Furthermore, administration of exogenous BHB also rescues the neurogenesis defect in Kmt2d 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.

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 andS4.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).

Acknowledgments

Footnotes

Conflict of interest statement: J.S.B. and H.T.B. have a pending patent for the use of a ketogenic diet and injection of BHB for treatment of Mendelian disorders of the epigenetic machinery.

This article is a PNAS Direct Submission.

Data deposition: The hippocampal gene expression datasets have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. {"type":"entrez-geo","attrs":{"text":"GSE90836","term_id":"90836","extlink":"1"}}GSE90836).

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1611431114/-/DCSupplemental.

Footnotes

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