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

References

  • 1. Ng SB, et al Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet. 2010;42(9):790–793.[Google Scholar]
  • 2. Lederer D, et al Deletion of KDM6A, a histone demethylase interacting with MLL2, in three patients with Kabuki syndrome. Am J Hum Genet. 2012;90(1):119–124.[Google Scholar]
  • 3. Miyake N, et al KDM6A point mutations cause Kabuki syndrome. Hum Mutat. 2013;34(1):108–110.[PubMed][Google Scholar]
  • 4. Fahrner JA, Bjornsson HTMendelian disorders of the epigenetic machinery: tipping the balance of chromatin states. Annu Rev Genomics Hum Genet. 2014;15:269–293.[Google Scholar]
  • 5. Ming GL, Song HAdult neurogenesis in the mammalian brain: significant answers and significant questions. Neuron. 2011;70(4):687–702.[Google Scholar]
  • 6. Bjornsson HT, et al Histone deacetylase inhibition rescues structural and functional brain deficits in a mouse model of Kabuki syndrome. Sci Transl Med. 2014;6(256):256ra135.[Google Scholar]
  • 7. Shimazu T, et al Suppression of oxidative stress by β-hydroxybutyrate, an endogenous histone deacetylase inhibitor. Science. 2013;339(6116):211–214.[Google Scholar]
  • 8. Hasselbalch SG, et al Blood-brain barrier permeability of glucose and ketone bodies during short-term starvation in humans. Am J Physiol. 1995;268(6 Pt 1):E1161–E1166.[PubMed][Google Scholar]
  • 9. Sleiman SF, et al Exercise promotes the expression of brain derived neurotrophic factor (BDNF) through the action of the ketone body beta-hydroxybutyrate. Elife. 2016;16:5e15092.[Google Scholar]
  • 10. Lee MG, et al Functional interplay between histone demethylase and deacetylase enzymes. Mol Cell Biol. 2006;26(17):6395–6402.[Google Scholar]
  • 11. Freeman JM, et al The efficacy of the ketogenic diet-1998: a prospective evaluation of intervention in 150 children. Pediatrics. 1998;102(6):1358–1363.[PubMed][Google Scholar]
  • 12. Courcet JB, et al Clinical and molecular spectrum of renal malformations in Kabuki syndrome. J Pediatr. 2013;163(3):742–746.[PubMed][Google Scholar]
  • 13. Kung AL, et al Gene dose-dependent control of hematopoiesis and hematologic tumor suppression by CBP. Genes Dev. 2000;14(3):272–277.[Google Scholar]
  • 14. Alarcón JM, et al Chromatin acetylation, memory, and LTP are impaired in CBP+/- mice: a model for the cognitive deficit in Rubinstein-Taybi syndrome and its amelioration. Neuron. 2004;42(6):947–959.[PubMed][Google Scholar]
  • 15. Kurdistani SKChromatin: a capacitor of acetate for integrated regulation of gene expression and cell physiology. Curr Opin Genet Dev. 2014;26:53–58.[Google Scholar]
  • 16. Castonguay Z, Auger C, Thomas SC, Chahma M, Appanna VDNuclear lactate dehydrogenase modulates histone modification in human hepatocytes. Biochem Biophys Res Commun. 2014;454(1):172–177.[PubMed][Google Scholar]
  • 17. During MJ, et al Glucagon-like peptide-1 receptor is involved in learning and neuroprotection. Nat Med. 2003;9(9):1173–1179.[PubMed][Google Scholar]
  • 18. Chehrehasa F, Meedeniya AC, Dwyer P, Abrahamsen G, Mackay-Sim AEdU, a new thymidine analogue for labelling proliferating cells in the nervous system. J Neurosci Methods. 2009;177(1):122–130.[PubMed][Google Scholar]
  • 19. Clarke K, et al Kinetics, safety and tolerability of (R)-3-hydroxybutyl (R)-3-hydroxybutyrate in healthy adult subjects. Regul Toxicol Pharmacol. 2012;63(3):401–408.[Google Scholar]
  • 20. Garthe A, Kempermann GAn old test for new neurons: refining the Morris water maze to study the functional relevance of adult hippocampal neurogenesis. Front Neurosci. 2013;7:63.[Google Scholar]
  • 21. Lim S, et al D-β-hydroxybutyrate is protective in mouse models of Huntington’s disease. PLoS One. 2011;6(9):e24620.[Google Scholar]
  • 22. Wheless JWHistory of the ketogenic diet. Epilepsia. 2008;49(Suppl 8):3–5.[PubMed][Google Scholar]
  • 23. Gasior M, Rogawski MA, Hartman ALNeuroprotective and disease-modifying effects of the ketogenic diet. Behav Pharmacol. 2006;17(5-6):431–439.[Google Scholar]
  • 24. Huang PH, Plass C, Chen CSEffects of histone deacetylase inhibitors on modulating H3K4 methylation marks - a novel cross-talk mechanism between histone-modifying enzymes. Mol Cell Pharmacol. 2011;3(2):39–43.[Google Scholar]
  • 25. Chen Y, et al Lysine propionylation and butyrylation are novel post-translational modifications in histones. Mol Cell Proteomics. 2007;6(5):812–819.[Google Scholar]
  • 26. Kim DY, Vallejo J, Rho JMKetones prevent synaptic dysfunction induced by mitochondrial respiratory complex inhibitors. J Neurochem. 2010;114(1):130–141.[Google Scholar]
  • 27. Kim DH, et al Crucial roles of mixed-lineage leukemia 3 and 4 as epigenetic switches of the hepatic circadian clock controlling bile acid homeostasis in mice. Hepatology. 2015;61(3):1012–1023.[Google Scholar]
  • 28. Cohen HY, et al Calorie restriction promotes mammalian cell survival by inducing the SIRT1 deacetylase. Science. 2004;305(5682):390–392.[PubMed][Google Scholar]
  • 29. Elliott R, Ong TJNutritional genomics. BMJ. 2002;324(7351):1438–1442.[Google Scholar]
  • 30. Ordovas JM, Corella DNutritional genomics. Annu Rev Genomics Hum Genet. 2004;5:71–118.[PubMed][Google Scholar]
  • 31. García-Cañas V, Simó C, León C, Cifuentes AAdvances in Nutrigenomics research: novel and future analytical approaches to investigate the biological activity of natural compounds and food functions. J Pharm Biomed Anal. 2010;51(2):290–304.[PubMed][Google Scholar]
  • 32. Yum MS, Ko TS, Kim DWβ-Hydroxybutyrate increases the pilocarpine-induced seizure threshold in young mice. Brain Dev. 2012;34(3):181–184.[PubMed][Google Scholar]
  • 33. Yum MS, Ko TS, Kim DWAnticonvulsant effects of β-hydroxybutyrate in mice. J Epilepsy Res. 2012;2(2):29–32.[Google Scholar]
  • 34. Yum MS, et al β-Hydroxybutyrate attenuates NMDA-induced spasms in rats with evidence of neuronal stabilization on MR spectroscopy. Epilepsy Res. 2015;117:125–132.[PubMed][Google Scholar]
  • 35. Carvalho B, Bengtsson H, Speed TP, Irizarry RAExploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics. 2007;8(2):485–499.[PubMed][Google Scholar]
  • 36. Irizarry RA, et al Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003;31(4):e15.[Google Scholar]
  • 37. Irizarry RA, et al Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003;4(2):249–264.[PubMed][Google Scholar]
  • 38. Carvalho BS, Irizarry RAA framework for oligonucleotide microarray preprocessing. Bioinformatics. 2010;26(19):2363–2367.[Google Scholar]
  • 39. Gentleman RC, et al Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5(10):R80.[Google Scholar]
  • 40. Huber W, et al Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015;12(2):115–121.[Google Scholar]
  • 41. Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JDThe sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 2012;28(6):882–883.[Google Scholar]
  • 42. Leek JT, Storey JDA general framework for multiple testing dependence. Proc Natl Acad Sci USA. 2008;105(48):18718–18723.[Google Scholar]
  • 43. Leek JT, Storey JDCapturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 2007;3(9):1724–1735.[Google Scholar]
  • 44. Ritchie ME, et al limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47.[Google Scholar]
  • 45. Smyth GKLinear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3(1):1–25.[PubMed][Google Scholar]
  • 46. Benjamini Y, Hochberg YControlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol. 1995;57(1):289–300.[PubMed][Google Scholar]
  • 47. Feron OPyruvate into lactate and back: from the Warburg effect to symbiotic energy fuel exchange in cancer cells. Radiother Oncol. 2009;92(3):329–333.[PubMed][Google Scholar]
  • 48. White H, Venkatesh BClinical review: ketones and brain injury. Crit Care. 2011;15(2):219.[Google Scholar]
  • 49. Zhang M, et al AR-42 induces apoptosis in human hepatocellular carcinoma cells via HDAC5 inhibition. Oncotarget. 2016;7(16):22285–22294.[Google Scholar]
  • 50. Zhao Q, Stafstrom CE, Fu DD, Hu Y, Holmes GLDetrimental effects of the ketogenic diet on cognitive function in rats. Pediatr Res. 2004;55(3):498–506.[PubMed][Google Scholar]
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