Pilot Clinical Trial of Modified Atkins Diet for Kabuki Syndrome
Phase: EARLY_PHASE1
Conditions: Kabuki Syndrome
Sponsor: Hugo W. Moser Research Institute at Kennedy Krieger, Inc.

 
Date of last protocol revision: ____3/7/2022______ 
Principal Investigator: _Jacqueline Harris___ 
JHM IRB Application Number: ___IRB00250195___ 
 
 
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Pilot Study of Modified Atkins Diet in Kabuki Syndrome 
ID:00250195 
NCT 04722315 
Date of Last Approval: 1/31/2024 
 

 
Date of last protocol revision: ____3/7/2022______ 
Principal Investigator: _Jacqueline Harris___ 
JHM IRB Application Number: ___IRB00250195___ 
 
 
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1. 
Abstract 
Kabuki syndrome is a rare genetic disorder characterized by intellectual disability and a 
unique cognitive profile. Studies in a mouse model of Kabuki syndrome have 
demonstrated hippocampal memory defects and a disruption of adult neurogenesis in the 
the dentate gyrus. Interestingly, these deficits were normalized in postnatal life with 
agents that inhibit histone deacetylases, indicating that Kabuki syndrome may be a 
treatable cause of intellectual disability. Preliminary data shows that patients with 
Kabuki syndrome have deficits in visuospatial reasoning and memory. This proposal 
aims to build upon the basic science and clinical work to evaluate a potential treatment 
using disease-specific outcome measures. If successful, these studies will yield insights 
into the pathogenesis of Kabuki syndrome and lead to the first therapeutic strategy. 
 
2. 
Objectives  
Objective 1: Test whether HDAC inhibition through modified Atkins diet modifies the 
neurocognitive or neurobehavioral phenotype in individuals with Kabuki syndrome. 
Previously, a ketogenic diet has been shown to ameliorate cognitive and 
neurohistological defects in a mouse model of Kabuki syndrome. This proposal aims to 
conduct a pilot study of 10-15 adult patients with Kabuki syndrome given 12 weeks of 
HDAC inhibition through diet and determine whether performance on the cognitive 
assessment protocol changes. 
 
 
3. 
Background  
Kabuki syndrome (KS; MIM 147920) is a genetic disorder occurring in about 1 in every 
32,000 births characterized by five cardinal features; dysmorphic facial features, skeletal 
anomalies, persistence of fetal fingertip pads, postnatal growth deficiency, and 
intellectual disability (ID). The most common variants in patients with KS are found in 
KMT2D – a histone methyltransferase that adds mono-, di- and trimethylation to K4, 
changes found at enhancers and actively transcribed promoters. Mutations in KDM6A – 
a histone demethylase that removes H3K27me3, a modification seen in closed chromatin 
– represent another known, but less common cause of KS (MIM 300867).  Mutations in 
KMT2D or KDM6A thus result in widespread changes in normal cellular transcription 
due to loss of histone modifications resulting in too much closed chromatin. Kabuki 
syndrome is thus an excellent example of a Mendelian disorder of histone machinery 
(MDEM), most of which, like KS, result in intellectual disability. In addition to 
information about a specific rare disease, understanding more about the cellular 
mechanisms resulting in impaired cognition in KS gives insight into the whole group of 
MDEMs. Understanding these as a group, in turn, may provide a window into the 
mechanisms underlying normal cognition and memory and learning, and pathologic 
states – specifically intellectual disability.  
Intellectual disability (ID) is a heavy burden on patients, family and society. Many 
genetic syndromes result in intellectual disability; however, although the causative genes 
of these syndromes are known, little is understood about how these variants lead to 
intellectual disability. Only recently, basic science has begun to try to characterize the 
mechanisms underlying cognitive impairment. This work has led to treatment trials in 
diseases such as Fragile X syndrome and Angelman syndrome. The Bjornsson lab has 
demonstrated that Kmt2d is highly expressed in the granule cell layer of the dentate 

 
Date of last protocol revision: ____3/7/2022______ 
Principal Investigator: _Jacqueline Harris___ 
JHM IRB Application Number: ___IRB00250195___ 
 
 
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gyrus. Kmt2d +/βGeo mice have many physical features of humans with KS as well as 
abnormalities in visuospatial memory and deficits in neurogenesis in the dentate gyrus 
region of the hippocampus seen in association with a thinner granule cell layer. 
Importantly, these cognitive and histopathologic deficits were corrected with postnatal 
administration of a histone deacetylase inhibitor and with the ketogenic diet. The dentate 
gyrus – and postnatal neurogenesis in this region – has been linked to spatial pattern 
separation and thus tests that examine visuospatial reasoning and memory at least 
partially localize to this brain region. While problems with visuospatial areas of 
cognition are far from a 1:1 correlation with dentate gyrus neurogenesis, there is 
certainly an important correlation. Thus, we would expect this neuroanatomical region 
to be abnormal in individuals with KS if mouse studies are predictive. Our recently 
published study of 23 patients solidified the visuospatial/verbal differences in the KS 
cognitive profile and more specifically linked the weaknesses in the profile to the 
dentate gyrus region. Additionally, by comparing the KS patients to age and IQ-matched 
controls, we established that this cognitive phenotype is specific to Kabuki syndrome 
and different from what is seen in other causes of ID. In addition, impaired neurogenesis 
in the hippocampus has been strongly linked to anxiety and anecdotally we have noticed 
a significant burden of anxiety in patients with Kabuki syndrome. Thus it is important to 
examine emotion and behavior in totality as well as anxiety in depth in this population 
and determine whether anxiety moderates the cognitive performance. As a next step, a 
biologically relevant and evidence-based treatment must be selected as an intervention 
for a clinical trial.  
The Bjornsson lab has demonstrated that in the Kmt2d +/βGeo mice, a ketogenic diet is 
equally effective in reversing the visuospatial deficits and increasing neurogenesis in the 
dentate gyrus. This is a treatment that is used clinically for many conditions including 
ones that affect the central nervous system like epilepsy. Modified Atkins diet has been 
shown to be effective in these conditions in place of stricter ketogenic diet and is easier 
for patients to tolerate. The pilot treatment trial we propose here could lead to a larger 
trial which could have immediate benefit to patients and change clinical practice. The 
Bjornsson lab demonstrated in 2016 that neurogenesis and memory deficits in the mouse 
model of KS was not only rescued by administration of HDAC inhibitor AR-42, but that 
it was also rescued with the ketogenic diet (Figure 2). Beta hydroxybutyrate, a ketone 
body that is actively transported into the central nervous system and enters the 
hippocampus during ketosis, is a potent HDAC inhibitor. Modified Atkins diet (MAD) 
has been shown to be an effective, safer to initiate, and easier to comply with substitute 
for the ketogenic diet in other CNS processes like epilepsy. Thus we believe the 
rationale is there to attempt a low-risk pilot study using this intervention in patients with 
KS. The Neurology teams at Johns Hopkins include nutritionists, clinicians, and 
researchers who have extensive experience with MAD and they will be available for 
consultation and for any diet-related needs. 12 weeks was chosen because that is the 
minimum amount of time used to see effect in studies on the ketogenic diet or MAD. 
Additionally, 8 weeks is the approximate length of time of neurogenesis of a new 
neuron. Since we suspect neurogenesis plays a role in cognitive performance in KS, the 
12 week duration allows for neurogenesis to take place. To date, no study of treating 
epilepsy in KS with ketogenic diet or MAD exists. 
 
 

 
Date of last protocol revision: ____3/7/2022______ 
Principal Investigator: _Jacqueline Harris___ 
JHM IRB Application Number: ___IRB00250195___ 
 
 
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4. 
Study Procedures 
a. Participants with Kabuki syndrome 18 years and older will be recruited to 
participate. Recruitment will stop once fifteen participants are consented. This 
number allows for the ~30% rate of dropout expected based on difficulty complying 
with the diet in order to have data from 10 participants. Exclusion criteria would be 
inability to tolerate or comply with modified Atkins diet, inability to do repeat blood 
and urine testing, and inability to travel to Baltimore for 2 study visits 3 months 
apart. Participants will begin whenever they have their initial visit and conclude 12 
weeks later. See Figure 1. 
 
 
 
 
 
 
Table 1: Neurocognitive and Neurobehavioral Testing 
Protocol (Repeated 
Day 1 and Week 12) 
Purpose of Test 
Area of Cognition or Behavior 
Evaluated 
Neurocognitive Subtest Current Battery 
 
 
 
 
Cognitive 
Assessment Protocol 
 
 
 
 
 
Outcome Measure 
Development 
Visuospatial reasoning 
Benton Judgement of Line Orientation 
Visuospatial perception, construction, 
and memory 
Brief Visuospatial Memory Test, NIH 
Toolbox Picture Story Memory 
Language  
Wechsler verbal portion of IQ testing 
Visual motor integration 
Beery Developmental Test of Visual Motor 
Integration 
Visual perception 
Beery Developmental Test of Visual 
Perception 
Executive function – inhibition, attention, 
and switching 
NIH Toolbox Flanker Inhibition and Card 
Sorting 
Visuospatial perception and construction 
Wechsler Intelligence Scale for Children -V 
Block Design 
Neurobehavioral 
Questionnaires 
 
Characterize Cognitive 
Phenotype and Brain-
Behavior Relationship 
Anxiety and Behavioral Phenotype 
Caregiver Rating Scales: SCARED and 
Child Behavior Checklist (CBCL) or Adult 
Behavior Checklist (ABCL) and NIH 
Toolbox Emotion Measures 
Verbal Hippocampal 
Measure 
Brain-Behavior 
Relationship 
Verbal memory 
Hopkins Verbal Learning Test 
12 weeks 
Daily: Diet logs 
Twice weekly: 
Urine ketones 
Every 3 weeks: 
Blood draw 
Initial Study Visit 
Cognitive and 
Behavioral testing 
Initial Blood Draw 
Modified Atkins Diet 
Education 
End Week 12 
Blood draw 
Cognitive 
assessment 
Behavioral 
questionnaires 
FINISH 
Figure 1: Study Flow 
 

 
Date of last protocol revision: ____3/7/2022______ 
Principal Investigator: _Jacqueline Harris___ 
JHM IRB Application Number: ___IRB00250195___ 
 
 
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The study flow is outlined in Figure 1. These consented adult participants will 
participate in an initial study visit. These participants will undergo cognitive and 
neurobehavioral testing and also will have baseline labs drawn and will meet with a 
study team member trained in modified Atkins diet for education. The labs are standard 
of care for diet initiation to rule out contraindications (CBC, CMP, lipids, UA, urine 
amino acids, free and total carnitine, Vitamin D, selenium). Blood will also be taken for 
genome-wide DNA methylation analysis to look for the known abnormal signature in 
Kabuki syndrome and see if it changes over time with the diet. Participants and/or their 
caregivers will keep a daily diet log and/or will be asked to download the free Carb 
Manager application onto their smartphone. They will send the logs and data back 
weekly. The application is optional, only if participants prefer it to keeping their own 
logs. Participants will be given urine ketone strips and asked to use and record in their 
diet log twice weekly. Participants will have blood ordered and drawn remotely every 3 
weeks and sent securely to the study team. Beta-hydroxybutyrate will be measured on 
this sample as well as genome-wide DNA methylation measured every 3 weeks to see if 
it changes over the course of the trial. At the 6 week mark participants will also securely 
send a urine sample for measurement of urine ketones and amino acids to investigate 
metabolism while on the diet. Participants will return to Baltimore at the end of 12 
weeks for a one day visit to repeat the cognitive assessment protocol, neurobehavioral 
measures, and repeat the initial lab tests including genome-wide DNA methylation 
(Figure 1). 
 
 
b. The study will last for 12 weeks for each participant. There will be 2 on site study 
visits. Participants will then return home for the 12 week diet. They then will return 
to Baltimore for a 1 day study visit.  
 
c. This study is not blinded for participants or investigators because that would be too 
difficult logistically since the participants have to keep the diet. Additionally, 
because this is just a very small pilot study, blinding is not necessary.  
 
d. Participants will receive all standard of care and treatments. None will be stopped.  
 
e. No placebo group will be used because this is only a pilot study and placebo groups 
will come in later studies.  
 
f. If participants cannot tolerate and/or adhere to the diet during the 12 weeks by their 
own self report and diet logs, they will be removed from the study. 
 
g. Participants can go back to their typical diet after the study ends or if they end the 
study early. 
 
 
h. Participants will have blood drawn 5 times and urine collected 2 times. Blood and 
urine collection at the initial and final study visits will be done at KKI. Most of the 
blood and urine will be sent to JHH core lab and are standard of care for diet 

 
Date of last protocol revision: ____3/7/2022______ 
Principal Investigator: _Jacqueline Harris___ 
JHM IRB Application Number: ___IRB00250195___ 
 
 
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initiation and monitoring to rule out contraindications or severe side effects (CBC, 
CMP, lipids, UA, urine amino acids, free and total carnitine, Vitamin D, selenium). 
Another 2 purple top tubes of blood will also be taken and transported to the 
Bjornsson lab by a study team member to run a genome-wide DNA methylation 
array to look for the known abnormal signature in Kabuki syndrome and see if it 
changes over time with the diet. The total additional blood volume taken beyond the 
standard of care labs for the diet will be 6 mL. In addition, participants will have 
blood ordered and drawn remotely every 3 weeks and sent securely to the study 
team. Once the study team receives it, one vial will go to JHH core lab and one to 
the Bjornsson lab. Beta-hydroxybutyrate will be measured on this sample by JHH 
core lab every 3 weeks and the other tube will again be taken to the Bjornsson lab to 
perform genome-wide DNA methylation arrays at 6 weeks to see if it changes over 
the course of the trial.  
 
5. 
Inclusion/Exclusion Criteria 
We will recruit 15 total participants with clinically-definite and genetically-confirmed 
Kabuki syndrome type 1 age 18 years and older. Clinical diagnosis of KS will be made 
based on recently published consensus diagnosis criteria. Genetic confirmation of a 
pathogenic mutation in KMT2D will also be required. Exclusion of participants younger 
than 18 years old is based on: 1) adults being able to consent to their own diet therapy, 
2) ability to adhere to the diet, and 3) ability to standardize one cognitive battery to 
compare across and between participants. Other exclusion criteria include presence of 
another known genetic syndrome, a health problem that would make a modified Atkins 
diet harmful, inability to travel to Baltimore for 2 visits separated by 12 weeks. 
Recruitment of participants will be done solely by asking adults already participating in 
IRB00240569 to participate in this study as well. No recruitment will be done of 
participants not already enrolled in the other study.  
 
6. 
Drugs/ Substances/ Devices 
a. The Bjornsson lab demonstrated in 2016 that neurogenesis and memory deficits in 
the mouse model of KS was not only rescued by administration of HDAC inhibitor 
AR-42, but that it was also rescued with the ketogenic diet (Figure 2). Beta 
hydroxybutyrate, a ketone body that is actively transported into the central nervous 
system and enters the hippocampus during ketosis, is a potent HDAC inhibitor. 
Modified Atkins diet (MAD) has been shown to be an effective, safer to initiate, and 
easier to comply with  substitute for the ketogenic diet in other CNS processes like 
epilepsy. Thus we believe the rationale is there to attempt a low-risk pilot study 
using this intervention in patients with KS. The Neurology teams at Johns Hopkins 
include nutritionists, clinicians, and researchers who have extensive experience with 
MAD and they will be available for consultation and for any diet-related needs. 12 
weeks was chosen because that is the minimum amount of time used to see effect in 
studies on the ketogenic diet or MAD. Additionally, 8 weeks is the approximate 
length of time of neurogenesis of a new neuron. Since we suspect neurogenesis plays 
a role in cognitive performance in KS, the 12 week duration allows for neurogenesis 
to take place. To date, no study of treating epilepsy in KS with ketogenic diet or 
MAD exists. AR42 and Vafidemstat were chosen as in vitro comparisons (no in vivo 
use of these drugs) because of the previous evidence from the Bjornsson lab that 

 
Date of last protocol revision: ____3/7/2022______ 
Principal Investigator: _Jacqueline Harris___ 
JHM IRB Application Number: ___IRB00250195___ 
 
 
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both HDAC inhibition and LSD1 inhibition also ameliorate the phenotype in mice 
like ketogenic diet does.  
 
7. 
Study Statistics 
a. Primary outcome variable: Change in cognitive testing protocol before and 
after 12 weeks of the diet 
b. Secondary outcome variables: 1) Change in anxiety measure scores after 12 
weeks on the diet. 2) Change in genome-wide DNA methylation array 
signature while on the diet. 
c. Statistical plan including sample size justification: We will recruit 15 
participants to this study with a goal of having 10 participants who complete 
the whole 12 weeks. We will only analyze data from participants who 
complete the whole 12 weeks. This number is completely generated based on 
the rarity of the disease model and therefore how many participants were felt 
were feasible to recruit. This is a very early stage, non-masked trial with no 
control group so no power analysis was done. To analyze the data, we will do 
intra-subject comparisons of the testing measures before and after 12 weeks 
of the diet, controlling for practice effects and for the fact the cognitive 
assessment protocol will be repeated 3 times in these participants. We will 
perform regression analysis to determine if the change is dependent on BHB 
levels. We will investigate whether scores on a measure of anxiety and if 
genome-wide DNA methylation analyses change after 12 weeks of diet and 
also if these potential changes moderate any change seen on cognitive 
assessment protocol.  
d. Participants will only stop early based on inability to tolerate the diet. With 
only 15 participants, there will be no interim data analysis to stop early.  
 
 
8. 
Risks 
a. The main risk of this study is the modified Atkins diet. Potential risks of the 
diet include kidney stones, constipation, acidosis, diminished growth, weight 
loss, and hyperlipidemia. The rest of the proposed research presents no more 
than minimal physical, psychological, legal, or financial risk to participants. 
Neurological examination is part of a routine physical examination and 
involves no more than minimal risk to the participants. Neuropsychological 
testing can take a prolonged amount of time and can cause anxiety and 
discomfort in participants. Venipuncture can cause discomfort and mild 
bruising or bleeding at the site. Risk of infection is minimal. Patients may be 
disturbed by seeing their blood drawn. Risk of using the CarbManager 
application is minimal.  Participants do not enter name or date of birth. They 
do enter a username (which will be their subject ID), sex, and year of birth. 
However sex and year of birth can be skipped.  Other than that, participants 
only enter diet logs daily.  The participant then generates weekly reports 
through the app that will be saved as a pdf to their device which they then 
will securely email to the study team.  Use of the app is optional for 
participants and they can opt to just type their diet logs and securely email 
them 

 
Date of last protocol revision: ____3/7/2022______ 
Principal Investigator: _Jacqueline Harris___ 
JHM IRB Application Number: ___IRB00250195___ 
 
 
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b. Labs and an exam will be done at the initial study visit to ensure that 
participants are healthy enough for 12 weeks of diet. Additionally, 
participants will be thoroughly educated about the diet at their initial study 
visit including potential adverse effects. Weekly check-ins with participants 
will be done to ensure they are complying with the diet and hear about any 
adverse effects. Subjects will be allowed to take breaks during 
Neuropsychological testing if significant anxiety or discomfort occurs.  We 
will reinforce at each study visit that subjects can stop study procedures at 
any time if needed.   
c. Any problems should be reported directly to Dr. Harris and she will be 
responsible for reporting the adverse events and responding to them. This 
study does have a DSMB consisting of 4 JHH faculty members.  
d. Any physical data forms will be kept in a locked office in a locked cabinet to 
which only the PI has the key.  The linking document with patient identifiers 
and study ID numbers will be kept on a password protected computer in the 
locked office, within a password protected file. This file will be kept separate 
from all data files including imaging data and testing results.  These files will 
be deidentified and marked with a study identifier only and stored on a 
secure server  - JHH OneDrive. Data collected through the CarbManager 
app, for those who choose to use it, will not have any identifiable information 
in it and will be emailed securely to the study team. 
e. Participants may incur a financial toll by having to travel to Baltimore. We 
will minimize this by making the needed travel clear in screening.  
 
9. 
Benefits 
a. There is a possibility that patients may experience improvement in their 
cognition after 12 weeks on the diet. Other benefits of the study include 
furthering the scientific knowledge about Kabuki syndrome specifically and 
brain-behavior relationships in general 
 
 
10. 
Payment and Remuneration 
a. Participants will not receive any payment as part of this study but will be 
provided lunch and parking during the study visits.  
 
11. 
Costs 
a. Participants will not incur significant costs as part of this study. 
Neurobehavioral testing and laboratory costs will be paid for by PI’s grant 
funding. Participants will be responsible for their own travel costs to 
Baltimore. Participants will also be responsible for the cost of their own food 
during the diet period.