Epigenetic Regulation of Stress-related Genes in Relation to MDMA-Assisted Psychotherapy Treatment for Post-Traumatic Stress Disorder
Phase: PHASE3
Conditions: PTSD
Sponsor: University of Southern California

Epigenetics and MDMA-Assisted Psychotherapy for PTSD 
 
A substudy of “A Multi‐Site Phase 3 Study of MDMA‐Assisted Psychotherapy for PTSD” 
(ClinicalTrials.gov Identifier: NCT03537014).”  
 
 
December 6, 2023 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Study Protocol 
For a detailed description of the planned data collection for the parent clinical trial see “A Multi‐Site 
Phase 3 Study of MDMA‐Assisted Psychotherapy for PTSD” (ClinicalTrials.gov Identifier: NCT03537014). 
The current substudy is concerned only with collecting additional salivary DNA samples from research 
participants in the main clinical trial that will be sent to the PI at USC for evaluation and co‐registration 
with psychometric and clinical scale data on a subject‐by‐subject basis, for those subjects that volunteer 
to be included in this substudy. The parent study is 18 weeks in duration and involves 20 planned study 
visits. 
 
For the current substudy, the site coordinators at participating sites in the multi‐site clinical trial 
will collect saliva from research participants in the parent study at the following time points: 
1) Collect saliva prior to first MDMA (vs placebo) treatment session at the Baseline Visit 3 or Visit 4 
for the Phase 3 parent study, prior to the first MDMA (vs placebo) treatment session. 
2) Collect saliva following final MDMA (vs placebo) treatment session at Primary Outcome 
Visit 19 or Visit 20 in the Phase 3 parent study, approximately 18 weeks after the first MDMA (vs 
placebo) treatment session. 
3) Collect saliva at 1 year follow up time point (optional, for subjects in the MDMA group only) 
4) Collect saliva at Integrative Session after last MDMA treatment session for subjects in the 
Placebo group 
The collection of saliva will be accomplished using the Oragene DNA OG‐500 salivary DNA kits 
(https://www.dnagenotek.com/ROW/products/collection‐human/oragene‐dna/500‐series/OG‐ 
500.html). 
The salivary samples take no more than 2‐3 minutes to collect by passive drool into the salivary 
collection kit. 
After capping, these salivary samples will be stored at room temperature and will then be sent 
back to the PI at USC for epigenetic analysis of gene methylation patterns. 
 
 
 

Statistical considerations for the study 
The statistical power calculations for the parent study were made by fitting a Mixed‐Effect Model 
Repeated Measure (MMRM) model to CAPS‐4 data from the MAPS Phase 2 study MP1 to obtain 
covariance parameter estimates. The previous Phase 2 MP1 study followed a similar design with 
outcomes measured by CAPS‐4 outcome scores, which allowed for estimation of within‐subject 
covariance parameters. With a sample size of 50 participants per treatment group in the 
modified Intent‐to‐Treat (mITT) population, this study has 90% power to detect a treatment 
effect, using a two‐sided test with an alpha of 0.0499. 
 
For the purposes of the current substudy analyzing the impact of the treatment on epigenetic 
regulation of candidate genes we have identified other studies in the literature showing significant 
effects with similar size population, demonstrating that we can expect treatment effects on 
epigenetic regulation with a large enough effect size to be discernible from this sample size. 
In addition to standard statistical approaches with corrections for multiple comparisons to assess the 
methylation changes on the target genes and gene networks, a second level of statistical analysis to be 
accomplished will be the assessment of the correlations between the change from baseline in PTSD and 
Depression symptoms (and related psychometrics) and the change from baseline in the methylation 
patterns of the target genes/gene networks obtained.