CpH methylome analysis in human cortical neurons identifies novel gene pathways and drug targets for opioid use
Sheila T Nagamatsu1,2,3, Gregory Rompala4, Yasmin L Hurd4
1Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States.
Introduction:
DNA methylation (DNAm), an epigenetic mechanism, has been associated with opioid use disorder (OUD) in preclinical and human studies. However, most of the studies have focused on DNAm at CpG sites. DNAm at non-CpG sites (mCpHs, where H indicates A, T, or C) has been recently shown to have a role in gene regulation and to be highly abundant in neurons. However, its role in OUD is unknown. This work aims to evaluate mCpHs in the human postmortem orbital frontal cortex (OFC) in the context of OUD.
Methods:
A total of 38 Postmortem OFC samples were obtained from the VA Brain Bank (OUD = 12; Control = 26). mCpHs were assessed using reduced representation oxidative bisulfite sequencing in neuronal nuclei. Differential analysis was performed using the "methylkit" R package. Age, ancestry, postmortem interval, PTSD, and smoking status were included as covariates. Significant mCpHs were set at q-value < 0.05. Gene Ontology (GO) and KEGG enrichment analyses were performed for the annotated genes of all differential mCpH loci using String, ShinyGO, and amiGO software. Further, all annotated genes were analyzed using the Drug gene interaction database (DGIdb).
Results:
A total of 2,352 differentially methylated genome-wide significant mCpHs were identified in OUD, mapping to 2,081 genes. GO analysis of genes with differential mCpH loci showed enrichment for nervous system development (p-value = 2.32E-19). KEGG enrichment analysis identified axon guidance and glutamatergic synapse (FDR 9E-4-2.1E-2). Drug interaction analysis found 3,420 interactions between the annotated genes and drugs, identifying interactions with 15 opioid-related drugs, including lofexidine and tizanidine, both previously used for the treatment of OUD-related symptoms.
Conclusion:
Our findings suggest a role of mCpHs for OUD in cortical neurons and reveal important biological pathways and drug targets associated with the disorder.
Insights
This study explored DNA methylation at non-CpG sites (mCpHs) in the brain for opioid use disorder (OUD). Findings reveal mCpHs play a role in OUD and identify potential drug targets.
Area of Science:
- Neuroscience
- Epigenetics
- Genomics
Background:
- DNA methylation (DNAm) is an epigenetic mechanism implicated in opioid use disorder (OUD).
- Most research focuses on DNA methylation at CpG sites, overlooking non-CpG sites (mCpHs).
- mCpHs are abundant in neurons and play a role in gene regulation, but their role in OUD is unknown.
Purpose of the Study:
- To investigate the role of mCpHs in the human postmortem orbital frontal cortex (OFC) in the context of OUD.
- To identify potential biological pathways and drug targets associated with OUD through mCpH analysis.
Main Methods:
- Analysis of 2,352 differentially methylated mCpHs in 38 postmortem OFC samples (12 OUD, 26 control).
- Utilized reduced representation oxidative bisulfite sequencing in neuronal nuclei.
- Performed Gene Ontology and KEGG enrichment analyses, alongside drug interaction analysis.
Main Results:
- Identified 2,352 differentially methylated mCpHs genome-wide, mapping to 2,081 genes.
- Enrichment analysis revealed involvement in nervous system development, axon guidance, and glutamatergic synapses.
- Drug interaction analysis identified 3,420 interactions, including with 15 opioid-related drugs.
Conclusions:
- mCpHs play a significant role in OUD within cortical neurons.
- The study highlights key biological pathways and potential drug targets for OUD treatment.
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