No association between peripheral serotonin-gene-related DNA methylation and brain serotonin neurotransmission in the healthy and depressed state

Clin Epigenetics. 2024 May 27;16(1):71. doi: 10.1186/s13148-024-01678-y.


Background: Methylation of serotonin-related genes has been proposed as a plausible gene-by-environment link which may mediate environmental stress, depressive and anxiety symptoms. DNA methylation is often measured in blood cells, but little is known about the association between this peripheral epigenetic modification and brain serotonergic architecture. Here, we evaluated the association between whole-blood-derived methylation of four CpG sites in the serotonin transporter (SLC6A4) and six CpG sites of the tryptophan hydroxylase 2 (TPH2) gene and in-vivo brain levels of serotonin transporter (5-HTT) and serotonin 4 receptor (5-HT4) in a cohort of healthy individuals (N = 254) and, for 5-HT4, in a cohort of unmedicated patients with depression (N = 90). To do so, we quantified SLC6A4/TPH2 methylation using bisulfite pyrosequencing and estimated brain 5-HT4 and 5-HTT levels using positron emission tomography. In addition, we explored the association between SLC6A4 and TPH2 methylation and measures of early life and recent stress, depressive and anxiety symptoms on 297 healthy individuals.

Results: We found no statistically significant association between peripheral DNA methylation and brain markers of serotonergic neurotransmission in patients with depression or in healthy individuals. In addition, although SLC6A4 CpG2 (chr17:30,236,083) methylation was marginally associated with the parental bonding inventory overprotection score in the healthy cohort, statistical significance did not remain after accounting for blood cell heterogeneity.

Conclusions: We suggest that findings on peripheral DNA methylation in the context of brain serotonin-related features should be interpreted with caution. More studies are needed to rule out a role of SLC6A4 and TPH2 methylation as biomarkers for environmental stress, depressive or anxiety symptoms.

Keywords: 5-HT; Depression; Early life stress; Epigenetics; Human brain imaging; Mood disorders; PET; Serotonin 4 receptor; Serotonin transporter; TPH2; Tryptophan hydroxylase 2.

MeSH terms

  • Adult
  • Brain* / metabolism
  • Cohort Studies
  • CpG Islands / genetics
  • DNA Methylation* / genetics
  • Depression* / genetics
  • Depression* / metabolism
  • Epigenesis, Genetic* / genetics
  • Female
  • Humans
  • Male
  • Middle Aged
  • Positron-Emission Tomography
  • Receptors, Serotonin, 5-HT4 / genetics
  • Receptors, Serotonin, 5-HT4 / metabolism
  • Serotonin Plasma Membrane Transport Proteins* / genetics
  • Serotonin* / blood
  • Serotonin* / metabolism
  • Synaptic Transmission* / genetics
  • Tryptophan Hydroxylase* / genetics
  • Young Adult


  • Serotonin Plasma Membrane Transport Proteins
  • Tryptophan Hydroxylase
  • SLC6A4 protein, human
  • Serotonin
  • TPH2 protein, human
  • Receptors, Serotonin, 5-HT4