DNA hypomethylation at specific CG-sites within TRAK1 is linked to the neurocognitive profile in Klinefelter syndrome

Klinefelter syndrome (47,XXY; KS) impacts neurodevelopment. Furthermore, KS is associated with widespread alterations in the epigenome and transcriptome. Whether these epigenetic and transcriptomic alterations can be linked to the neurocognitive phenotype remains to be elucidated. We performed a comprehensive, integrative analysis of the neurocognitive profile and the methylome in blood from males with KS (n = 65) and male controls (n = 63) (Cohort 1). The results were validated in a second cohort of males with KS (n = 22) and male controls (n = 16) in which transcriptome data was also available (Cohort 2). The findings were further validated in neural precursor cells derived from human induced pluripotent stem cells from 47,XXY (n = 3) and 46,XY (n = 3) amniotic cells. In cohort 1, we identified five CG-sites within the TRAK1 gene which were hypomethylated in males with KS compared to male controls. TRAK1 hypomethylation was positively correlated with several neurocognitive variables among males with KS. In cohort 2, we identified a similar methylation pattern and demonstrated that the methylation levels at the five CG-sites were correlated with a high expression level of a specific short TRAK1 transcript (ENST00000341421.7). Neural precursor cells (NPCs) established from 47,XXY amniotic cells also exhibited hypomethylation at the five CG-sites and strong upregulation of ENST00000341421.7 compared to NPCs established from 46,XY amniotic cells. In conclusion, we demonstrate that the DNA methylation level at specific CG-sites within TRAK1, a gene highly expressed in the brain, is correlated with the neurocognitive phenotype of KS, implying a possible epigenetic underpinning for the observed neurocognitive impairments in KS.