Epigenetic signature of GOMAFU, MALAT1, NEAT1 lncRNAs in children with specific learning disorders: expression differences.

Specific Learning Disorder (SLD) is a neurodevelopmental condition characterized by significant difficulties in reading, writing, or mathematics, despite normal intellectual functioning. Emerging evidence suggests that long non-coding RNAs (lncRNAs), which are transcripts longer than 200 nucleotides, play critical roles in neural development and cognitive function. This study aimed to investigate the differential expression of three lncRNAs long intergenic non-protein coding RNA 66 (GOMAFU), long intergenic non-protein coding RNA 47 (MALAT1), and nuclear paraspeckle assembly transcript (NEAT1) in children diagnosed with SLD compared to healthy controls. The study group consisted of 38 individuals with SLD and 35 healthy controls. A total of 73 participants were included: 38 children with SLD and 35 age- and sex-matched healthy controls. Total RNA was extracted from peripheral blood samples, and the expression levels of the selected lncRNAs were analyzed using quantitative PCR (qPCR). Two housekeeping genes, GAPDH and ACTB, were used for normalization. Expression data were analyzed using the ΔΔCt method. GOMAFU was significantly upregulated in the SLD group when normalized against both GAPDH and ACTB (p = 0.004, fold change (FC) ≈ 29). MALAT1 showed no statistically significant difference with either reference gene. NEAT1 was not significant when normalized to GAPDH, but was significantly upregulated when normalized to ACTB (p = 0.015). Subgroup analysis revealed that GOMAFU was significantly downregulated in children with severe SLD compared to those with non-severe SLD (ACTB normalization). No significant expression differences were found between male and female participants for any of the lncRNAs. These results suggest that GOMAFU may be strongly associated with SLD pathogenesis and severity, offering potential as a biomarker.