Comprehensive Transcriptomic Investigation of Rett
Syndrome Reveals Increasing Complexity Trends from Induced Pluripotent
Stem Cells to Neurons with Implications for Enriched Pathways
posted on 2023-11-08, 19:04authored byYusuf
Caglar Odabasi, Sena Yanasik, Pelin Saglam-Metiner, Yasin Kaymaz, Ozlem Yesil-Celiktas
Rett syndrome (RTT)
is a rare genetic neurodevelopmental disorder
that has no cure apart from symptomatic treatments. While intense
research efforts are required to fulfill this unmet need, the fundamental
challenge is to obtain sufficient patient data. In this study, we
used human transcriptomic data of four different sample types from
RTT patients including induced pluripotent stem cells, differentiated
neural progenitor cells, differentiated neurons, and postmortem brain
tissues with an increasing in vivo-like complexity to unveil specific
trends in gene expressions across the samples. Based on DEG analysis,
we identified F8A3, CNTN6, RPE65, and COL19A1 to have differential
expression levels in three sample types and also observed previously
reported genes such as MECP2, FOXG1, CACNA1G, SATB2, GABBR2, MEF2C,
KCNJ10, and CUX2 in our study. Considering the significantly enriched
pathways for each sample type, we observed a consistent increase in
numbers from iPSCs to NEUs where MECP2 displayed profound effects.
We also validated our GSEA results by using single-cell RNA-seq data.
In WGCNA, we elicited a connection among MECP2, TNRC6A, and HOXA5.
Our findings highlight the utility of transcriptomic analyses to determine
genes that might lead to therapeutic strategies.