Dysregulation of RUNX1 isoforms drives mitochondrial defects during neural differentiation in down syndrome

Down syndrome (DS) is distinguished by neurodevelopmental abnormalities, with mitochondrial dysfunction. The Runt-related transcription factor 1 (RUNX1) gene, located within the Down Syndrome Critical Region (DSCR), is known to encode three major isoforms (RUNX1a, RUNX1b and RUNX1c) that play essential roles in neurodevelopmental processes. Our previous research demonstrated that RUNX1 overexpression induces mitochondrial dysfunction in DS-induced pluripotent stem cells (DS-iPSCs). However, the functional impacts of altered expression levels of these RUNX1 isoforms on mitochondrial function, as well as the regulatory mechanisms governing their expression in neural stem cells (NSCs), remain to be elucidated. In this study, our results revealed that DS-NSCs exhibited reduced oxidative phosphorylation and an increased number of mitochondria with structural damage. Consistently elevated RUNX1b and RUNX1c transcription levels were consistently observed in DS peripheral blood mononuclear cells, iPSCs and NSCs. Overexpression of RUNX1c in NSCs not only suppressed RUNX1a expression but also resulted in a substantial decrease in mitochondrial ATP production rate and a significant elevation in reactive oxygen species (ROS) levels. In contrast, knockdown of RUNX1c not only reduced ROS levels but also restored the impaired oxidative phosphorylation in DS-NSCs. Furthermore, our findings revealed that the downregulation of LINC01426, a long non-coding RNA located adjacent to RUNX1, during the neural differentiation of DS-iPSCs resulted in the overexpression of RUNX1c, owing to the reduced interaction with the splicing factor. These findings collectively indicate that the LINC01426-mediated activation of RUNX1c isoforms contributes to mitochondrial dysfunction and morphological abnormalities, ultimately leading to impaired neural differentiation in DS.