Tuberous sclerosis complex (
TSC) is a
congenital disorder characterized by cortical malformations and concomitant
epilepsy caused by loss-of-function mutations in the mTOR suppressors TSC1 or TSC2. While the underlying molecular changes caused by mTOR activation in
TSC have previously been investigated, the drivers of these transcriptional change have not been fully elucidated. A better understanding of the perturbed transcriptional regulation could lead to the identification of novel pathways for therapeutic intervention not only in
TSC, but other genetic
epilepsies in which mTOR activation plays a key role, such as
focal cortical dysplasia 2b (FCD). Here, we analyzed
RNA sequencing data from cortical tubers and a tsc2-/- zebrafish. We identified differential expression of the
transcription factors (TFs) SPI1/PU.1, IRF8, GBX2, and IKZF1 of which SPI1/PU.1 and IRF8 targets were enriched among the differentially expressed genes. Furthermore, for SPI1/PU.1 these findings were conserved in
TSC zebrafish model. Next, we confirmed overexpression of SPI1/PU.1 on the
RNA and
protein level in a separate cohort of surgically resected
TSC tubers and FCD tissue, in fetal
TSC tissue, and a Tsc1GFAP-/- mouse model of
TSC. Subsequently, we validated the expression of SPI1/PU.1 in dysmorphic cells with mTOR activation in
TSC tubers. In fetal
TSC, we detected SPI1/PU.1 expression prenatally and elevated
RNA Spi1 expression in Tsc1GFAP-/- mice before the development of
seizures. Finally, in vitro, we identified that in astrocytes and neurons SPI1 transcription was driven by H2 O2 -induced oxidative stress, independent of mTOR. We identified SPI1/PU.1 as a novel TF involved in the pro-inflammatory gene expression of malformed cells in
TSC and FCD 2b. This transcriptional program is activated in response to oxidative stress and already present prenatally. Importantly, SPI1/
PU.1 protein appears to be strictly limited to malformed cells, as we did not find SPI1/
PU.1 protein expression in mice nor in our in vitro models.