Abstract
Pilocytic astrocytomas (PA), the most common pediatric brain tumors, exhibit MAPK pathway alterations leading to its constitutive activation. They are also associated with low proliferation index due to the oncogene-induced senescence (OIS), sustained by senescence-associated secretory phenotype (SASP) factors. Little is known about the downstream consequences of MAPK activation leading to OIS-SASP, and of the molecular implications of MAPK pathway inhibition in senescent PA cells. Senescent DKFZ-BT66 cells derived from a primary KIAA::BRAF-fusion positive PA were used to generate RNA-sequencing and phospho-/proteomic datasets, before and after treatment with the MEK inhibitor (MEKi) trametinib for different time-spans. A multi-omics factor analysis tool (MEFISTO) and single sample gene set enrichment analysis (ssGSEA) were used to identify key OIS effectors and differentially regulated pathways upon MAPK inhibition. Trametinib treatment inhibited OIS and SASP signatures across all omics levels in the senescent DKFZ-BT66 cells, associated with reduced sensitivity towards senolytics drugs, indicating inhibition of senescence features upon MEKi. MEFISTO analysis identified key effectors involved in MAPK-induced OIS in the senescent PA cells. We built a pathway network using a prior knowledge network approach allowing to map the direct downstream effectors of MAPK leading to OIS-SASP. We identified several parallel pathways (JAK/STAT, p38, GSK3B) potentially involved in OIS and under the control of the MAPK pathway. In addition, ssGSEA showed that pathways related to upstream MAPK activators (SOS1, CK2, several RTKs) were predicted to be upregulated upon treatment, highlighting putative targets to be further investigated. Our data suggest that MAPKi reverses OIS signaling in senescent PA cells, while inducing the activation of MAPK upstream regulators, identifying putative co-targets for the treatment of PA. Further validation of the targetability of these pathways is pending. Furthermore, the identification of the MAPK-related OIS-SASP genes provides insight into the regulation of OIS-SASP by the MAPK pathway.