@phdthesis{01HCYBJTB9H842EN2QH2V4R5FR,
  abstract     = {{Neuroblastoma (NB) is the most common extra-cranial solid childhood cancer with a relapse rate of nearly 50% in high-risk NB cases, after which limited treatment options are available. Additionally, intensive multimodal treatment often leads to long-term side effects in survivors, highlighting the urgency for more precise therapy options to improve therapeutic effectiveness while minimizing adverse effects. Therefore, a comprehensive understanding of the molecular pathways and factors influencing NB progression is essential for the development of novel targeted therapeutic strategies.
The genomic landscape of NB exhibits a relatively low mutational burden. However, it is characterized by highly recurrent chromosomal structural rearrangements. Additionally, NB cells can co-opt normal developmental programs, relying on developmental master transcription factors (TFs) for survival and tumor progression. Using a targeted search for lineage-dependent TFs important in neurogenesis and affected by copy number alterations, we identified the neuronal-specific TF SOX11 as the sole protein-coding gene in the shortest region of overlap for amplicons at chromosome 2p distal to MYCN. We additionally characterized SOX11 as a dependency TF based on its specific expression in the normal sympatho-adrenal lineage and adrenergic (ADRN) NB tumors and cell lines, its regulation by multiple ADRN specific (super-)enhancers and its strong dependency on high SOX11 expression in ADRN NBs.
Using transcriptome analysis after SOX11 knockdown and overexpression, we have successfully identified the SOX11 regulome, encompassing the regulatory factors and pathways that play a significant role in shaping the ADRN NB phenotype. This revealed regulation by SOX11 of multiple functions related to cell migration, cytoskeleton, neuronal differentiation and a broad regulatory effect on multiple epigenetic regulatory factors and protein complexes. Furthermore, in order to gain a more comprehensive understanding of the specific target genes directly bound by SOX11, we employed SOX11 CUT&RUN-sequencing in adrenergic NB cells and the mesenchymal NB cell line SH-EP following SOX11 overexpression. This revealed a direct effect of SOX11 on multiple core and subunit specific SWI/SNF components as well as several other proteins implicated in diverse epigenetic regulatory processes.
The two distinct NB differentiation states, namely adrenergic (ADRN) and mesenchymal (MES), are characterized by specific core regulatory circuitries (CRC) consisting of interconnected lineage-specific TFs regulated by super-enhancers. We identified SOX11 as integral part of the ADRN CRC based on SOX11, as well as other CRC members, binding to the SOX11 promoter and enhancer landscape. Furthermore, SOX11 directly regulates other CRC members and partial collapse of the ADRN CRC is observed after SOX11 knockdown. However, SOX11 knockdown alone is inadequate to induce a complete ADRN-to-MES transition, implying that additional factors are required for lineage switching in NB. Based on current data and the direct effect of SOX11 op chromatin remodeling, we postulate that SOX11 plays a role in epigenetic plasticity and maintenance of the ADRN CRC. 
Lineage specific functions of SOX TFs are highly dependent on recruitment of interactions partner. We used rapid immunoprecipitation and mass spectrometry (RIME) to map the interactome of SOX11 showing interaction with spliceosome complex proteins and other splicing regulators. SOX11 overexpression indeed influences alternative splicing events, suggesting a dual role in RNA splicing by interacting with splicing regulators as well as controlling their transcription. In silico analysis further shows strong dependency on interaction between SOX11 and the paraspeckle protein NONO, particularly in high-risk MYCN-amplified NB cases, with our data suggesting an interplay between SOX11 and NONO in RNA splicing.
Overall, these findings suggest that SOX11 acts as a multifaceted epigenetic regulator through direct regulation of the SWI/SNF complex and interaction with the splicing machinery, with current data suggesting a role in epigenetic plasticity and maintenance of the ADRN CRC in NB. In addition, we identified multiple promising therapeutic targets which are under further investigation facilitating the identification of potential drug targets.}},
  author       = {{Louwagie, Amber}},
  language     = {{eng}},
  pages        = {{VII, 239}},
  publisher    = {{Ghent University. Faculty of Medicine and Health Sciences}},
  school       = {{Ghent University}},
  title        = {{Molecular characterization of SOX11 as multifaceted epigenetic regulator in neuroblastoma}},
  year         = {{2023}},
}