Abstract 3662: Plasticity of transcriptional and epigenetic cellular states in neuroblastoma is driven by core lineage transcription factors
Authors: Nes Johan van , Groningen Tim van , Valentijn Linda , Zwijnenburg Danny , Westerhout Ellen M. , Hamdi Mohamed , Koster Jan , Versteeg Rogier 
Published: August 2019

Abstract
Background: Cellular identity in development and disease is driven by Core Regulatory Circuitries (CRCs) of lineage transcription factors that associate with super-enhancers. We showed that neuroblastoma includes two types of tumor cells with divergent gene expression profiles. Undifferentiated mesenchymal (MES) cells and lineage-committed adrenergic (ADRN) tumor cells have divergent phenotypes, super-enhancer (SE) landscapes and Core Regulatory Circuitries (van Groningen et al., Nature Genetics, 2017).
Results: We study five pairs of MES- and ADRN-type cell lines, each of which are derived from the tumor of individual patients. These isogenic cell lines can show spontaneous bidirectional transdifferentiation. As the mechanisms of reprogramming in cancer are poorly understood, we studied the mechanism of MES and ADRN transdifferentiation. We identified a MES-specific Core Regulatory Circuitry consisting of 20 super enhancer-associated transcription factors. Amongst them were NOTCH and MAML transcription factors. Indeed MES cells were found to have an active NOTCH signaling. Inducible expression of NOTCH3-IC in ADRN cells induced a step-wise reprogramming of the ADRN transcriptome towards a dedifferentiated MES state. This transition induced genome-wide remodeling of the H3K27ac landscape and a switch from ADRN SEs to MES SEs. The NOTCH3-IC transgene activated a transcriptional feed-forward cascade including NOTCH ligands, -receptors and -cofactors to amplify the NOTCH signaling levels. Blocking of this endogenous feed-forward loop with a γ-secretase inhibitor showed that this cascade was essential to achieve MES reprogramming. The endogenous NOTCH feed-forward cascade maintained the induced MES state, also after abrogating expression of the NOTCH3-IC transgene. The induced MES cells and stable MES cell lines were resistant to chemotherapy, highlighting their clinical importance. Accordingly, we found that MES cells are strongly enriched in post-treatment samples, suggesting that MES cells play a role in resistance and relapse development. Since neuroblastoma is presumed to originate from the sympathetic nervous system, we analyzed normal sympathetic lineage development at single-cell resolution. We found that MES tumor cells resembled non-malignant precursor cells of the sympatho-adrenal (SA)-lineage, while ADRN cells expressed SA-lineage differentiation genes.
Conclusions: Our results demonstrate that the divergent transcriptional states of cancer cells resemble stages of normal lineage development. Lineage TFs induce transdifferentiation via remodeling of the epigenetic and transcriptional landscapes, mimicking spontaneous interconversion. Plasticity of CRCs and lineage identity may have profound implications for treatment strategies in neuroblastoma.
Citation Format: Johan van Nes, Tim van Groningen, Linda Valentijn, Danny Zwijnenburg, Ellen M. Westerhout, Mohamed Hamdi, Jan Koster, Rogier Versteeg. Plasticity of transcriptional and epigenetic cellular states in neuroblastoma is driven by core lineage transcription factors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3662.