TCF4 is a key mediator of cell identity in neuroblastoma and vulnerable to protein degradation by multiple epigenetic factors [RNA-seq]

Neuroblastomas (NBs) are aggressive pediatric tumors that are responsible for up to 15% of all pediatric cancer deaths. Two differentiation states exist in NB tumors, a majority of more committed ADRN tumor cells and a minority of neural crest cell (MES/NCC)-like cells. The transition between identity states is governed by different sets of master TFs that collectively form core regulatory circuitries (CRC) that drive high expression of downstream lineage-specific genes. In this study we aim to discover new lineage dependency factors in NB. Here, we identified the E-box transcription factor TCF4 (E2-2) not previously reported in NB to be a critical factor shared across both NB states and play important role in driving NB oncogenesis. We performed multiple functional and high-throughput analysis to delineate the unrecognized function of TCF4 in NB To determine the consequences of TCF4 knockdown, we transduced two representatives NB cell lines Kelly (ADRN) and SK-N-AS (MES) with three doxycycline-inducible shRNA expression vectors targeting TCF4 KD (#2 and #3). we first performed RNA-seq analysis after TCF4 KD in Kelly and SK-N-AS cells to identify TCF4-regulated genes. We next examined the genome-wide occupancy of TCF4 by chromatin immunoprecipitation sequencing (ChIP-seq) analysis in Kelly and SK-N-AS cells. To identify TCF4 direct targets, we integrated the ChIP-seq and RNA-seq data for TCF4 KD in both NB cells