Tumor-suppressive disruption of cancer subtype-associated super enhancer circuits by small molecule treatment

Abstract

Transcriptional cancer subtypes which correlate with traits such as tumor growth, drug sensitivity or the chances of relapse and metastasis, have been described for several malignancies. The core regulatory circuits (CRCs) defining these subtypes are established by chromatin super enhancers (SEs) driving key transcription factors (TFs) specific for the particular cell state. In neuroblastoma (NB), one of the most frequent solid pediatric cancer entities, two major SE-directed molecular subtypes have been described: A more lineage-committed adrenergic (ADRN) and a mesenchymal (MES) subtype. Here, we found that a small isoxazole molecule (ISX), a frequently used pro-neural drug, reprogrammed SE activity and switched NB cells from an ADRN subtype towards a growth-retarded MES-like state. The MES-like state shared strong transcriptional overlap with ganglioneuroma (GN), a benign and highly differentiated tumor of the neural crest. Mechanistically, ISX suppressed chromatin binding of N-MYC, a CRC-amplifying transcription factor, resulting in loss of key ADRN subtype-enriched components such as N-MYC itself, PHOX2B and ALK, while concomitently, MES subtype markers were induced. Globally, ISX treatment installed a chromatin accessibility landscape typically associated with low risk NB. In summary, we provide evidence that CRCs and cancer subtype reprogramming might be amenable to future therapeutic targeting.

Super-Enhancers and Their Parts: From Prediction Efforts to Pathognomonic Status

“…Moreover, in infant neuroblastoma 2, major SE-directed molecular subtypes have been described, namely the ADRN and MES subtypes. The ISX drug has been shown to reprogramme SE activity and switch NB cells from an ADRN subtype towards a growth-retarded MES-like state, sharing strong transcriptional overlap with GN, a benign and highly differentiated tumour of the neural crest, opening new insights into cancer therapy [ 175 ].…”

“… SE hijacking. TFs increase in expression and overexpression, leading to pathological gene activation Cell growth, proliferation, transdifferentiation Isoxazole (ISX-9) [ 175 ] NB — SH-SY5Y (subclone with adrenergic (ADRN) phenotype) derived from SK-N-SH cells, 5 CD133-primary samples (2/5 had an isogenic pair of ADRN phenotype), SH-EP2 (subclone with undifferentiated mesenchymal (MES) phenotype) derived from SK-N-SH cells, 3 CD133+ primary samples (all with an isogenic pair of ADRN phenotype) — (1) DBH , CHGA , DLK1 (2) ASCL1 , EYA1 , GATA3 , HAND1 , SIX3 ( ZNF536 , PHOX2A , KLF13 , SOX11 , GATA2 , KLF7 , TFAP2B , ISL1 , HEY1 , DACH1 , PHOX2B , PBX3 , SATB1 ) (3) WNT5A , IGFBP2 , FN1 , IL13RA1 (4) MEOX1 , MEOX2 , SIX1 , SIX4 , SOX9 , SMAD3 WWTR1 ( PRRX1 , CREG1 , ELK4 , DCAF6 , ID1 , MAML2 , NOTCH2 , CBFB , IFI16 , ZNF217 , EGR3 , ZFP36L1 ABEP1 ) (1) known markers of adrenergic differentiation (2) 18 ADRN-specific TFs. Although PHOX2B and PHOX2A are ADRN-specific, SEs associated with them are also found in some MES lines.…”