BET Inhibitors Target the SCLC-N Subtype of Small-Cell Lung Cancer by Blocking NEUROD1 Transactivation

Abstract

Small cell lung cancer (SCLC) is a recalcitrant malignancy that urgently needs new therapies. Four master transcription factors (ASCL1, NEUROD1, POU2F3, and YAP1) have been identified in SCLC, and each defines the transcriptome landscape of one molecular subtype. However, these master transcription factors have not been found directly druggable. We hypothesized that blocking their transcriptional coactivator(s) could provide an alternative approach to target these master transcription factors. Here, we identify that BET proteins physically interact with NEUROD1 and function as transcriptional coactivators. Using CRISPR knockout and ChIP-seq, we demonstrate that NEUROD1 plays a critical role in defining the landscapes of BET proteins in the SCLC genome. Blocking BET proteins by inhibitors led to broad suppression of the NEUROD1-target genes, especially those associated with superenhancers, resulting in the inhibition of SCLC growth in vitro and in vivo. LSAMP, a membrane protein in the IgLON family, was identified as one of the NEUROD1-target genes mediating BET inhibitor sensitivity in SCLC. Altogether, our study reveals that BET proteins are essential in regulating NEUROD1 transactivation and are promising targets in SCLC-N subtype tumors. Implications: Our findings suggest that targeting transcriptional coactivators could be a novel approach to blocking the master transcription factors in SCLC for therapeutic purposes.

Functional Characterisation of the ATOH1 Molecular Subtype Indicates a Pro-Metastatic Role in Small Cell Lung Cancer

“…However, as the NE gene expression signature was retained upon ATOH1 depletion (Figure S4), additional factors, for example, MYC overexpression 16 , are likely required to promote full NE to Non-NE transition in ATOH1-driven SCLC. The need for additional signals to fully induce a NE to Non-NE transition is similarly posited in studies of ASCL1 and NEUROD1 depletion in SCLC, where morphological changes or a NE to Non-NE transition were not observed 77,78,83,84 .…”

mTOR inhibition overcomes RSK3-mediated resistance to BET inhibitors in small cell lung cancer

“…We recently found that a subset of SCLC expressing NEUROD1 (the SCLC-N subtype) is particularly susceptible to BETis due to the dependence of NEU-ROD1 transactivation on BET family proteins (7). However, BETi has only modest antitumor activity in the SCLC-N subtype tumors in vivo (7), which necessitates a combinatorial strategy to augment its antitumor effects in both SCLC-N and other molecular subtypes of SCLC. Several previous studies have reported that inhibitors targeting PARP, HDAC6, or BCL2 synergized with BETis in SCLC (8)(9)(10)(11).…”

“…Previous studies reported that mouse SCLC was exquisitely susceptible to BETis ( 5 ), but human SCLC lines had a much broader range of sensitivity ( 6 ). We recently found that a subset of SCLC expressing NEUROD1 (the SCLC-N subtype) is particularly susceptible to BETis due to the dependence of NEUROD1 transactivation on BET family proteins ( 7 ). However, BETi has only modest antitumor activity in the SCLC-N subtype tumors in vivo ( 7 ), which necessitates a combinatorial strategy to augment its antitumor effects in both SCLC-N and other molecular subtypes of SCLC.…”

Selectivity Mechanism of Pyrrolopyridone Analogues Targeting Bromodomain 2 of Bromodomain-Containing Protein 4 from Molecular Dynamics Simulations

“…Several small-molecule BET inhibitors were developed for early clinical development or in preclinical studies. − High efficacy and positive results were found for BET inhibitor treatment of hematological malignancies, − such as ovarian cancer, metastatic prostate cancer, breast cancer, and small-cell lung cancer . However, some probes designed as early tools exhibited weak and poorly selective binding; thus, it was necessary to develop novel well-characterized probes to ascertain the function of bromodomain family members. − In addition, some pan-BD inhibitors (defined as having similar inhibitory activity for BD1 and BD2 of BET proteins including the eight bromodomains) have potential applications for academic research or drug development, such as JQ1, I-BET151, ZEN-3694, − OTX-015, , NHWD-870, and ABBV-075 (Figure S1).…”