Abstract 1457: NELFE regulates chromatin accessibility to affect MYC induced transcription

Abstract Liver cancer incidence rates have more than tripled in the last 40 years and is projected to increase more than 40% in the next decade. Although progress has been made, there is still limited therapeutic options. Due to the various etiological factors associated in HCC development and late stage in which it is diagnosed, the five-year survival rate is only 20%. Molecularly, more than 80% of HCC has an alteration in MYC signaling. Yet, MYC remains undruggable and studies over the recent years show that targeting proteins that regulate MYC is a promising approach in developing anti-cancer therapies. One such protein is the RNA binding protein (RBP) Negative Elongation Factor E (NELFE). We recently demonstrated for the first-time that NELFE recruits MYC via protein-protein interactions to the chromatin to control the expression of pro-survival genes. Consistent with the role of NELFE as a regulator of MYC in these cancers, we showed that patients with aberrant NELFE expression concurrently have active MYC signaling and poor outcome. These studies suggest that the NELFE/MYC interplay may be important for HCC maintenance. Thus, our hypothesis is that NELFE modulates the chromatin landscape to facilitate MYC-induced transcription to promote HCC. To investigate NELFE’s effect on MYC-induced transcription, we performed NELFE and MYC ChIP-sequencing and ATAC-sequencing analyses on CRISPR/Cas9-mediated NELFE knockout HCC cells. We found NELFE depletion resulted in significant reduction in nucleosomal accessibility and MYC binding to the chromatin near promoter-proximal regions. Although NELFE depletion alters the chromatin landscape, we found it rarely interacts with the chromatin, specifically within MYC bound regions, suggesting that the MYC/NELFE interaction is facilitated by a third protein. NELFE co-immunoprecipitation followed by mass spectrometry analyses identified the protein SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily B, Member 1 (SMARCB1) as a potential MYC cofactor that facilitates the NELFE/MYC interaction. Immunoblotting analyses show NELFE interacts with SMARCB1 and MYC and loss of NELFE significantly reduced SMARCB1/MYC interactions, indicating that NELFE facilitates chromatin accessibility through SMARCB1, which is required for MYC-induced transcription. Future studies include investigating SMARCB1’s oncogenic role in HCC through NELFE/MYC signaling. Citation Format: Kai Zhang, Anna Barry, Ryan Lamm, Hien Dang. NELFE regulates chromatin accessibility to affect MYC induced transcription [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1457.