NELFE and SMARCB1 cooperate to regulate chromatin accessibility and allow MYC-driven gene activation in hepatocellular carcinoma

Liver cancer is a serious and growing problem in the United States, with cases having more than tripled since 1980. Although there have been some advances in diagnosis and treatment, the five-year survival rate remains below 20%. Hepatocellular carcinoma (HCC), the most common type of liver cancer, often involves aberrant activation of the MYC gene, which helps cancer cells grow and survive. Unfortunately, MYC is very difficult to target directly with drugs. As such, researchers are interested in understanding proteins that control or support MYC's activity. One such protein is NELFE, which regulates gene expression by regulating how genes are turned on and off. We believe NELFE is important because it helps MYC access and activate its target genes, promoting cancer growth. To study this, we used CRISPR/Cas9 to remove NELFE from liver cancer cells and performed ATAC-seq and ChIP-seq experiments to see how this affected MYC and the structure of DNA. We found that without NELFE, the DNA became less accessible, and MYC was less able to bind near important genes. However, NELFE does not directly bind to these MYC sites, suggesting it works together with another protein. Mass spectrometry of NELFE identified SMARCB1, a component of the SWI/SNF chromatin remodeling complex, as a major interacting partner that links NELFE to MYC. Although SMARCB1 is widely known as a tumor suppressor in many cancers, in our liver cancer system, it appears to act as an oncogene, promoting cancer growth. We also showed that NELFE and SMARCB1 form special phase-separated structures in cells that help organize DNA, influencing both paused and non-paused genes. These structures keep the chromatin open, allowing MYC to be more active and interact with its target genes. Moreover, when NELFE is missing, SMARCB1 and MYC cannot interact properly, leading to reduced gene activation by MYC. In summary, NELFE helps MYC promote liver cancer by working with SMARCB1 to change how DNA is organized. Understanding this relationship could lead to new treatments for liver cancers that depend on MYC.