Super-enhancer Activates Master Transcription Factor NR3C1 Expression and Promotes 5-FU Resistance in Gastric Cancer

Area of Science:

• Oncology
• Molecular Biology
• Genomics

Background:

• 5-fluorouracil (5-FU) resistance is a major challenge in gastric cancer (GC) treatment.
• Super enhancers (SEs) play a critical role in cancer cell survival under drug pressure.

Purpose of the Study:

• To investigate the role of SEs in 5-FU resistance in GC.
• To identify key transcription factors (TFs) regulated by SEs that contribute to 5-FU resistance.
• To explore therapeutic strategies targeting SEs and identified TFs to overcome 5-FU resistance.

Main Methods:

• Chromatin immunoprecipitation-sequencing (ChIP-Seq) to map SE landscapes in GC.
• siRNA screen to identify master TFs regulated by SEs.
• Fluorescence recovery after photobleaching (FRAP) to study NR3C1 phase separation.
• Cleavage Under Targets and Tagmentation (CUT&Tag) sequencing to analyze SEs and NR3C1 co-binding.
• Pharmacological inhibition using JQ1 and Cort108297 in patient-derived organoids (PDOs) and xenografts (PDXs).

Main Results:

• SEs were mapped in GC, revealing a master TF, Nuclear Receptor Subfamily 3 Group C Member 1 (NR3C1), activated by SEs.
• High NR3C1 expression, driven by SEs, correlated with 5-FU resistance in patient-derived organoids (PDOs).
• NR3C1 forms phase separation, promoting SE-related gene transcription; its inhibition or SE destruction reconfigures enhancers, increasing 5-FU sensitivity in PDOs and PDXs.

Conclusions:

• SE-driven NR3C1 is a key mechanism promoting 5-FU resistance in gastric cancer.
• Targeting SEs or inhibiting NR3C1 offers promising therapeutic strategies to enhance 5-FU efficacy.
• Enhancer reprogramming by disrupting SEs or inhibiting NR3C1 reduces 5-FU-related gene transcription, improving treatment outcomes.