STAG2 mutations alter CTCF-anchored loop extrusion, reduce cis-regulatory interactions and EWSR1-FLI1 activity in...

Area of Science:

• * Molecular biology
• * Cancer genetics
• * Epigenetics

Background:

• * STAG2 (Stromal Antigen 2) is frequently mutated in cancers.
• * STAG2 loss of function (LOF) correlates with aggressive Ewing sarcoma.
• * Ewing sarcoma is driven by the EWSR1-FLI1 oncogene, causing aberrant transcription.

Purpose of the Study:

• * To investigate how STAG2 LOF affects the Ewing sarcoma transcriptome and oncogenic transcription.
• * To elucidate the mechanisms by which STAG2 LOF influences EWSR1-FLI1 activity and gene regulation.

Main Methods:

• * Utilized isogenic Ewing sarcoma cell lines with and without STAG2 function.
• * Performed transcriptome-wide analyses to assess gene expression changes.
• * Investigated DNA binding patterns of key proteins (EWSR1-FLI1, CTCF/cohesin) and histone modifications.
• * Analyzed dynamic loop extrusion and promoter-enhancer interactions using genome-wide techniques.

Main Results:

• * STAG2 LOF significantly altered the Ewing sarcoma transcriptome but did not impact EWSR1-FLI1, CTCF/cohesin, or H3K27 acetylation binding.
• * STAG2 LOF disrupted anchored dynamic loop extrusion at CTCF sites and reduced promoter-enhancer interactions.
• * Expression of EWSR1-FLI1-regulated genes at GGAA microsatellite neo-enhancers was significantly affected.
• * Down-modulation of cis-mediated EWSR1-FLI1 activity correlated with increased cell migration and invasion.

Conclusions:

• * STAG2 LOF fine-tunes EWSR1-FLI1 oncogenic transcription through altered CTCF-anchored loop extrusion.
• * Disruption of promoter-enhancer interactions by STAG2 LOF impacts Ewing sarcoma aggressiveness.
• * Findings reveal a novel regulatory mechanism involving STAG2 in Ewing sarcoma progression.