Abstract 1929: Stag2-cohesin mediates 3d genome dynamics to regulate MYCN driven oncogenic transcriptome in neuroblastoma.

Abstract Neuroblastoma(NB) is characterized by an abnormal transcriptome driven by a network of core regulatory circuitry (CRC) transcription factors (TFs) and cell type-specific enhancer landscapes. Neuroblastoma arises due to defects in cellular differentiation, either through a failure to terminally differentiate or a reversion to a pluripotent-like state. While CRC TFs are known to bind cell type-specific enhancers and promoters to define transcriptomes necessary for proper differentiation, their functional interplay with 3D nuclear architectural proteins, such as cohesin (comprising SMC1A, SMC3, RAD21, and STAG1 or STAG2), remains largely unexplored. 3D genome organization plays a critical role in defining the cell type-specific transcriptional landscape by facilitating enhancer-promoter looping, which undergoes dynamic rewiring during differentiation. Beyond their canonical roles in DNA replication and repair, cohesin mediates chromatin looping between enhancers and promoters, enabling precise regulation of target gene expression. Understanding how CRC TFs collaborate with cohesin to establish and maintain NB-specific transcriptional programs could provide valuable insights into the mechanisms underlying neuroblastoma pathogenesis and differentiation defects. To define roles of STAG1- and STAG2-cohesin in MYCN target regulation, genome-wide RNA-seq and ChIP-seq analyses were performed to uncover the distinct yet overlapping roles of these complexes in regulating the oncogenic transcriptome of NB cells. STAG1 Knockdown (KD) has minimal impact on NB cell proliferation or transcriptional activity. In contrast, STAG2 KD reduces cell proliferation, accompanied by downregulation of MYCN target genes and upregulation of neuronal differentiation genes. Genome-wide ChIP-seq analysis revealed that MYCN/STAG1 peaks are associated with promoters of canonical MYCN target genes. In contrast, MYCN/STAG2 peaks are primarily associated with promoters and enhancers of neural differentiation genes. STAG2 KD decreases chromatin-bound MYCN, particularly at enhancers and promoters, with no change in total MYCN protein levels. This reduction correlates with the observed downregulation of MYCN target genes. In contrast, STAG1 KD does not affect MYCN chromatin binding. Ectopic induction of MYCN in MYCN-nonamplified SHEP cells significantly increased STAG2 chromatin binding, whereas STAG1 binding remains unchanged. In contrast, chromatin-bound STAG1 and STAG2 levels remained unaffected by MYCN KD despite the reduction in their total protein levels. These findings underscore the critical role of STAG2-cohesin in sustaining the NB oncogenic transcriptome by selectively modulating MYCN chromatin binding. This study highlights STAG2-cohesin's functional specialization, establishing it as a pivotal regulator of cohesin dynamics and NB transcriptional programs. Citation Format: Jee-Youn Kang, Kaitlyn Tremble, Zhihui Liu, Carol J. Thiele. Stag2-cohesin mediates 3d genome dynamics to regulate MYCN driven oncogenic transcriptome in neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1929.