Hypoxia-induced phase separation of ZHX2 drives 3D chromatin remodeling and cancer metastasis (RNA-Seq)

Hypoxia and dysregulation of three-dimensional (3D) chromatin architecture can both activate oncogenic transcriptomic profiles, thus contributing to tumor malignancy. But how hypoxia regulates 3D chromatin architecture remains unknown. Here, we find that the transcription factor, zinc fingers and homeoboxes 2 (ZHX2), generates liquid-liquid phase separation (LLPS) under hypoxia, thus promoting its occupancy on chromatin and activating transcription for a cluster of oncogenes, that is enriched by metastatic genes distinct from targets of hypoxia-inducible factor (HIF) and pathologically relevant to breast cancer. Mechanistically, hypoxia induces the LLPS of ZHX2 via a proline-rich intrinsically disordered region (IDR) in the nuclear localization sequence (NLS), thereby enhancing the phosphorylation of ZHX2 at S625 and S628 that incorporates CCCTCbinding factor (CTCF) in condensates to reorganize chromatin looping, consequently resulting in oncogenic super-enhancer formation and breast cancer metastasis. This fundamental mechanism provides significant insight into oncogene activation and suggests a phase separation-based therapeutic strategy for cancer. We conducted RNA-seq experiments in T47D cells under normoxia, hypoxia, and hypoxia with ZHX2 knockdown (KD). Our aim was to identify a specific set of genes that exhibit both hypoxia-inducible characteristics and are positively regulated by ZHX2 under hypoxic conditions. Additionally, we assessed gene expression changes in T47D cells treated with 0.5% and 1% 1,6-hexanediol under hypoxic conditions for 24 hours to detect alterations in gene expression following phase separation disruption. We conducted RNA-seq experiments in T47D cells under hypoxia to identify a specific set of genes that exhibit both hypoxia-inducible characteristics and are positively regulated by ZHX2 phase separation under hypoxic conditions.