Cohesin protein STAG2 regulates expression of IRF9 and interferon signaling in melanoma via enhancer loop reprogramming [RNA-seq]

The cohesin complex participates in the organization of 3D genome through generating and maintaining DNA loops. Stromal antigen 2 (STAG2), a core subunit of the cohesin complex, is frequently mutated in various cancers. However, the impact of STAG2 inactivation on 3D genome organization and subsequent gene expression in cancer remain poorly understood. Here we show that depletion of STAG2 in melanoma cells leads to expansion of topologically associating domains (TADs) and enhances the formation of H3K27Ac-associated DNA loops at sites where binding of STAG2 is switched to its paralog STAG1. We further identify Interferon Regulatory Factor 9 (IRF9) as a major direct target of STAG2 in melanoma cells via integrated RNA-Seq, STAG2 ChIP-Seq and H3K27Ac HiChIP analyses. We demonstrate that loss of STAG2 activates IRF9 through modulating the 3D genome organization, which in turn enhances type I interferon signaling and increases the expression of PD-L1. Our findings not only establish a previously unknown role of the STAG2 to STAG1 switch in 3D genome organization, but also reveal a functional link between STAG2 and interferon signaling in cancer cells, which may contribute to malignant phenotype in STAG2-mutant cancer. We investigated how STAG2 KD affact 3D genome structure and its related functional consequnece in malignant phenotype in STAG2-mutant melanomas.

黏连蛋白复合物（cohesin complex）通过生成并维持DNA环，参与三维基因组的构象构建。基质抗原2（Stromal antigen 2, STAG2）作为黏连蛋白复合物的核心亚基，在多种癌症中高频发生突变。然而，STAG2失活对癌症中三维基因组组织及后续基因表达的影响机制仍未被充分阐明。本研究发现，在黑色素瘤细胞中敲低STAG2会导致拓扑关联结构域（topologically associating domains, TADs）发生扩增，并在STAG2结合位点被其旁系同源蛋白STAG1替代的区域，增强了与组蛋白H3赖氨酸27乙酰化（H3K27Ac）相关的DNA环形成。通过整合RNA测序（RNA-Seq）、STAG2染色质免疫共沉淀测序（ChIP-Seq）及H3K27Ac HiChIP测序分析，本研究进一步鉴定出干扰素调节因子9（Interferon Regulatory Factor 9, IRF9）是黑色素瘤细胞中STAG2的主要直接靶标。实验证实，STAG2缺失通过调控三维基因组构象激活IRF9，进而增强I型干扰素信号通路，并提升程序性死亡受体配体1（PD-L1）的表达水平。本研究的发现不仅明确了STAG2向STAG1的转换在三维基因组组织中此前未被报道的功能，还揭示了STAG2与癌细胞干扰素信号通路之间的功能性关联，该关联可能参与STAG2突变型癌症的恶性表型形成。此外，本研究还探讨了STAG2敲低对STAG2突变型黑色素瘤中三维基因组结构的影响，及其对恶性表型的相关功能后果。