Loss of ZNF408 Is Linked to Immune Escape in Breast Carcinogenesis [CUT&Tag]
Understanding cancer immune escape is important to the comprehension of cancer development and to the development of cancer immunotherapy. We report here that ZNF408, encoded by a gene linked to familial exudative vitreoretinopathy (FEVR) and autosomal recessive retinitis pigmentosa (RP), is physically associated with the chromatin remodeler SETD1A/COMPASS complex in breast cancer cells. The ZNF408/SETD1A/COMPASS complex orchestrates the transcriptional activation of a cohort of genes via histone H3K4 trimethylation, particularly STING1 that are critically involved in innate immune response, leading to the release of multiple cytokines and activation of cytotoxic lymphocyte cells in tumor microenvironment. ZNF408 enhances STING expression and promotes anti-tumor immune responses both in vitro and in vivo. Importantly, the expression of ZNF408 is downregulated in breast carcinomas, and its level of expression is positively correlated with that of STING1 and negatively correlated with the histological grade of breast cancer. High ZNF408 is also correlated with high CD8+ T cell infiltration and favorable prognosis of breast cancer patients. Our study uncovers an important role for ZNF408 in innate immune response, supporting further investigations of the ZNF408-SETD1A/COMPASS-STING1 axis in cancer immune escape as well as in other ZNF408-associated diseases including FEVR and RP. Overall design: The study comprises ATAC-seq samples from MCF-7 cells with 2 replicates, RNA-seq samples with 3 replicates each for both wild-type and ZNF408 knockdown conditions, and CUT&Tag samples for SETD1A with 2 replicates. There are no replicates for CUT&Tag samples targeting ZNF408 and H3K4me3. This setup includes control samples for RNA-seq and comparative analysis across conditions to explore the effects of ZNF408 knockdown on gene expression and chromatin state.