Mdig shapes 3D chromatin architecture of immune checkpoint genes and limits metastasis of triple negative breast cancer cells

Abstract

Despite decades of progress in metastasis research, the identity of bona fide metastasis-driving genes remains elusive. By shifting the focus from individual genes to the three-dimensional (3D) architecture of the genome, we identify the mineral dust-induced gene (mdig) as a chromatin-topology regulator that suppresses immune-checkpoint activation and metastasis in triple-negative breast cancer (TNBC). Re-expression of mdig in mdig-knockout (KO) cells markedly reduced liver metastasis, whereas mdig loss activated epithelial-mesenchymal transition (EMT), T-cell exhaustion, and antigen-presentation pathways. Across multiple cancer types, high mdig expression predicted improved responses to immune checkpoint blockade (ICB). Mechanistically, mdig depletion derepressed inhibitory checkpoint genes, including PD-L1, PD-L2, LGALS9, and PLXNB1/2, accompanied by increased H3K9me3 and H3K36me3 at these loci. Hi-C profiling revealed that mdig maintains topologically associating domains (TADs) and long-range repressive loops at checkpoint loci; loss of mdig disrupted these structures, enabling coordinated activation of immune-evasion programs. Genome-wide analyses showed extensive TAD remodeling in mdig KO cells, with pronounced alterations on chromosome X. Collectively, these findings position mdig as a key chromatin-architectural regulator of immune evasion and metastatic behavior, underscoring its potential as a biomarker for ICB responsiveness in TNBC and beyond. Significance statementMetastasis remains the leading cause of cancer mortality, yet bona fide metastasis-driving genes remain difficult to define. By examining three-dimensional genome architecture rather than individual gene function, we identify mdig as a chromatin-topology regulator that restrains immune evasion and metastasis in triple-negative breast cancer. Loss of mdig disrupts TAD structures and long-range repressive loops at immune-checkpoint loci, enabling coordinated activation of EMT, antigen-presentation, and T-cell-exhaustion programs. Restoring mdig expression markedly reduces liver metastasis, and high mdig levels across cancers predict improved responses to immune-checkpoint blockade. These findings establish mdig as a key regulator of chromatin organization and a potential biomarker for immunotherapy responsiveness.