Nucleolar stress-induced heterochromatin disengagement triggers tumour intrinsic immunogenicity

<title>Abstract</title> Various cellular stresses release immunogenic molecules and elicit immunosurveillance to detect and eliminate potential threats, thus safeguarding organismal health. Nucleolar stress is characterized by the disruption of nucleolar morphology and function, leading to impaired ribosome biogenesis and activation of stress response pathways. However, the regulatory mechanisms linking nucleolar stress to tumour-intrinsic immunogenicity and its therapeutic implications remain unclear. Utilizing CRISPR screens to identify cancer-specific immunogenic regulators, we identified nucleolar OTUD4 (an ovarian tumour domain-containing deubiquitinase) as a repressor of immunogenicity by preserving nucleolar homeostasis. OTUD4 depletion induced nucleolar stress, thereby enhancing immunogenicity and retarding tumor growth in preclinical models. Mechanistically, OTUD4 functioned as a phospho-activated K63 deubiquitinase, catalyzing the K63-linked deubiquitination of nucleophosmin 1 (NPM1) to stabilize its oligomerization. Consequently, OTUD4 deletion promoted NPM1 hyperubiquitination and depolymerization, thereby driving the release of NPM1-binding heterochromatin H3K9me3. The heterochromatin remodeling derepressed endogenous retroelements (ERV) that subsequently stimulated cytosolic DNA-sensing pathways to trigger the type I interferon response and upregulate the expression of antigen presentation genes. Concurrently, ERV-encoded retroviral antigens augmented tumour-intrinsic antigenicity. A pharmacological screen revealed that the casein kinase II inhibitor CX-4945 phenocopied OTUD4 ablation by dephosphorylating and inactivating OTUD4 activity. Clinically, OTUD4 amplification or a high OTUD4-nucleolus gene signature inversely correlated with patient survival and immunotherapy resistance. Our findings position nucleolar stress as a central driver of tumour-intrinsic immunogenicity, and propose a clinical rationale for leveraging nucleolar stress inducers to sensitize immunologically cold tumours to immunotherapy.