Systematic multivariate analysis of chromatin complex dependencies reveals Set1C/COMPASS as a melanoma-enriched epigenetic vulnerability.

Abstract

Epigenetic dysregulation is a common feature of cancer. It creates vulnerabilities arising from an increased reliance on chromatin-based mechanisms that sustain malignant transcriptional states. While many chromatin regulators are broadly required for cellular viability, others function in a context-dependent manner across distinct oncogenic settings, tissue lineages, and differentiation states. Moreover, chromatin regulators often operate within multi-subunit complexes; thus, epigenetic vulnerabilities emerge from coordinated complex activities. Here, we integrate large-scale genetic dependency maps from human cancer cell lines with curated epigenetic complex annotations to perform a systematic, multivariate analysis of complex-level epigenetic dependencies across cancer lineages. Our analysis reveals that dependencies frequently cluster among functionally related chromatin complexes and that biologically related cancer types (e.g., hematologic malignancies) share similar dependency patterns, consistent with shared underlying epigenetic requirements. Focusing on melanoma, we identify multiple enriched epigenetic complex dependencies, including complexes previously associated with recurrent genetic alterations or melanocyte lineage regulation, as well as a previously unrecognized vulnerability involving the H3K4 methyltransferase complex Set1C/COMPASS. This dependency is not restricted to a specific melanoma differentiation state, but genetic depletion of CXXC1 (a critical complex-specific subunit) suggests that CXXC1-dependent melanoma cells require Set1C/COMPASS activity to maintain global H3K4 trimethylation (H3K4me3) and proliferation. Integrative modeling links Set1C/COMPASS dependency to MYC- and E2F-driven transcriptional programs, which are suppressed upon complex inhibition. Together, this work combines integrative, multivariate analysis of lineage-enriched epigenetic dependencies with genetic perturbation, transcriptional profiling, and single-cell analysis to uncover an enriched epigenetic dependency on Set1C/COMPASS in melanoma cells.