Chromatin Organization Governs Transcriptional Response and Plasticity of Cancer Stem Cells [CUT&Tag]

The organization of chromatin, governed by physicochemical interactions, nucleosome positioning, and histone modifications, regulates transcription to influence cellular plasticity and cell fate. We explored whether the organization of chromatin into nanoscale packing domains is involved in regulating transcriptional programs that govern stemness and responses to chemotherapy. Specifically, chromatin packing domains are a unit of chromatin structure at the single-cell level playing a critical role in regulating cellular transcriptional plasticity and access to the transcriptional landscape. Using an optical spectroscopic nanosensing technology, partial wave spectroscopic (PWS) microscopy, we show that ovarian cancer-derived cancer stem cells (CSCs) display upregulation of nanoscale chromatin packing domains (P<0.05) compared to non-CSCs cells. CUT&Tag sequencing with antibodies for repressive H3K27me3 and active H3K4me3 and H3K27ac marks identified 4438 H3K27me3 differentially enriched regions (P<0.05), of which 2786 were detected in CSCs, supporting chromatin packing domain upregulation in ovarian CSCs. Additionally, more poised genes with both H3K4me3 and H3K27me3 marks were identified in CSCs (n=2292) vs. non-CSCs (n=932), supporting the increased transcriptional plasticity of CSCs. Corresponding to the distinct organization of chromatin marks in CSCs, comparative transcriptomic analyses yielded a higher intercellular transcriptional heterogeneity in global gene expression at baseline in CSCs vs. non-CSCs. In response to cisplatin, genes with low baseline expression levels underwent the highest upregulation in CSCs, demonstrating transcriptional plasticity under the stress of chemotherapy. Treatment of CSCs with epigenome targeting drugs downregulating chromatin packing domain formation promoted cellular differentiation. In particular, the Dot1L inhibitor (Dot1Li) downregulated chromatin domains and blocked transcriptional plasticity. This resulted in the reversal of stemness features and inhibition of tumor initiation capacity. The results support that CSCs harbor upregulated chromatin packing domains, contributing to transcriptional and cell plasticity that epigenome modifiers can target.