Single-cell multi-omics defines H3K27me3 remodelling in intervertebral disc degeneration with implications for regenerative intervention

Abstract

Utilizing key developmental cues and refining their orchestrating role in degeneration represents a promising strategy for understanding and treating intervertebral disc (IVD) degeneration, a major cause of chronic lower back pain. Here, we focus on notochordal cells (NCs), which originate from the embryonic notochord and reside in the developing nucleus pulposus. These distinctly vacuolated cells exhibit robust regenerative effects and hold promise for new therapeutic approaches. Dogs, like humans, suffer from the consequences of IVD degeneration. As the IVD matures and degenerates, NCs are replaced by smaller non-vacuolated NP cells (NPCs). The dog was employed as a model to capture, at the single-cell level, the heterogeneity of resident cells by studying the nucleus pulposus tissue at three stages (i.e., juvenile, young adult and degenerate adult). Here, we integrated transcriptomic data with repressive histone H3 lysine 27 trimethylation (H3K27me3) profiles at the single-cell level to assess changes in chromatin states and gene expression across this IVD degeneration-associated cell phenotypic transition. H3K27me3 enrichment on key genes involved in IVD development and homeostasis, such as Brachyury (TBXT), aligns with the observed attenuation during ageing and degeneration seen in both dog and human IVDs. This study further demonstrates that eliminating repressive histone marks, together with CRISPR-mediated gene transactivation, enhances TBXT gene expression in human NPCs derived from degenerated aged discs. Our findings underscore how extensive insights gained through single-cell omics can lead to the identification of crucial cellular cues that may enable degenerate NPCs to regain a healthier phenotype.

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Funding

EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)(825925)

Friends of Veterinary Medicine fund, housed at Stichting Utrechts Universiteitsfonds - grant reference number 2610577

China Scholarship Council (CSC)(Xiaole Tong)

EU-HK Research Cooperation Co-funding Mechanism - grant reference number: E-HKU703/18

EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)(101053581)

Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)(TOP - 714.016.001)

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)(P2BSP3-174991)

Human Frontier Science Program (HFSP)(LT000209/2018-L)

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