Spatial transcriptomic profiling reveals local and domain-establishing regulatory signaling networks within the bone marrow
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PROVIDER: PRJNA950246 | ENA |
REPOSITORIES: ENA
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Project description:The application of single-cell RNA sequencing (scRNAseq) to the bone field has led to significant advancements in our understanding of skeletal stem cell (SSC) heterogeneity, yet disparity remains in the characterization of these cells in the context of their native environment. To resolve these limitations, we combined scRNAseq and spatial transcriptomics in adult femurs to provide endogenous, in vivo context. First, predictive modeling was used to determine the spatial location of SSCs within the bone marrow. These results localized CXCL12-abundant reticular cells to the bone marrow, while PDGFRα+SCA1+ were found to enrich within the outer periosteum. Correlative analyses were next used to define the cellular niche composition, identifying smooth muscle cells, as well as endothelial cell and macrophage subtypes overrepresented within the SSC niche. Using cell-cell communication prediction and spatial transcriptomics, we defined ligand-receptor pairs specifically expressed within the niche and mapped their expression back to niche-resident cells. Finally, these SSC niches were placed in the context of bone microdomains. Signaling gradients derived from the vasculature and bone surfaces were unbiasedly assessed using SpatialTime. This data indicated a striking, spatially-restricted activation of metabolic and major morphogenetic pathways. This project demonstrates the ability of this technique to spatially localize SSC subpopulations, define the cellular components of the stem cell niche, unravel cell-cell communication and place this niche in the context of its bone microdomain to gain a comprehensive understanding of local and global SSC regulatory networks within the bone.
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Project description:EP300 and CBP are paralogous, multidomain histone acetyltransferases (HATs) that regulate gene expression by binding to and acetylating diverse proteins. With widespread effects on gene regulation, these enzymes are attractive targets for therapeutic development. Discovery efforts for chemical inhibitors typically target protein domains that are amenable to probe binding. In some cases, probes have been identified for more than one domain within a single protein, including high potency inhibitors of both the catalytic HAT domain and bromodomain (BRD) that mediate the enzymatic and protein binding (“reader”) activities of EP300/CBP. In cancer cell systems, combination inhibition of both domains is more toxic than single inhibitor alone, indicating that inhibition of individual domain functions may elicit differential effects. Thus, we hypothesized that determining the relative effects of domain-specific inhibition of EP300/CBP on tumor cell growth may elucidate exceptional-responding tumor types to one inhibitor or the other. This would permit a broader therapeutic index by enabling reduced dosing of domain-targeted inhibitors, while maintaining enhanced inhibition of cancer cell growth. Here, using high-throughput cell line-based screening, we demonstrate that targeting the HAT or BRD domains of EP300/CBP using the chemical probes A485 and CCS1477 has differential effects in select tumor types. Group 3 medulloblastoma (G3MB) cells were especially sensitive to EP300/CBP BRD inhibition, as compared with HAT inhibition. Structurally, these effects are mediated by the difluorophenyl group in the catalytic core of CCS1477. Mechanistically, the effects of bromodomain and HAT-domain specific inhibition are distinct, with bromodomain inhibition causing rapid early disruption of genetic dependency networks that are required for G3MB growth. These studies provide a domain-specific structural foundation for drug discovery efforts targeting EP300/CBP and identify a selective role for the EP300/CBP bromodomain in maintaining genetic dependency networks in G3MB cells.
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