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Spatial transcriptomics of murine bone marrow megakaryocytes at single-cell resolution

ABSTRACT: Spatial transcriptomics of murine bone marrow megakaryocytes at single-cell resolution

PROVIDER: PRJNA932772 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23372500_1.fastq.gz	Fastqsanger.gz
	SRR23372500_2.fastq.gz	Fastqsanger.gz
	SRR23372600_1.fastq.gz	Fastqsanger.gz
	SRR23372600_2.fastq.gz	Fastqsanger.gz
	SRR23372501_1.fastq.gz	Fastqsanger.gz

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Spatial transcriptomics of murine bone marrow megakaryocytes at single-cell resolution

Project description:Megakaryocytes are bone marrow (BM) resident cells that derive from hematopoietic stem cells. A pivotal function of megakaryocytes is the generation of platelets through the release of long protrusions called proplatelets into sinusoidal vessels. single-cell RNA-sequencing on murine BM megakaryocytes has previously revealed transcriptional heterogeneity with segmentation into four distinct categories. These studies postulated functions beyond platelet production with evidence for immunoregulatory and stem cell niche supporting subtypes, as well as a cycling population. The spatial context and transcriptional heterogeneity of megakaryocytes is of great interest as localization of for instance the vasculature is a necessity for platelet production. For single-cell RNA sequencing this spatial orientation is however lost due to the dissociation of tissues. Recent technological advances have enabled the interrogation of gene expression profiles of tissues in situ. This enables the integration of morphological, situational and transcriptional information to classify cells in the context of their microenvironment. In the following we present, for the first time, the application of this technology to BM megakaryocytes at a single cell level.

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Spatial transcriptomics of murine bone marrow megakaryocytes at single-cell resolution.

Project description:BackgroundWhile megakaryocytes are known for making platelets, recent single-cell RNA sequencing data have revealed subpopulations of megakaryocytes with predicted immunoregulatory and bone marrow niche-supporting roles. Although these studies uncovered interesting information regarding the transcriptional variation of megakaryocytes, the generation, localization, and regulation of these subsets have not yet been studied and therefore remain incompletely understood. Considering the complex organization of the bone marrow, we reasoned that the application of spatial transcriptomic approaches could help dissect megakaryocyte heterogeneity within a spatiotemporal context.ObjectivesThe aim of this study was to combine spatial context and transcriptomics to assess the heterogeneity of murine bone marrow megakaryocytes in situ at a single-cell level.MethodsBone marrow sections were obtained from femurs of C57BL/6J mice. Using the murine whole transcriptome array on the Nanostring GeoMx digital spatial profiling platform, we profiled 44 individual megakaryocytes (CD41+ by immunofluorescence) in situ throughout the bone marrow, both adjacent and nonadjacent to the endothelium (directly in contact with vascular endothelial-cadherin-positive cells).ResultsPrincipal component analysis revealed no association between transcriptomic profile and adjacency to the vasculature. However, there was a significant effect of proximal vs distal regions of the bone. Two and 3 genes were found overexpressed in the proximal and distal sides, respectively. Of note, proplatelet basic protein and platelet factor 4, 2 genes associated with platelet production, had higher expression in proximal megakaryocytes.ConclusionThis study indicates a possible effect of spatial location on megakaryocyte heterogeneity and substantiate further interest in investigating megakaryocyte subpopulations in the context of their spatial orientation.

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Gene expression data from wildtype and Grin1 deleted bone marrow megakaryocytes

Project description:N-methyl-D-aspartate receptors (NMDARs) are glutamate-gated cation channels with high calcium permeability. Their activity supports megakaryocytes proliferation and maturation, however their downstream effects on the megakaryocyte transcriptome remain poorly elucidated. We used Clariom S Pico Arrays to profile the transcriptome changes caused by loss of Grin1 in mouse bone marrow megakaryocytes.

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