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In a recent study published in the journal NatureA large research team in the United States has combined single-cell ribonucleic acid (RNA) sequencing and high-resolution fluorescence in situ hybridization to determine the identity of different cell types that spatially cooperate to form complexes. Morphological structure of the heart.

Research: Spatially organized cell communities shape the developing human heart. Image credit: beerkoff / ShutterstockResearch: Spatially organized cell communities shape the developing human heart. Image credit: beerkoff / Shutterstock

background

Each of the complex structures of the human heart has specific roles that contribute to efficient heart function, and impairment of any of these functions can lead to congenital heart disease in children and valvular heart disease and myocardial disease in adults. Birth defects, such as heart disease, can occur. However, despite the heart’s important role in the human body, the organization and function of cardiac structures and how they interact remain poorly understood.

About research

In this study, the researchers used a single-cell RNA sequencing (scRNAseq) approach along with multiplexed error-robust fluorescence in situ hybridization (MER-FISH). This strategy allowed us to combine single-cell transcriptomics and spatial biology to visualize, analyze, and quantify RNA transcripts of large numbers of genes from a single cell.

They started by identifying the cell lineages that are part of the developing heart. This helped determine how different types of heart cells assemble into complex structures and coordinate to regulate the function of the human heart. scRNAseq was performed in replicates and analyzed on human hearts at different stages of growth starting from 9 weeks post-conception to 16 weeks.

The resulting over 140 million single cells were transcriptionally sorted into five cellular compartments: cardiomyocytes, endothelial cells, mesenchymal cells, neurons, and blood cells. Within these cellular compartments, analysis of genetic markers identified 12 cell classes, and subsequent cluster analysis identified 39 cell populations and 75 subpopulations.

We then used MER-FISH to spatially map cardiac cells and investigate the cellular mechanisms that guide cardiac remodeling and morphogenesis, including ventricular wall development. The tissues of the cells identified using scRNAseq, particularly those during development, such as myocardial wall compaction, were investigated using MER-FISH imaging.

This study then aimed to decipher the assembly of these specific cardiovascular cells into cellular neighborhoods, where they come together to form multicellular structures that contribute to cardiac function. The scientists also investigated the organizational and cellular complexity of specific regions, such as the ventricles, by exploring cells within the ventricles that were identified, isolated, and mapped using MER-FISH. Additionally, we used a mouse model to investigate cell-cell interactions. alive In experiments, human-derived pluripotent stem cells were used for similar evaluations. in vitro experiment.

a, Left, Schematic diagram of the experiment. Right, scRNA-seq identifies a diverse range of distinct cardiac cells that make up the developing human heart, as shown by uniform manifold approximation and projection (UMAP) of approximately 143,000 cells.  b. Schematic diagram shows how 238 cardiac cell-specific genes were spatially identified using MERFISH. Pseudo-colored dots mark the positions of individual molecules of 10 specific RNA transcripts.  c, Approximately 250,000 MERFISH-identified cardiac cells are clustered into specific cell populations as shown by UMAP and colored accordingly (d).  d, Identified MERFISH cells were spatially mapped across 13 anterior cardiac sections (left) and shown according to major cell classes (right).  e, Combined embedding between MERFISH and age-matched scRNA-seq datasets enabled transfer of cell labels and imputation of her MERFISH genes.  f, Co-occurrence heatmap shows the correspondence between cell annotations of MERFISH cells and cell annotations transferred from the 13 pcw scRNA-seq dataset.  g, Gene imputation performance was spatially validated by comparing the normalized gene expression profiles of marker genes measured by MERFISH with the corresponding imputed gene expression profiles. epi, epicardial;  MV, mitral valve;  P-RBC, platelet-erythrocyte; TV, tricuspid valve. Scale bar, 250 μm (g).  Illustrations in a were created using his BioRender (https://www.biorender.com).be, Left, Schematic diagram of the experiment. Right, scRNA-seq identifies a diverse range of distinct cardiac cells that make up the developing human heart, as shown by uniform manifold approximation and projection (UMAP) of approximately 143,000 cells. b, A schematic diagram shows how 238 cardiac cell-specific genes were spatially identified using MERFISH. Pseudo-colored dots mark the positions of individual molecules of 10 specific RNA transcripts. capproximately 250,000 MERFISH-identified cardiac cells were clustered into specific cell populations as indicated by UMAP and colored accordingly. d. dIdentified MERFISH cells were spatially mapped across 13 anterior cardiac sections (left) and shown according to major cell classes (right). eJoint embedding between MERFISH and age-matched scRNA-seq datasets enabled cell label transfer and MERFISH gene imputation. fThe co-occurrence heatmap shows the correspondence between the cell annotations of MERFISH cells and the cell annotations transferred from the 13 pcw scRNA-seq dataset. g, gene imputation performance was spatially validated by comparing the normalized gene expression profiles of marker genes measured by MERFISH with the corresponding imputed gene expression profiles. epi, epicardial; MV, mitral valve; P-RBC, platelet-erythrocyte; TV, tricuspid valve. Scale bar, 250 μm (g).illustration of be Created using BioRender (https://www.biorender.com).

result

This discovery shows that different cardiac cell types belong to specific subpopulations that are part of specific communities, with functional specialization defined according to the anatomical region and cellular ecology in which they reside. It became clear. The cardiomyocyte lineage was the largest cellular compartment identified using MER-FISH. The study also found that cells belonging to non-cardiomyocyte cellular compartments also undergo segregation into populations and subpopulations and contribute to the formation of specific structures and regions of the heart.

Cardiomyocyte subpopulations in the ventricular region demonstrated the ability to build complex layered structures on the ventricular wall and form cell communities with other subpopulations of cardiac cells. moreover, alive and in vitro Experiments performed to understand cell-cell interactions have revealed that the spatial organization of cardiac cell subpopulations during ventricular wall morphogenesis occurs through different signaling pathways.

The study also found that the heart region is made up of spatially organized combinations of isolated populations of cells called cell communities. These cell communities differed in the number and type of cell populations, and within these communities, the neighbors of each cardiac cell within a 150-micrometer radius were defined. These interacting cell populations also had distinct cell signaling pathways.

conclusion

Overall, this study found that cardiomyocytes are the largest compartment of cell types in the developing heart, with all cell types exhibiting distinct structural and regional distributions within the heart. Specific cell populations also form cell communities in various combinations, and signaling pathways between cell populations within a community define their structure and function. This research helped understand the development of the human heart’s complex structure and provided a potential means to treat structural heart disease.

Reference magazines:

  • Farrar, E.N., Hu, R.K., Khan, C., Chan, Q., Lu, T., Ma, Q., Tran, S., Chan, B., Carlin, D., Monell, A., Blair, A.P., Wang, Z., Eschbach, J., Li, B., Destici, E., Ren, B., Evans, SM, Chen, S., Zhu, Q., and Chi, N.C. (2024). Spatially organized cell communities form the developing human heart. Nature. DOI: 10.1038/s4158602407171z, https://www.nature.com/articles/s41586-024-07171-z

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