Researchers Develop New Technique for Studying the 3D Organization of Cells in Tissue at the Single-Cell Level

Researchers Develop New Technique for Studying the 3D Organization of Cells in Tissue at the Single-Cell Level

A great deal of research has been conducted on bone marrow, which contains stem cells capable of creating blood cells through life. However, little is known about the spatial organization of cells within the bone marrow and how those cells interact. A better understanding of the organization of the bone marrow could help with the development of new treatments for hematological diseases such as leukemia.

A great leap forward has been made by researchers at the European Molecular Biology Laboratory (EMBL) and the German Cancer Research Center (DKFZ). The researchers have developed a new technique that has allowed them to visualize the three-dimensional organization of cells in the bone marrow at the single cell level.

Using their new technique, the researchers have revealed the cellular composition of bone marrow and how the cells interact with each other. They have also identified previously unknown cell types – niche cells – which play an important role in the regulation of blood stem cells.

The technique involves a combination of single-cell and spatial transcriptomics with new computational methods. Using their new technique, the researchers showed how the different cell types were organized in the bone marrow and they also accurately predicted how each would behave. This is the first time that spatial interactions between cells with a tissue have been calculated computationally from genomic data.

The researchers studied RNA in individual bone marrow cells and identified 32 different cell types, some of which were incredibly rare and were previously unknown to science. “We believe that these rare ‘niche cells’ establish unique environments in the bone marrow that are required for stem cell function and production of new blood and immune cells,” said Simon Haas, group leader at DKFZ. The researchers have made their data available to all free of charge in a 3D atlas, which can be accessed via a web app.

The researchers say their new technique can be used on other tissues and could be invaluable for studying the pathology of human diseases.

You can read more about the study in the paper – Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization – was recently published in the journal Nature Cell Biology. DOI: 10.1038/s41556-019-0439-6

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