Combining data from other technologies and a new technique called sci-Space could result in four-dimensional atlases showing gene expression across different cells during embryonic growth of mammals.These atlases would show how gene transcripts in individual cells reflect time, cell lineages, cell movement, and the location of the embryo. These atlases would also be able to illuminate gene expression's spatial regulation.The mammalian embryonic process is remarkable. A fertilized egg divides and then turns in weeks or months into a complex organism capable to perform a multitude of physiological processes. It also contains a variety cells, tissues, and anatomical structures.Understanding how mammals form, particularly at the single-cell level during embryonic growth, could help advance biomedical research and veterinary treatment of a wide range of conditions. These conditions include congenital malformations, inherited disorders, and developmental delays. Future regenerative medicine efforts may also benefit from understanding how organs are created.A team of scientists from UW Medicine, Howard Hughes Medical Institute, and Brotman Baty Institute for Precision Medicine demonstrated their sci-Space technique using mouse embryos.The July 2 issue of Science published their results. Sanjay R. Srivatsan, of the Department of Genome Sciences of the University of Washington School of Medicine and Mary C. Regier of UW Department of Bioengineering are the lead authors.AdvertisementJay Shendure (UW Medicine professor of genomic sciences and director at the Brotman Baty Institute and investigator at the Allan Discovery Center For Cell Lineage Tracing); Kelly R. Stevens (UW assistant professor in bioengineering); and Cole Trapnell (associate professor of genetic sciences). Regier and Stevens also work as investigators at UW Medicine Institute for Stem Cell and Regenerative Medicine Research.Researchers observed the orchestration genes in 120,000 cell nuclei. The DNA code is the same for all somatic cells in the body. Researchers gathered information about which genes were activated in these nuclei during the formation of mouse embryos. Researchers also looked into how embryonic cell locations affected the activation of genes during development.This technique is based on earlier work by these scientists and others who developed methods for whole-organism profiling to determine gene expression and DNA-code access in thousands of single cells during embryonic development. This was done to track the evolution and trajectory of different cell types.Normal development depends on how cells are organized spatially. This includes the physical positions that they take when an embryo forms. Missing or damaged cells, as well as misplacements or disruptions of cells, can lead to serious problems and even death in prenatal life.It has proved difficult to gain knowledge about spatial patterns in gene expression. It was difficult to test individual cells for gene transcripts over large areas of embryo. This has limited scientific understanding of the spatial organization of gene expression.AdvertisementScientists involved in the current study had previously developed a method for labeling cell nuclei. This technique was called sci-Plex. The scientists then used sci-RNA-sequencing to index single-cell RNA sequences.Sci-Space now allows scientists to analyze cell transcripts and spatial coordinates in order to identify thousands of genes whose expression is anatomically patterned. Some genetic patterns were found in neurons of the brain and spinal chord, while others were found in cardiac muscle cells.Scientists also used gene profile and spatial information to identify subtypes of cells. Although both blood vessels cells and heart muscle may express a certain growth factor gene, it is only the heart muscle cells that produce these growth factor receptors.Researchers also found that different cell types had different levels of spatial patterning in gene expression. Connective tissue progenitor cells, for example, showed high levels of spatially restricted gene transcription. This observation suggests that these cells behave differently in different parts of the body.Researchers also calculated the distance between cells and their gene expression profiles to determine the power of spatial location on a cell's transcript profile.Researchers noted that "For many cell types" the researchers observed in their paper that as the physical distance between them increased, so did their angular distance between the transcriptomes. They also noted that this trend can vary greatly. This was evident in particular brain and spinal cord cells.Other cell types had their genetic transcript profiles greatly affected by their location in the embryo. Certain cartilage cells are one of these, and they form part of the framework for the bones of the head or face.Researchers also examined gene expression dynamics during brain cell differentiation and migration in mouse embryonic development. Researchers examined the anatomical distribution of different brain cell trajectories. They used the Anatomical Reference Brain Atlas from Allen Institute as a guide.Researchers noted that cells from each trajectory occupied distinct brain regions. The researchers also found different levels of development maturity in different parts of the brain. These gradients revealed both new and established patterns of migration.The researchers believe sci-Space could be used in the future to create serial sections that span the whole embryo of a mouse and cover many points in time.Recent research was supported by the National Institutes of Health (Deutsch Forschungsgemeinschaft), Brotman Baty Institute and Paul G. Allen Frontiers Foundation.
