Developmental Biology Takes Advantage of Spatial Technologies

Spatial biology technologies are equipping developmental biologists with new tools for high-resolution gene expression analysis across tissues. These allow researchers to characterize and map the spatial organization of cell types, learning how they change at key points in development such as organogenesis. The creation of human tissue atlases supports the study of regulatory mechanisms controlling key developmental events, and may further our understanding of, and help to prevent, human pregnancy complications. This article focuses on how developmental biologists are using spatial technologies to advance our understanding of human development.

Building tissue maps with transcriptomics

Spatial technologies are invaluable for their ability to create tissue reference maps to facilitate the study of cell types, cell fate, and tissue architecture. Researchers are using Vizgen’s MERSCOPE^®, a single-cell spatial transcriptomic imaging platform that can profile the expression of hundreds to thousands of genes in situ, to characterize different types and states of cells across developmental stages. Recently, a group led by Arnold Kriegstein at the University of California, San Francisco (UCSF) used MERSCOPE to build a spatial map of annotated, cortical cell types of the human brain across prenatal and postnatal development, including excitatory neurons, interneurons, glial cells, and brain vasculature. “Their results shed light on lineage-specific mechanisms of normal cortical development,” says Jiang He, Scientific Co-founder and Senior Director of Scientific Affairs at Vizgen.

Another group at UCSF, led by Tomasz Nowakowski, used MERSCOPE to map the developing human thalamus in the first trimester, annotating regions, cell types, and marker genes. Additionally, a group headed by Peter Reddien at Massachusetts Institute of Technology and the Whitehead Institute for Biomedical Research used MERSCOPE to investigate cell fate in planarians, uncovering the spatial organization of distinct cell types. “Spatial platforms like MERSCOPE have the ability to build reference maps of different cell types in different tissues, and with such reference maps in hand, scientists are able to figure out what goes wrong in developmental diseases,” says He.

He believes that MERSCOPE’s customizability makes it particularly valuable to developmental biologists. “MERSCOPE offers custom gene panels, so that researchers can customize any gene panel they want in order to study different biological questions,” says He. “In developmental biology, since gene expression and cell type can change significantly throughout the course of disease, having a platform that offers complete custom solutions, high multiplexing capabilities, and high sensitivity is key.”

Transcriptome-proteome interplay during development

For multi-omic analyses, NanoString Technologies offers two platforms—the GeoMx^® Digital Spatial Profiler (DSP) and CosMx™ Single Molecular Imager (SMI)—for high-plex spatial biology with in situ hybridization or immunohistochemistry. “Our spatial platforms can digitally quantitate the whole transcriptome (18K+ mRNA targets) at single-cell resolution or stain and readout more than 500+ antibodies in one experiment,” says Margaret Hoang, Director of Research at NanoString Technologies.

Hoang believes that NanoString’s platform enables a new generation of researchers to use high-plex spatial technologies as a discovery tool in developmental biology. “We used GeoMx DSP to test the ability to catalog whole transcriptome profiles during organogenesis in mouse embryos,” says Hoang. They assayed substructures within nine different organs at four embryonic timepoints, and found that developmental transcriptional factors were differentially expressed across organs. “We have built some great analysis tools downstream of our spatial platforms for unbiased discovery of developmental mechanisms,” she says. “One such tool is InSituCor, which finds modules of co-expressed genes within a spatial neighborhood.”

In a collaboration studying early human embryos from ectopic pregnancies, NanoString and developmental biologists took a multiomics approach. They used a CosMx Wtx panel and InSituCor to analyze spatial transcriptomics data, and found 57 novel gene modules that corresponded with expected embryonic structures. “Additionally, we performed our GeoMx multiomics protocol, giving us a rich dataset using our whole transcriptome atlas (WTA, 18K+) and Immuno-oncology Proteome Atlas (IPA, 570+ antibodies) on the same spatially resolved anatomical structures,” says Hoang. “This gave us a chance to understand the interplay between transcriptome and proteome during human development.”

Combining spatial and single-cell approaches

Spatial transcriptomics across tissues and within single cells is supported by 10x Genomics’ sequencing-based Visium and Chromium platforms, respectively (compatible with optional protein detection as well). “By integrating whole transcriptome analysis with precise transcript localization, these platforms provide a comprehensive view of cellular diversity and interaction patterns during human development,” says Jyoti Sheldon, Senior Product Marketing Manager at 10x Genomics. Visium is an especially powerful tool for developmental biology in part because it combines whole transcriptome analysis with single-cell scale resolution. “This precision allows researchers to unravel the complex cellular interactions and differentiation processes that drive tissue development and organogenesis,” says Sheldon. “By mapping gene expression in the spatial context within the intricate architecture of developing tissues, Visium captures the dynamic spatial and temporal expression patterns that are critical for understanding developmental processes.”

Using Visium-based spatial transcriptomics and Chromium-based single-cell multiomics, a research group at the University of Cambridge constructed a single-cell atlas of the human maternal-fetal interface at the uterine-placenta border including key trophoblast cells. “By examining the spatial organization and gene expression patterns of cells in affected tissues, scientists can pinpoint the molecular underpinnings of developmental disorders,” says Sheldon. “This level of detail facilitates the understanding of disease mechanisms, including how cellular interactions and signaling pathways are disrupted during development.”

The atlas allowed the Cambridge researchers to study the entire process of trophoblast differentiation, along with the transcription factors involved. Because trophoblasts are crucial for the formation of maternal arteries and blood supply to the developing embryo, defects in this process can result in major obstetric complications such as preeclampsia, preterm labor, and stillbirth. Researchers from the Sloan Kettering Institute used Visium and Chromium to create an atlas of four to six week human embryos with spatial transcriptomics, characterizing cell types and spatial architecture during early organogenesis. Defects occurring during this developmental window can result in birth defects or miscarriage. Studies such as these two can enhance our understanding and improve in vitro models of the human placenta during early stages of pregnancy, and perhaps contribute to our ability to prevent future complications.