Sep 16, 2024
Spatial Omics at DcGC: Proof-Of-Concept Study of a Game-Changing Technique Shows Successful Application in Zebrafish
This image shows the spatial transcriptomics data from a zebrafish brain, where each of the 20 colors corresponds to a specific cell type. Distinctly colored clusters reveal unique gene expression patterns, offering unprecedented understanding of the processes involved in tissue repair and recovery.
Spatial transcriptomics, a new game-changing technique that simultaneously quantifies mRNA expression of a large number of genes directly in the tissue context, is now available at the DRESDEN-concept Genome Center (DcGC). A recent proof-of-concept study featuring the Brand group demonstrated that Xenium, one of the spatial transcriptomics techniques, can be successfully applied in zebrafish to monitor the transcription of up to 480 genes.
In recent years, single-cell sequencing and related omics technologies have revolutionized scientific research. However, these techniques couldn’t pinpoint the exact location of sequenced cells within the tissue. That is until now.
“One could detect different cell types in a tissue sample, even identify new cell types, but could not place these cells physically within the tissue,” says Dr. Julieta Aprea, lead of the Spatial Omics unit at the DcGC. “Spatial transcriptomics changes that. It merges transcriptomics with histology, allowing us to pick any cell in a tissue and see its transcriptome.”
Proof-Of-Concept Study
The team at the DcGC, in collaboration with the Histology Facility and the Light Microscopy Facility (core facilities of the CMCB Technology Platform), has been offering spatial omics since the spring of 2023. Xenium has been successfully used on human and mouse samples, where up to 5,000 different genes can be sequenced. Given that many groups at the CRTD are working with zebrafish, the DcGC decided to extend the technique’s application to this model organism as well. In collaboration with 10x Genomics, the DcGC took on a challenging project with Prof. Michael Brand’s group.
“Zebrafish are one of the amazing animals that can regenerate their nervous system. We wanted to follow regeneration of zebrafish brain, identifying which cells are destroyed by an injury, which are involved in the repair process, and which regenerate,” says Sebastian Eguiguren, a PhD student in the Brand group.
Traditional single-cell transcriptomics revealed different neuronal cell types and subtypes, including novel ones. “The question was, where are these cells located in the regenerating brain?” Sebastian adds.
The Key to Success: Sample Preparation
Successful spatial omics rely on meticulous sample preparation. That’s where Susanne Weiche from the CMCB Histology Facility team played a crucial role.
“As with single-molecule fluorescent in-situ hybridization, that the technique is based upon, quality sample preparation is essential. For this study, we focused on precise 4-micrometer paraffin sections of different areas of the fish brain,” explains Susanne Weiche.
“The dataset we obtained is simply incredible,” says Sebastian Eguiguren. “The outstanding quality of the data allows me to trace the gene expression patterns of nearly 500 genes distributed across various cell types in a regenerating zebrafish brain.”
The Spatial Genomics Workflows Available at the DcGC:
At the moment, the DcGC offers two different spatial genomics workflows: Xenium and Visium. You can read more about the techniques in our article here.
Explore Spatial Genomics at the DcGC
Are you interested in applying spatial omics to your research?
Contact the DcGC for a consultation. The experts at the DcGC and Histology Facility can guide you through the process, from experimental design to execution, ensuring support at every step.
