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3D-Seq: Localizing Spatial Gene Expression in 3-Dimensions on Single-Cell Level

Reference Number TO 03-00462


Spatial cellular information is crucial for understanding the complex crosstalk and communication between neigbouring cell-types during tissue development, differentiation and homeostasis. Overall, the three-dimensional resolution of the cellular tissue architecture can provide invaluable insights into all relevant molecular mechanisms and processes, reflecting the (patho-)physiological state of a defined tissue. Current methodologies focus on transcriptional profiling on defined plane coordinates in 2D revealing in situ sequencing data with limited depth and cellular resolution. To fully explore the individual cellular make-up in a given tissue sample at high spatial resolution, innovative approaches are required.

3D-Seq approach
3D-Seq approach


The invention relates to a novel “3D-Seq” technology that provides a solution for obtaining single-cell gene expression profiles in a spatial context. Spatial single-cell RNAseq can be carried out in any desired tissue sample by first compartmentalizing consecutive tissue sections and consequently mapping positional information for individual cells within each compartment with using only a single slide. By this means RNAseq data regarding identity, activity and functionality for individual cells will be assayed in the three-dimensional space to uncover tissue heterogeneity. A central feature of the presented technology is a newly designed grid providing a spatial (3D-)coordinate system that enables compartment specific combinatorial barcoding of single cells within the desired dimensions. The technology also comprises a computational solution to reveal the cellular transcriptome of individually captured cells in relation to their localization. The technology exhibits following advantages: • Novel versatile method for spatial transcriptomics in a given snap-frozen tissue sample • Fast turn-around time for sample processing and data acquisition • Easy retrieval of positional global gene expression data with single cell resolution • Deep sequence analysis rather than selected genes in multiplex-based in situ RNA sequencing • Applicable to all NGS platform technologies • Grid-system appropriate for assay systems beyond transcriptomics (other “Omics”)

Commercial Opportunity

Feasibility of technology has been shown with a first series of grid prototypes. 

Developmental Status

Technology is ready for further application in basic research, molecular pathology and/or biomarker discovery. This opportunity is available for research collaborations and/or licensing.

Patent Situation

European Patent application EP18184151 has been filed with priority of August 2018. 

Further Reading

Lein E, Borm LE, Linnarsson S. (2017) “The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing.” Science 358, 64-69