Open-Source Spatial Transcriptomics Platform Developed

A spatial transcriptomics platform called Nova-ST has been developed by researchers at VIB-KU Leuven. This open-source platform was developed to improve gene expression profiling in tissue samples by offering high-resolution spatial analysis at an affordable cost.

At the heart of Nova-ST lies a clever adaptation of Illumina NovaSeq 6000 S4 or the new generation Novaseq X sequencing flow cells, commonly used for large-scale DNA sequencing. These flow cells contain a dense nano-patterned surface riddled with tiny, randomly barcoded nanowells arranged in a hexagonal lattice. Each well acts as a capture site for mRNA molecules from a specific location within the tissue sample. This dense nano-patterned surface allows Nova-ST to achieve high spatial resolution, potentially capturing the footprint of single cells.

"We then use these capture sites to snag mRNA molecules while preserving their spatial coordinates," explains Suresh Poovathingal, first author of the study published in Cell Reports Methods. This approach enables researchers to create detailed gene activity maps across entire tissue sections.

The platform boasts several advantages, including cost-effectiveness, high spatial resolution potentially reaching single-cell level, and compatibility with various tissue types. Its open-source nature also promotes accessibility and customization.

Nova-ST is already being applied to advance research in neurodegeneration and cancer biology. For instance, it's being used to study neurodegenerative diseases' effects on neuromuscular junctions and to analyze immune cell distribution in tumors undergoing immunotherapy.

According to senior author Stein Aerts, "Nova-ST is a game-changer for research across multiple fields, from cancer biology to plant biology. By making this platform open source, we aim to empower scientists worldwide to explore and innovate."

As part of a broader effort to democratize spatial transcriptomics, Nova-ST joins other initiatives like Seq-Scope and Open-ST. The technique's protocols and computational pipeline are publicly available, enabling the scientific community to implement and further develop this transformative technology.