A new advance overcomes present limitations in spatial transcriptomics with a DNA nanotechnology-driven method called 'Light-Seq.' Light-Seq allows researchers to 'geotag' the full repertoire of RNA sequences with unique DNA barcodes exclusive to a few cells of interest. These target cells are selected using light under a microscope via a fast and effective photocrosslinking process, and their RNAs made available to next-generation sequencing with the help of a new DNA nanotechnology-driven technique. This entire process can then be repeated for different cell populations in the same sample.

 

Under the microscope, researchers often observe different cell types organizing themselves in peculiar patterns within tissues, or sometimes a rare cell type that stands out by occupying a unique position, exhibiting an unusual shape, or expressing a specific biomarker molecule. To determine the deeper meaning of their observations, they have developed approaches to also access cells' gene expression patterns (transcriptomes) by analyzing the gene-derived RNA molecules present within them, which they can match with cells' shapes, spatial positions, and molecular biomarkers.

 

However, these "spatial transcriptomics" approaches still only capture a fraction of a cell's total RNA molecules, and cannot deliver the depth and quality of analysis provided by single-cell sequencing methods, which were developed to investigate the transcriptomes of individual cells isolated from tissues or biofluids via next-generation sequencing (NGS) techniques. Nor do they allow researchers to only home in on specific cells based on their location in a tissue, which would greatly facilitate the pursuit of disjointed cell populations, or rare, difficult-to-isolate cells like rare brain cells with unique functions, or immune cells that invade tumors. In addition, because the original tissue environment is disrupted, many spatial transcriptomics and all single-cell sequencing methods prevent researchers from revisiting their samples to perform follow-up analysis, and they are costly because they require specialized instruments or reagents.

 

A new advance made at the Wyss Institute for Biologically Inspired Engineering at Harvard University now overcomes these limitations with a DNA nanotechnology-driven method called "Light-Seq." Light-Seq allows researchers to "geotag" the full repertoire of RNA sequences with unique DNA barcodes exclusive to a few cells of interest. These target cells are selected using light under a microscope via a fast and effective photocrosslinking process.

 

With the help of a new DNA nanotechnology, the barcoded RNA sequences are then translated into coherent DNA strands, which can then be collected from the tissue sample and identified using NGS. The Light-Seq process can be repeated with different barcodes for different cell populations within the same sample, which is left intact for follow-up analysis. With a performance comparable to single-cell sequencing methods, it significantly broadens the depth and scope of investigations possible on a tissue sample. The method is published in Nature Methods[BB1] .