Spatial Biology UK 25-26 April 2023 | London

Four of us, affiliated to the Wedge lab, Maria Jakobsdottir, Marian Love, Diego Sanchez Martinez, and Laura Woodhouse, recently attended a Spatial Biology meeting hosted by Oxford Global. Spatial technologies provide the ability to test the expression of multiple targets either at the protein, mRNA, or metabolite level across a part of a specimen section. This exciting field is still in its infancy and there was much discussion on how to ensure that such data is more than just a “pretty image” in a paper but could be uploaded to repositories and shared effectively between research groups. The meeting gave a useful overview of the different methods and instruments that are presently on the market, along with their applications. Many of the talks were delivered by company representatives, who shared their insights.

It was evident that diverse fields of research needed different information from the spatial biology readout and that the distinct machines had their own niches, with no one technology best for all scenarios. Throughout the conference, no ball-park prices were ever discussed, and a worry was that the cost of each assay may preclude the addition of adequate controls. Many researchers were interested in using Spatial systems to detect different cell types in a manner akin to flow cytometry but on a slide. Another set of investigators wanted to place their cell or gene of interest in context of a small battery of markers. For both such applications, cyclic immunostaining or mRNA in situ platforms would probably be ideal. However, where different antigens are detected in the visualisation process may be important for them to be robustly distinguished and this must be borne in mind when designing such assays.

Alternatively, the one-stain approach by Rarecyte, with novel methods to deconvolve fluorescent signals, allowed for twenty fluorescent probes to be detected simultaneously. A different technology, very effective in tissues with high-autofluorescence, was offered by both Ionpath and Standard Biotools’ Hyperion XTI, which use metal ion labelled antibodies and mass-spec to image slides. There are limits to the number of probes, approximately forty, as there are only so many metal ions with the correct properties that are of suitable purity for conjugation. Further, the tissue is destroyed after “visualisation”, so it can only be scanned once resulting in an upper limit to probe number.

As a group we aim to use a non-biased approach to investigate cancer evolution, with no one favourite gene, but a requirement to detect the expression of as many different genes as possible. The Visium chip by 10X Genomics offers a platform that detects any polyA-tailed transcripts within a 55-micron diameter spot, with 5000 spots available per capture. The resolution of Visgen’s Merscope or Nanostring’s CosMx will be superior, but these rely on specialised probes they are presently limited to 500 and 1000 different transcripts, respectively, although the aim is to further optimise these systems to increase probe number. We are interested in pre-cancer diagnosis, and the differences between a normal looking, pre-malignant and cancerous tissue from the same individual. The Nanostring GeoMx is the ideal system for this as it can capture a defined area of the slide, highlighted by immunofluorescent staining, and bound barcoded antibodies and mRNA probes can be released and quantified.

Much of the final choice of technology to use will come down to financial constraints and local prior expertise. The field is so new that much novel information is to be gained by spatial biology experiments. Which is the optimal platform for a particular research question may be different in the near future, as the diverse technologies are evolving and refining rapidly.