Cellular Position Tracking Using DNA Origami Barcodes

Project Information

CellTrack

Grant agreement ID: 724872

DOI

10.3030/724872

Project closed

EC signature date 3 May 2017

Start date 1 August 2017

End date 31 July 2022

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 923 262,50

EU contribution

€ 1 923 262,50

Coordinated by

KAROLINSKA INSTITUTET
Sweden

Periodic Reporting for period 4 - CellTrack (Cellular Position Tracking Using DNA Origami Barcodes)

Reporting period: 2022-02-01 to 2022-07-31

Summary of the context and overall objectives of the project

In this project we set out to investigate a novel barcoding system. The idea was to create readable “address labels” for individual cells in a tissue sample. These labels would be readable both by microscopy and by sequencing. If one could do this, one could use microcopy to image tissue along with the address labels, to record the location of each cell. Then separate the tissue into single cells, then sequence the messenger RNA (mRNA) of each cell together with each cells address labels. In the end this will (i) create a picture of what RNA each cell was expressing, and (ii) where each cells original location in the tissue was. This would be important for healthcare and medical research, as knowing the molecular biology of each cell (the mRNA), plus the spatial information (the location of each cell) is increasingly being seen as crucial for understanding how organs work in health and disease. The overall objective was to prove the first address label system like this using a technique called DNA origami. During the project we have come very close to realizing these goals and future research in the group will eventually reach the overarching goal. In pursuit of the action, we have made several other important steppingstones that have become interesting projects in their own right.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

We have performed a large amount of work on combinatorial production techniques to make large libraries of unique DNA origami nanostructures in one pot. We have also performed extensive work on making polygonal DNA origami nanostructures that interact with cells in a programmed manner and patterning of molecules on DNA origami. One significant result has been the development of a technology for patterning of antigens on the nanoscale, and then use these to look at how antibodies bind to patterns of antigens in a manner more detailed than was previously possible. We were able, for the first time to publish details of how antibodies bind to antigens separated by nanoscale distances, something we believe will have impact on vaccine design (Shaw, Högberg et al., Nat. Nanotech. 2019) And very recently we discovered, that antibodies can transport themselves, like bipedal walkers, on surfaces of nanopatterned antigens (Hoffecker, Högberg et al., Nat. Comp. Sci. 2022). Yet another significant achievement have been another project that sprang out of the original ideas in the project but ended up in a different niche, namely the use of precise, nanoscale, peptide spacing to induce apoptosis on demand (Wang, Högberg et al. ACS Nano 2021) – a project we hope will allow us to develop prototype cancer-targeting devices in the future. The project has so far led to 5 scientific publications and 1 patent application and there are a number of papers and patent applications resulting from the project that remain to be submitted.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The nano-barcodes we have developed within the period are unique in the way that they are trackable in both microscopy and sequencing in a way that goes well beyond the state of the art. All the results mentioned above represent significant progress beyond state of the art. In particular, the cell-tracking barcode sytem (the cell “address labels” described above) has progressed both the DNA origami technique itself and its applications beyond the state of the art. Further, the discovery and characterization of spatial tolerance of human antibodies and their walking dynamic a breakthrough beyond the state of the art that will help generate a lot of new knowledge about antibodies, immunology and eventually vaccines.

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