Pixelgen Publishes on Molecular Pixelation in Nature Methods

A novel approach to spatial proteomics of single cells has been unveiled by researchers from Pixelgen Technologies, the Karolinska Institute, Imperial College London, and the Royal Institute of Technology in Sweden. This innovative method, detailed in a peer-reviewed article in Nature Methods, marks the first instance of a sequencing-based technique that eliminates the need for optical tools to map protein locations within single cells.

The technology, named Molecular Pixelation (MPX), utilizes DNA-barcode-based strategies to identify and visualize the spatial organization of proteins on immune cell surfaces in three dimensions. Unlike traditional microscopy, which relies on fluorophore-labeled antibodies and immobilized samples, MPX offers enhanced multiplexing and throughput capabilities. It allows for a more comprehensive analysis by eschewing the limitations of two-dimensional data visualization.

MPX operates through the use of DNA-tagged antibodies, known as Antibody-Oligonucleotide Conjugates (AOCs), which bind to their respective protein targets on chemically fixed cells. This method does not necessitate sample immobilization or single cell compartmentalization, and assays are conducted in standard reaction tubes. Unique DNA pixels—nano-sized DNA spheres—establish associations between neighboring AOCs, facilitating the spatial analysis of protein arrangements. These associations are sequenced, and the resulting data is computationally reconstructed into spatial proteomics networks depicting individual cells.

The study showcased the capabilities of MPX using a diverse 80-plex protein panel that targeted T cells, NK cells, B cells, dendritic cells, and monocytes. MPX was able to generate single-cell-level data on protein abundance from peripheral blood mononuclear cells (PBMC) and identified both known and novel spatial protein patterns in chemokine-stimulated T-cells. This underscores MPX's potential in defining cell states based on the spatial arrangement of surface proteins.

Filip Karlsson, Pixelgen’s Chief Technology Officer and lead author of the study, emphasized the significance of spatial proteomics in understanding cell motility, activation, drug mechanisms, and target discovery. Karlsson believes MPX offers substantial advantages over traditional techniques and will be instrumental in developing therapies that reorganize cell surface proteins to modulate immune activities. This includes potential applications in pre-tuning immune synapses in CAR-T cell therapies for cancer, among other innovative medicinal and diagnostic developments.

Petter Brodin, MD, PhD, a Professor of pediatric immunology at the Karolinska Institute and Imperial College London, and co-author of the study, highlighted the value of this technology for research into cellular regulation and functional adaptation in response to environmental stimuli. Brodin noted that the spatial dimension provided by MPX adds a crucial layer of information beyond traditional protein and mRNA abundance measurements, offering new insights for future studies.

Founded in 2020, Pixelgen Technologies aims to revolutionize biological understanding by mapping the spatial relationships of cell surface proteins. The company, headquartered in Stockholm, Sweden, developed Molecular Pixelation to provide novel insights into cellular activity, thereby advancing the creation of better medicines and diagnostics.