Pixelgen Technologies Announces Peer-Review Publication on Molecular Pixelation Technology in Nature Methods

Researchers demonstrate first sequencing-based, optics-free method for spatial proteomics of single cells

Stockholm, May 8, 2024 – Pixelgen Technologies, a leader in spatial proteomics for single cells, announced today that researchers from Pixelgen, the Karolinska Institute, Imperial College of London, and the Royal Institute of Technology in Sweden have demonstrated a ground-breaking sequencing-based method for identifying the relative locations of highly-multiplexed immunologically relevant proteins in single cells, in a peer-reviewed article published in Nature Methods. The Molecular Pixelation (MPX) technology used in the study is the first to demonstrate spatial proteomics of single cells without light, enabling multiplexing, throughput, and spatial resolution in 3D for proteomics-level single cell research.

The study, titled “Molecular Pixelation: Spatial Proteomics of single cells by sequencing,” illustrates the ability of a DNA-barcode-based strategy to identify and visualize in 3D the spatial protein organization of immune cell receptors. How immune cell surface receptors are organized relative to each other, and their behavior control many of a cell’s vital functions. Researchers have traditionally studied spatial surface protein organization with microscopy, using fluorophore-labeled antibodies on immobilized samples or with flow cytometry. These approaches have limitations in multiplexing and sample throughput, and data is visualized only in two dimensions.

MPX uses DNA-tagged antibodies (Antibody-Oligonucleotide Conjugates, AOCs) bound to their protein targets on chemically fixed cells to survey cell surface protein arrangement in a highly multiplexed fashion. Sample immobilization or single cell compartmentalization is not required and assays are performed in standard reaction tubes. DNA pixels, which are unique nano-sized DNA spheres, are used to form associations between neighboring AOCs, allowing the spatial analysis of protein arrangement. The generated amplicons are then sequenced, and reads are computationally arranged into spatial proteomics networks of each single cell.

The study processed a heterogeneous 80-plex protein panel targeting T cells, NK cells, B cells, dendritic cells and monocytes. It demonstrated the ability of MPX to generate single cell-based data on protein abundance from peripheral blood mononuclear cells (PBMC). It also identified known and novel patterns of protein spatial organization in chemokine-stimulated T-cells. The results show the ability of MPX to define cell states based on spatial arrangement of surface proteins.

“This study highlights the importance of spatial proteomics of single cells, which could bring new insights into cell motility and activation, drug mode-of- action, and drug-target discovery based on spatial clustering and cell-to-cell communication,” said Filip Karlsson, Pixelgen Chief Technology Officer, and lead author on the paper. “We believe MPX has significant advantages over traditional technologies and will play an important role in guiding the development of therapies that aim to spatially reorganize cell surface proteins to support immune-modulatory activities, including pre-tuning immune synapses in CAR-T cells in cancer, and more broadly pave the way for a new generation of medicines and diagnostics.”

“Being able to analyze the spatial distribution and colocalization of proteins in individual white blood cells as demonstrated in this study has tremendous value for our research into how cells are regulated by cell-cell interactions and adapt their function in response to environmental factors,” added Petter Brodin, MD, PhD, Professor of pediatric immunology at Karolinska Institute and Imperial College London, and co-author of the paper. “This additional spatial dimension offers an orthogonal layer of information to the protein and mRNA abundance measurements we are used to studying and we are keen to learn what it will tell us in the future.”


About Pixelgen Technologies
Pixelgen Technologies AB was founded in 2020 by a team of passionate, experienced innovators and entrepreneurs with a vision to bring a new spatial understanding to biology by mapping cell surface proteins and their spatial inter-relationships. The company has developed Molecular Pixelation, a DNA-based visualization technology for analyzing cell surface proteins, to gain novel insights into cellular activity that will advance better medicines and diagnostics. Pixelgen is headquartered in Stockholm, Sweden.


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