FWF grant supports new method to study gene activity and proteins at single-cell resolution
The Austrian Science Fund (FWF) has awarded funding for a collaborative project led by Manuel Matzinger, deputy head of the Proteomics Technology Hub of IMP, IMBA and GMI and Viktoria Dorfer at the Research Center Hagenberg, University of Applied Sciences Upper Austria. The project aims to develop a workflow that allows researchers to analyse RNA and proteins from the same single cell, enabling a deeper understanding of how molecular processes shape cellular behaviour.
The project brings together expertise from across the Vienna BioCenter. Elly Tanaka (IMBA) contributes her neural tube organoid model, while Andreas Sommer (Next Generation Sequencing Facility, Vienna BioCenter Core Facilities) supports the transcriptomics work.
Cells constantly adjust which genes they express and which proteins they produce in response to developmental cues and environmental signals. While transcriptomics reveals gene activity, proteins ultimately determine cellular function. By integrating both layers of information within the same cell, the researchers aim to create a robust and scalable single-cell multiomics workflow that captures cellular states with unprecedented detail.
The team will combine automated methods for isolating single cells with improved approaches for measuring both proteins and RNA from the very same cell. In parallel, they will develop a computational platform that allows researchers to integrate and visualize these data. The software will be available as a web application and an R package, enabling scientists without specialized bioinformatics expertise to analyse their results.
Beyond developing new technology, the researchers will apply their approach to study how asymmetry arises during early nervous system development. Using neural tube organoids, they will isolate individual cells at early stages and analyse their RNA and proteins to identify the molecular signals that trigger the formation of distinct regions of the developing neural tube.
The workflow developed in this project could enable scientists to explore cellular heterogeneity across many biological systems, providing new insights into how cells diversify, organise into tissues, and respond to disease.
“Understanding how cells develop into a complex organism is one of the most fundamental questions in modern biology,” says Manuel Matzinger, deputy head of the Proteomics Technology Hub at IMP and IMBA. “While genes provide the blueprint for life, proteins ultimately determine cellular behaviour and function.” “We aim to bridge this gap by developing a new workflow that allows us to study these two layers of biology in the very same cell,” Matzinger adds. “This will give us a more comprehensive and time-resolved picture of cellular development than ever before.”
About the Vienna BioCenter Proteomics Tech Hub
The Proteomics Tech Hub, headed by Karl Mechtler and shared between three institutes at the Vienna BioCenter (IMBA, IMP and GMI), aims to advance cutting-edge proteomics methods with a strong focus on single-cell proteomics. The team establishes and designs novel protocols to improve the sensitivity of protein identification, protein quantification, and cross-linking technology.