7 June 2021

Single cell proteomics detects heterogeneity in complex cell systems

new study

In a newly published paper scientists from BRIC/ DanStem, Erwin M. Schoof and Benjamin Furtwängler et al. present a comprehensive mass spectrometry-based single-cell proteomics workflow that enables the characterization of complex cellular systems by quantifying the expression of over 1000 proteins in single-cells.

In this study the scientists composed the workflow using the state of the art mass spectrometry technology combined with a FACS compatible sample preparation and computational data analysis pipeline. They subsequently benchmarked the workflow to investigate its capabilities to detect changes in protein expression between different cell types. Finally, they applied the workflow to an exciting leukemia model system where they were able to successfully describe the cellular hierarchy and differentiation trajectories based on the single-cell protein expression data and even find evidence for an unexpected alternative trajectory.

In this study, we demonstrate that single-cell proteomics is ready to be scaled up to match current single-cell RNA sequencing methods, with the advantage of providing meaningful information about protein levels. The readout of the protein expression is important as these molecules ultimately fulfil the function of the gene, and mRNA is only an intermediate product in the cell which may not correctly match protein levels. Furthermore, with the integration of FACS in our workflow, we add another dimension of single-cell readout that has proven to be very valuable for deciphering complex cellular systems. Additionally, our computational pipeline provides the tools needed to make sense of this multidimensional data.

Professor Bo Porse

Similar to single-cell RNA sequencing, the introduction of a new analytical technology might facilitate new findings in many areas of biology. Large-scale characterizations of complex cellular systems using single-cell proteomics and potentially in combination with multi-omics approaches might reveal previously unknown cell states or differentiation trajectories. Additionally, measuring differences of protein and RNA expression, might reveal important post-transcriptional gene regulatory mechanisms. For example, the hematopoietic system is immensely important for the human health and it is maintained by an interplay of many different cell types serving specific functions. Treatment of diseases thereof, like acute myeloid leukaemia, remains challenging, as the underlying mechanisms have yet to be fully understood. Single-cell proteomics might add the additional dimension of information that is needed to elucidate the mechanisms of such malignancies.

The potential of single-cell proteomics has been revealed multiple times and incremental technological improvements were extensively discussed. Nonetheless, bringing these parts together in such a comprehensive manner and benchmarking the workflow with an experimental setup that closely resembles its future application will likely be a very important step in moving this field forward.

Professor Bo Porse
In the future the scientists want to apply the single-cell proteomics workflow to the hematopoietic system in the bone marrow and characterize health and disease on protein level and compare these results with other -omics approaches. Moreover, they continuously work on technological improvements to further increase the proteome depth of the workflow.
Schoof, E. M., Furtwängler, B., Üresin, N., Rapin, N., Savickas, S., Gentil, C., Lechman, E., Keller, U., Dick, J. E. and Porse, B. T. (2021) Quantitative single-cell proteomics as a tool to characterize cellular hierarchies. Nature Communications, 12.

*Mass spectrometry is an analytical tool useful for measuring the mass-to-charge ratio (m/z) of one or more molecules present in a sample.  These measurements can often be used to calculate the exact molecular weight of the sample components as well. Typically, mass spectrometers can be used to identify unknown compounds via molecular weight determination, to quantify known compounds, and to determine structure and chemical properties of molecules.

The Porse group