High speed fluorescence image-enabled cell sorting
Science 21 January 2022
10.1126/science.abj3013
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Cell sorting enters a new dimension
A new breakthrough technology, combining cell sorting and imaging, allows revolutionary insights into biological processes
Since its invention over 50 years ago, flow cytometric cell sorting has been one of the most potent tools in the biologist’s arsenal. It allows researchers to isolate cells of interest from complex mixtures, a process critical to understanding how cells function. This method has now received a massive upgrade, thanks to a technology described in a study led by researchers at EMBL Heidelberg and BD Biosciences, now published as a cover story in Science.
Developing novel technologies is central to the life sciences. Expanding this toolset allows researchers to perform more informative experiments and accelerates the development of treatments for diseases.
With traditional flow cytometry, researchers could so far only isolate cells on the basis of simple properties, such as protein expression levels. With the introduction of the new high-throughput image-enabled cell sorting (ICS) platform, developed by BD Biosciences and road-tested by EMBL Heidelberg, researchers can now capture and analyse high-resolution rapid-fire snapshots of cells, allowing them to isolate cells based on features from image data, such as where a protein or biomarker is localised in a cell. Such features provide rich information of the inner workings of a cell and were previously invisible to the flow cytometer.
Researchers of EMBL’s Steinmetz and Cuylen groups along with the Flow Cytometry Core Facility used this new method to develop novel experimental strategies and apply them to ground-breaking applications. From separating out cells in different phases of cell division to conducting rapid genome-wide screens – this study greatly expands the range of questions life sciences researchers can ask.
Sorting using cellular ‘snapshots’
Each of the approximately 37 trillion cells in our body is unique: they come in different shapes and sizes and express genes at different levels and localisations to fulfil the diversity of cellular functions. Changes in such properties are often associated with diseases. ICS provides researchers with a new way to investigate these differences by isolating cells with specific properties that could so far only be analysed through imaging.
“We’ve been longing for years to have a system that would allow us to picture each cell before sorting according to measurements from such images,” said Malte Paulsen, former Head of EMBL’s Flow Cytometry Core Facility, and currently Head of Platforms and Laboratory, DanStem Institute, University of Copenhagen, Denmark. “This is exactly what ICS achieves at a very high throughput.” The entire process of data acquisition, image reconstruction, image analysis, and sorting occur within microseconds, allowing ICS to work at speeds up to 15,000 cells per second.
EMBL has been the first institution in the world to put this novel technology to the test in several innovative applications. In one such application, the researchers used ICS to isolate cells from different phases of mitosis, the universal process by which cells divide and which, when deregulated, can cause cancer or developmental disorders.
Within minutes of ICS run time, the authors were able to enrich thousands of cells from each stage of mitosis with very high purity. “I was truly amazed when I saw the first sorts of the different mitotic stages,” said Sara Cuylen-Haering, one of the corresponding authors of the study. “Until now, this had been impossible, and it will allow exciting downstream studies of the isolated stages.”
Peeking inside genomes
Another advantage of this new technology lies in the field of functional genomics. Here, genetic screens allow researchers to figure out which of the 18,000 genes in our genome contribute to a specific cellular phenotype. Combining genetic screens with image-based readouts is extremely powerful as it can provide rich insights into processes at subcellular scale. While such screens have been time-consuming and technologically challenging so far, ICS significantly expands their scope, enabling researchers to ‘look under the hood’ of each cell.
To demonstrate this, the EMBL team used ICS to study the NFkB pathway, which is central to cellular immunity. By disrupting the function of all human protein-coding genes in cultured cells and then sorting these cells using the ICS system, the authors identified several novel regulators of the pathway.
“Even for heavily studied pathways like that of NFkB, we could discover new elements in addition to recapitulating almost all of the known genes,” said Daniel Schraivogel, lead author of the study. “Identifying new gene functions can be game changing for biomedical research; such revelations can explain disease mechanisms and lead to novel drug targets.”
“The potential to carry out genomic screens with microscopic resolution is extremely exciting as it enables us to identify functions for many more elements of the genome,” said Lars Steinmetz, a corresponding author on the study. “The speed of this technology also accelerates the potential for scientific discovery – the entire process of a genome-scale screen can now be decreased to hours rather than days or weeks.”
Nurturing industry-academia collaborations
This study is emblematic of one of EMBL’s core missions – to actively engage in technology transfer and industry relations. “This project would not have been possible in an academic or industry setting alone,” said Steinmetz. “In this paper, we brought these two arms of science together and demonstrated a technology that promises to advance our ability to collect functional information for every part of the genome.”
In addition to genomics research, cell biology, and immunology, the new technology will have applications in fields such as infection biology and planetary biology, two themes in EMBL’s new programme, ‘Molecules to Ecosystems’.
“The development of ICS, which uses BD’s novel CellViewTM Image Technology, represents a culmination of more than a decade of work by a truly multidisciplinary team of more than 100 scientists and engineers,” said Eric Diebold, worldwide vice president of R&D for BD Biosciences and a corresponding author of the paper. “This joint publication between EMBL and BD Biosciences is a fantastic example of how academia and industry can partner together to accelerate scientific and technological progress for the benefit of research and human health.”
