VIB Tech Watch Innovation Lab update 10x genomics’ tech fuels single-cell studies at VIB

20 April 2018
The 10x Genomics’ GemCode Technology makes it possible to study the genetic and transcriptional information of an organism at the single-cell level. Early in its development, this technology was spotted by the VIB Tech Watch initiative, which gave the VIB scientists a competitive advantage. Over the last few months, scientists from multiple VIB research centers have used the technology to investigate biology at a scale never seen before.

Unprecedented insights at an unprecedented scale
The field of cancer biology will be significantly ,impacted by this technology. “It was previously believed that tumors form a uniform, homogeneous population,” says Diether Lambrechts (VIB-KU Leuven Center for Cancer Biology). “However, large-scale single-cell data allowed us to generate a catalog of the tumor microenvironment transcriptome at single-cell resolution. Specifically, we were able to identify multiple discrete cell populations.”

Peter Carmeliet (VIB-KU Leuven Center for Cancer Biology) agrees: “10x Genomics’ single-cell technology has allowed us to obtain unprecedented insight into the metabolic signature of tumor endothelial cell subpopulations.” Bart Lambrecht (VIB-UGent Center for Inflammation Research) is also confident that the hundreds of parameters obtained on individual cells will eventually result in the discovery of biomarkers for the successful treatment of immune-mediated diseases.

One experiment, thousands of individual cells profiled
The technology is broadly applicable and will affect multiple fields in life sciences. Abbas Jariani, PhD student in the lab of Kevin Verstrepen (VIB-KU Leuven Center for Microbiology), used the 10x Genomics GemCode to analyze yeast populations. He is enthusiastic about his first results: “We gathered transcriptome data for thousands of individual yeast cells in just one experiment!”

The same holds true for the research performed in the lab of Stein Aerts (VIB-KU Leuven Center for Brain & Disease Research), who comments on his recent work (Davie et al., 2017, BioRxiv): “The 10x Chromium allowed us to profile the transcriptome of more than 100,000 fruit fly brain cells, achieving a nearly 1x cell coverage of the entire brain. In combination with our computational method SCENIC, this dataset enabled the discovery of cell-type transcription factor networks at single-cell resolution.”

An enthusiastic response
The value of this platform for the VIB scientists is reflected in the fact that multiple VIB centers have now incorporated the 10x Genomics GemCode into their workflows. In addition, interest in this technology is continuously increasing, illustrated by the more than 100 scientists who attended the 10x Genomics VIB workshop in October 2017, held in Ghent.

VIB looks forward to the ongoing collaboration, in which the newest applications for this technology will be explored. Halina Novak, VIB Tech Watch and Innovation Manager: “The Chromium System and GemCode technology have multiple applications, from single-cell genomics, whole genome and exome sequencing to the assembly of full-length single-cell V(D)J sequences for investigating the immune system. Ultimately, this will allow many researchers across life sciences to rapidly advance their research.”


Generating novel research questions
Multiple new research questions and accompanying technological challenges arise from the new single-cell sequencing studies. For example, the recent discovery of numerous discriminatory tumor biomarker panels favor targeted sequencing approaches to increase throughput while lowering cost. Even more so, the interest in spatial localization of RNA and proteins in situ to validate the single-cell sequencing data is increasing. Below is a list of a few companies on the Tech Watch radar that provide advanced solutions for next-generation single-cell applications:

AKOYA BIOSCIENCES has developed the CODEX technology platform (will be evaluated by the ‘VIB Tech Watch Flexible Innovation Lab’ from March 2018) to visualize up to 50 proteins in situ using oligo-labeled antibodies and a fluidic staining device (Y Goltsev, et al., Biorxiv, 2017).

IONPATH has developed a technology for in situ detection of up to 50 proteins, DNA and/or RNA in parallel at subcellular resolution based on mass spectrometry (Angelo et al., Nat Med, 2014).

FLUIDIGM has developed the Hyperion system, which combines CyTOF with imaging capabilities, allowing in situ detection of up to 37 proteins at subcellular resolution.

MISSIONBIO has developed the Tapestri platform to perform ‘SiC-seq’ for targeted single cell gene panel DNA sequencing (Lan et al., 2017, Nat. Biotech) and ‘Abseq’ for single cell protein profiling using droplet microfluidic barcoding (Shahi et al., 2017, Sci Rep).

We are watching 70 additional companies active in single-cell analysis technologies. Please reach out to the Tech Watch team if you would like to know more. To keep up with the hottest technology trends in Life Sciences, follow the Tech Watch team on Twitter: @VIBTechWatch.

Sofie De Prijck and Niels Van Damme (VIB-UGent Center for Inflammation Research)