Launch of Single Cell Accelerator drives VIB to forefront of single cell research

25 July 2018
VIB is one of the earliest adopters of disruptive single-cell technologies to boost research in this ground-breaking field. The VIB ‘Single Cell Accelerator’ program is being launched to aid access to multiple innovative platforms and to foster technology development tools. This new program will run through VIB’s Tech Watch initiative and will inject additional funding and technological support in emerging single-cell technologies. This will enable VIB to establish its position at the forefront of this rapidly moving research field. Janssen is the first pharma company to collaborate with VIB in the Single Cell Accelerator, showcasing the great value of this initiative.
Single-cell technologies are changing Life Science research
Recently there has been a huge rise in emerging single-cell technologies across the globe. These technologies have rapidly enhanced the molecular understanding of functional cell states underlying diseases such as cancer, inflammatory and neurodegenerative illnesses; which are the focus area of about 50 research groups at VIB. Toon Swings, from the VIB-KU Leuven Center for Microbiology (lab of Jan Michiels), is particularly excited about the evolution in single-cell culturing, isolation and manipulation technologies in the field of microbiology, and states that this “will enable scientists to study the human microbiome in unmatched detail in relation to human health conditions.”
Back in 2016, the VIB Tech Watch team invested in one of the first 10X Genomics Chromium platforms in Europe, enabling single-cell RNA sequencing. Since then, VIB has been working at the cutting edge of the single-cell field by testing emerging applications and developing complementary technologies in house, as well as downstream data analysis tools. As a result, single-cell analysis is now considered an essential and routine tool for understanding and addressing fundamental research questions. Diether Lambrechts (Science Director of the VIB-KU Leuven Center for Cancer Biology), one of the early-adaptors of the 10X Genomics Chromium platform, explains that his research highly benefited from this platform since “the large-scale single-cell data allowed us to generate a catalog of the tumor microenvironment transcriptome at single-cell resolution, enabling us to identify multiple discrete cell populations.”
Single Cell Accelerator to boost cutting edge single-cell research
To remain at the forefront of this cutting-edge single-cell field, VIB launches a new initiative: the ‘Single Cell Accelerator’ (SCA). Halina Novak, Technology Innovation Manager at VIB, states that “through this initiative, significant additional funding will be injected to evaluate, develop and integrate emerging breakthrough single-cell technologies. Areas of great interest include spatial omics for validation of single-cell sequencing data to localize the distinct cellular subsets ‘in situ’, single-cell manipulation technologies for immune profiling, isolation, CRISPR screens, culturing, pharmacogenetics, cellular extraction / cell building and single-cell genomics”.
Janssen first industrial partner to plug into Single Cell Accelerator
VIB’s expertise in the single-cell field is also of great value for Biotech and Pharma, and long-term collaborations are being established in the SCA.  Janssen Pharmaceutica NV, part of the Janssen Pharmaceutical Companies of Johnson & Johnson, is the first pharma partner in the SCA. “This collaboration will help us to combine forces to develop and evaluate emerging single-cell technologies, which we hope will allow both parties to excel rapidly in the single-cell field,” says Silvie Van den Hoecke, SCA project manager. 
Single-cell technology evaluation, implementation and development in and beyond VIB
Martin Guilliams and Charlotte Scott from the VIB-UGent Center for Inflammation Research will use the SCA initiative to investigate spatial and multi-omics technologies which will contribute to their participation in the ‘Human Cell Atlas’ (HCA) program, an international initiative to characterize all cell types in the human body at the single-cell level, which will serve as a basis to understand human health and disease. By profiling healthy and diseased liver samples at the single-cell level, Martin Guilliams and Charlotte Scott will contribute significantly to this program, hereby adding that “on-going single-cell sequencing efforts and subsequent spatial omics technologies will no doubt rewrite scientific textbooks over the next decade. In the HCA we will collectively investigate individual cell subset in all major tissues (liver, brain, lung, eye, placenta, etc.) and for the most prominent diseases (cancer, asthma, hepatitis, etc.) will be determined for the human but also for all major model systems, revolutionizing biomedical research and ultimately bringing new cures to the clinic.”
Yvan Saeys (VIB-UGent Center for Inflammation Research), and Stein Aerts (VIB-KU Leuven Center for Brain & Disease Research) note that the wealth of data generated on the single-cell platforms presents unprecedented opportunities for bioinformatics and data analysis. This resulted in the ‘in-house’ development of bioinformatics pipelines, including gene regulatory network analysis (SCENIC, Aerts lab), lightning-fast single-cell visualization tools (SCope, Aerts lab), and automated flow analysis (FlowSOM, Saeys lab). The latter has recently shown to be one of the best performing methods for automated cell type identification for flow and mass cytometry data.

More recently, the group of Yvan Saeys started to work on novel tools to have a better understanding on the cell developmental dynamics, using single-cell data. Their large-scale benchmarking study comparing such algorithms attracted a lot of attention at the most recent Human Cell Atlas meeting in Hinxton. Even more exciting time are ahead, states Yvan Saeys since “multi-omics technologies are able to capture more and more complementary types of information from the same single cell. The spatial resolution that is already offered by some technologies will lead to novel modelling tools that will allow us to better study cell dynamics and intercellular communication, and I think this is one of the most appealing prospects offered by these new technologies.” Moreover, pioneering VIB groups are also significantly investing in the development of single-cell technologies, for instance in the lab of Stein Aerts, who is now focusing on single-cell epigenomics of single cells. The Aerts lab is also developing new approaches to capture single cells in nanoliter droplets using microfluidic (lab-on-a-chip) devices, allowing flexible analysis of RNA or chromatin from tens of thousands of single cells in parallel.
More info on the VIB Single Cell Accelerator via  

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