The Single Cell Accelerator drives VIB to the forefront of single-cell research

22 September 2018
VIB was one of the earliest adopters of disruptive single-cell technologies, boosting research in this ground-breaking field. In April 2018, the VIB ‘Single Cell Accelerator’ program was launched to aid access to multiple innovative single cell 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 into emerging single-cell technologies.

Single-cell technologies are changing life sciences research 
There has been a huge rise in the development and use of emerging single-cell technologies across the globe. These technologies have rapidly enhanced the molecular understanding of functional cell states underlying diseases such as cancer and inflammatory and neurodegenerative illnesses, which encompass the focal areas of about 50 research groups at VIB.

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 and downstream data analysis tools in house. As a result, single-cell analysis is now considered an essential and routine tool used to address fundamental research questions in about 50 research groups at VIB.

Diether Lambrechts (VIB-KU Leuven Center for Cancer Biology), one of the early adopters of the 10X Genomics Chromium platform, agrees that his research has benefited enormously from this platform: “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 for the first time.”

VIB Single Cell Accelerator 
A new initiative, the ‘VIB Single Cell Accelerator’ (SCA), was launched at the VIB seminar in April 2018. Through this initiative, VIB scientists will have access to significant additional funding in 2018-2019 to evaluate, develop and integrate emerging breakthrough single-cell technologies at VIB. The SCA will initially run for two years, and VIB groups can apply for SCA funding through the Tech Watch application process. Technology platforms will be placed in the Technology Innovation Lab (physically embedded in a host lab space, a PI’s lab or a core facility), and these projects will be managed by trained technology specialists. These experts will troubleshoot to optimize the technologies and subsequently train VIB scientists in the labs to disseminate their expertise.

Halina Novak, Technology Innovation Manager at VIB, says: “By combining disruptive single-cell platforms, technology development projects, specialized data analysis and modeling tools to process omics data, and coupling this expertise with respective research themes, this program enables VIB to excel rapidly in the single-cell field.” Areas of great interest to VIB in the SCA include spatial omics for the validation of single-cell sequencing data to localize distinct cellular subsets in situ, single-cell manipulation technologies for immune profiling, isolation, culturing, pharmacogenetics, cellular extraction/cell building and single-cell genomics.

Single-cell technology evaluation, implementation and development 
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 that will contribute to their participation in the ‘Human Cell Atlas’ (HCA) program. This international initiative seeks 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, they will contribute significantly to this program.

“Ongoing single-cell sequencing efforts and subsequent spatial omics technologies will no doubt rewrite scientific textbooks over the next decade,” Martin Guilliams asserts. “Through the HCA, we will collectively investigate individual cell subsets in all major tissues for the most prominent diseases.
This will be determined for humans as well as major model systems, revolutionizing biomedical research and ultimately bringing new cures to the clinic.”

Toon Swings, Life Sciences Technology Specialist and until recently part of the Jan Michiels Lab at the VIB-KU Leuven Center for Microbiology is particularly excited about the evolution in single-cell culturing, isolation and manipulation technologies in the field of microbiology. “This will enable scientists to study the human microbiome in unmatched detail in relation to human health conditions,” he explains.

Inspiring novel in-house analytics and modeling techniques 
Yvan Saeys (VIB-UGent Center of Inflammation Research), and Stein Aerts (VIB-KU Leuven Center for Brain & Disease Research) note that the wealth of data generated by single-cell platforms presents unprecedented opportunities for bioinformatics and data analysis. This resulted in the in-house  development of  ioinformatics 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 began work
on novel tools to gain a better understanding of 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 times are ahead,” states Yvan Saeys. “Multi-omics technologies are able to capture more and more complementary types of information from the same cell. The
spatial resolution that is already offered by some technologies will lead to novel modeling 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.”

VIB takes the lead in developing new single-cell technologies 
Pioneering VIB groups are also investing significantly in the development of single-cell technologies, such as the Stein Aerts Lab, which is now focusing on single-cell epigenomics. The Aerts Lab is also developing new approaches to capture single cells in nanoliter droplets using microfluidic devices, allowing the flexible analysis of RNA or chromatin from tens of thousands of single cells in parallel.​

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