By scaling up single-cell sequencing studies, scientists can discover rare cell types, better understand disease states, and track changes in cells over time. However, processing, assaying, and analyzing large numbers of single cells is costly, time-consuming, and labor-intensive.
Giovanna Prout
chief executive officer
scale bioscience
Scale Biosciences is leading the way to remove barriers to scale-up 100 million cell challengewhere they, along with several other companies and organizations, pledged to provide grants for notable single-cell research. Winners will leverage cutting-edge technology to help sequence and analyze more cells than ever before. In this Innovation Spotlight, Giovanna Prout talks about the motivation for developing this challenge to support biomedical research at the single-cell level.
What inspired you to develop this challenge?
We are driven by the success of the global scientific community in discoveries in biology. We want to provide access to new and impactful tools that can generate ideas for large-scale single-cell transcriptome studies without worrying about implementation or cost burden. Ta. This challenge was also born out of our desire to introduce a community of industry partners who can work together to make such programs a reality. By partnering with the Chan Zuckerberg Initiative (CZI), Ultima, NVIDIA, and Bioturing, we are able to offer challenge winners and non-winners free or reduced costs to execute their ambitious projects.
What currently limits single-cell research?
Single-cell research has traditionally been limited by cost and technical limitations that lead to inflexibility in how studies are designed. The technology, which was introduced almost a decade ago, is reaching its limits. Scale Biosciences is taking the baton and commercializing technology that is easy to use without sacrificing performance or reproducibility, enabling single-cell experiments on an unprecedented scale. For example, our new QuantumScale RNA platform allows processing up to 2 million cells or nuclei with the flexibility to scale from 1 to thousands of samples or conditions in an easy, streamlined workflow that takes just 1.5 days. We also introduced pricing that allows researchers to significantly scale up their experiments. The cost is less than 1 cent per cell and only $100 per sample.
Why is scale-up so important in single-cell research?
This is a very important question. Because we know that more is not always better. But in this case, it’s good. Human development, health, and disease are extremely complex. Understanding its complexity requires further research that incorporates more diversity, including age, ancestry, gender, and sample type. Scaling up experiments also facilitates large-scale complex genetic screens in drug development by allowing more conditions and replicates to be run at once, allowing for faster and more powerful target selection and validation. . Additionally, while AI-based models are trained and validated for predictive science, they must be fed with more diverse data. These themes are also reflected in the projects selected to be fully funded by the 100 Million Cell Challenge.
Why did you choose 100 million as your target number?
When we started this project, we thought 100 million cells was ambitious. Nothing like this has ever been done before. But the scientific community is pretty amazing. They showed us how much latent demand there is for large-scale projects at the right price. Still, I believe we’ve just scratched the surface of what researchers do with tools like ours.
What were the key parameters you were looking for in these proposals?
We were looking for projects that could have an impact on human health. The 50 million cell-equivalent projects selected for full funding included projects focused on four areas of biomedical research:
- Global health equity: Research across multiple continents and diverse populations across ages and ancestry.
- Disease characterization: Observe many patients and tissues over time to fully understand disease-specific mechanisms.
- Cancer biology: new approaches to understanding treatment response
- Therapeutic Innovation: New Platforms for Disease Disruption and Drug Development
How did researchers respond to this opportunity?
We have seen a tremendous response to the program, with projects totaling nearly 1 billion cells submitted by researchers from 27 countries. Many researchers study critical challenges in global health. We received over 140 unique proposals.
How has this challenge evolved over time?
The response from the research community was so strong that the challenge was expanded to fully or partially fund projects involving more than 600 million cells in total.
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This challenge truly represents an unprecedented level of industry collaboration. We originally announced a program with Ultima Genomics and NVIDIA as partners to provide grants for projects worth 100 million cells. CZI then joined, bringing new capabilities to the program and resources to fully fund 50 million cell equivalents of research. Following an overwhelming response, Bioturing joined in and the partners agreed to work together to extend partial grants to all projects that meet certain eligibility criteria, supporting research on over 600 million cells. I did.
What was the final result of this challenge?
We will present a fully-funded project at the American Society of Human Genetics meeting in Denver in November 2024, and will receive samples from program participants and return data on hundreds of millions of cells. looking forward to it.
What are some of the award-winning projects?
The selected projects span an incredible range of applications, from expanding the first global atlas of pediatric health care to investigating population-specific differences in cancer outcomes.
Below is the complete list of winners.
- Federico Gaiti, Princess Margaret Cancer Center: Elucidating the molecular dependence of glioblastoma cells involved in neuronal crosstalk
- Caleb Webber, Dementia Research Institute UK: Zebrafish whole brain disease modeling
- Sophia George, University of Miami: Cancer patient cohort tissues and PBMC samples from the African Caribbean Single Cell Network
- Kevin Matthew Byrd, Virginia Commonwealth University: Mapping the pediatric inhalation interface at single-cell resolution
- David Van Heel, Queen Mary University of London: In-depth omics of South Asian populations to improve the health of communities in the UK and around the world
- Tom Tahon, Ghent University: Molecular drivers of human T cell development
- Drew Nevin, Garvan Medical Research Institute: Identifying patients at risk for drug-induced cardiotoxicity
- Luis Barreiro, University of Chicago: Revealing the diversity of immunity in diverse human populations
- Barbara Treutlein, ETH Zurich: Predictive modeling of cell state-specific responses to small molecule perturbations in human organoids
- Zach Lewis, Allen Institute for Brain Science: sympathetic nervous system atlas
- John Tsang, Yale University/Chan Zuckerberg Biohub New York: Deciphering the immune health of the world’s population
- Konstantin Tsoanas, MIT: A protein platform to perturb human PBMCs with transcriptome reads
- Christine Distesch, University of Washington: Single-cell transcriptome analysis of sex differences in normal human development and genetic conditions with abnormal numbers of sex chromosomes
- April Foster, Wellcome Sanger Institute: Perturbation signaling for understanding human development
