Recently, Bernd Bodenmiller from the University of Zurich gave a webcast for nature.com on using mass cytometry to study single cell signaling networks in biology and disease. The talk consisted of an introduction, an overview of the Fluidigm CyTOF instrument, a summary of Bernd’s recent paper in Nature Biotechnology, and his current work with collaborators in ovarian cancer. If you missed it, the talk is still hosted on Nature’s webcast page and is also summarized for you below.
The talk started with Dr. Bodenmiller talking about his current focus and a list of what attributes would make an ideal method for examining cell signaling. He stated that the ideal method would have four things: the ability to detect a high number of conditions, comprehensive measurement of signaling network states, the ability once the data were collected to correlate signaling network functions and phenotype to the signaling network state, and finally, single cell resolution.
He has used the CyTOF throughout his post-doctoral work, for his Nature Biotechnology paper, and is actively using it for his current projects and so explains how it works with a degree of familiarity. The CyTOF allows for minimal compensation between channels, and so many more parameters can be acquired when compared to a traditional flow cytometer.
These attributes make the instrument an attractive option for doing exploratory or big picture work in signaling networks, but Bernd and his collaborators found that when attempting very large experiments the time and cost associated is prodigious. To help mitigate both of these difficulties, they developed a technique called Mass-tag Cellular Barcoding which by labeling each well of a 96 well plate with a unique combination of isotopes, allows them to stain and run 96 wells in one tube, saving time and reagents. Subsequently, they have applied these methods to many biological and clinically relevant problems, including ovarian cancer.
In the Q&A section, Bernd answered technical questions concerning mass cytometry and single cell barcoding. Furthermore, he emphasized that most antibodies used fluorescence flow cytometry can be used for mass cytometry. He also commented on the utility of mass cytometry for evaluating pharmacokinetic and pharmacodynamic properties of cellular inhibitors.
Finally, a couple questions were posed about data analysis and management, which are summarized below.
Q: Can SPADE be used on traditional flow cytometry files?
A: Yes, SPADE can be used on flow and mass cytometry data. You can download and install SPADE, or run and visualize SPADE on Cytobank’s servers.
Q: For a cellular biologist, data analysis can seem overwhelming. For institutions that are interested in starting mass cytometry, would you consider establishing close collaborations with biostatisticians and computer scientists?
A: More and more software tools are used to analyze mass cytometry data, including Cytobank, where dose titration and SPADE analysis can be performed. There do exist implemented, publicly available methods out there as well. Everyone has specific biological questions, and sharing data with bioinformaticians is a good way to do this.
Bernd summarized his talk by concluding that mass cytometry, coupled with effective analysis, is a powerful new tool for screening and systems biology.
Our goal at Cytobank is to build a platform that enables such analyses. These include providing high level overviews of large complex datasets using advanced visualizations and algorithms with direct links to the underlying data and associated annotation delivered to your web-enabled device. Thus providing the ability to collaborate across multiple discplines and institutions.
If you’ve got questions about mass cytometry, analysis algorithms like SPADE, or would just like us to take a look at your data, please don’t hesitate to send an email to email@example.com.