Application for ISAC Council
Jonathan M. Irish, Ph.D., Assistant Professor, Vanderbilt University, USA
: I trained in cancer biology, immunology, and computational biology at Stanford with Garry Nolan during my Ph.D. research and with Ron Levy during my postdoctoral studies. My lab at Vanderbilt focuses on how signaling specifies cell identity in healthy tissues and human diseases. For my thesis research, I created a new technique to measure signaling responses in individual cancer cells and applied this to show that cytometry measurements of signaling stratify leukemia patient clinical outcomes (Irish et al., Cell
2004). I also helped write code to create heatmaps of cytometry data that ultimately grew into the web-based analysis platform Cytobank (Kotecha, Krutzik, and Irish, Current Protocols in Cytometry
2010). I co-founded Cytobank Inc. and remain involved as a board member and advisor. As a postdoc, I trained in clinical tumor immunology research and applied techniques I had created to dissect B cell receptor (BCR) signaling in lymphoma and healthy B cells, revealing lymphoma negative prognostic (LNP) cells (Irish et al., Blood
2010). With the support of a K99/R00 grant from NIH/NCI, I transitioned to independence and moved to Nashville to found my lab at Vanderbilt University. Vanderbilt's early investment in mass cytometry (CyTOF) and emphasis on collaborative translational research helped launch my lab and adapt phospho-flow, mass cytometry, and single cell analysis methods for solid tumors, including melanoma, lung cancer, and brain tumors (Nicholas et al., Cytometry A
2016; Leelatian et al., Cytometry B
2017; Diggins et al., Nature Methods
2017). Last year, I launched Vanderbilt’s paired shared resources, the Cancer & Immunology Core and the Mass Cytometry Center of Excellence. Lab website: http://my.vanderbilt.edu/irishlab/
Cytometry has been an essential, driving part of my scientific research for 20 years, and I enjoy developing new methods and teaching cytometry techniques. I still remember being nervous about whether the signaling experiments would work at the first phospho-flow hands-on workshop I helped teach, the 2003 EMBO Practical Course in Advanced Cytometry (it went well, with some group-specific variations). Since then, I’ve taught hands-on courses on phospho-flow, mass cytometry, and advanced analysis, including new course modules at Vanderbilt emphasizing cytomic approaches (e.g. “Bioinformatics II: Discovery Oriented Data Science” and “Computational Immunology”). Teaching these courses has also led to great opportunities to collaborate on cytometry. For example, I met Kanutte Huse, Ph.D. at a phospho-flow course I helped organize in Bergen, Norway in 2008. Kanutte spent a productive year as a Visiting Research Fellow in my lab at Vanderbilt in 2012, published multiple collaborative manuscripts with our group, and was recently named an ISAC Marylou Ingram Scholar. My lab member and I have enjoyed doing webinars with Fluidigm and Expert Cytometry and speaking on cytometry at CYTO, AAI, Keystone Symposia, and other conferences. I was especially honored to be invited to give a Frontiers talk at CYTO in 2015. I’ve been able to take on roles at CYTO including Speaker, Session Chair, and Workshop organizer, and I now hope to take on a growing leadership role as part of the ISAC Council.
Vision for Cytometry & ISAC
: Cytometry is a truly cross-platform ‘omic technology, and it has been thrilling to see quantitative single cell biology technologies emerge, mature, and push the boundaries of the number and type of features that can be measured. I look forward to a time when I will be able to use cytometry to reveal and characterize a new population of cells in a clinical patient sample and then search for this population in an online atlas of previously observed cell types. Maybe this atlas would indicate others have seen cells with similar features and would indicate where these types of cells are found, what they look like, what genes they express, and how they signal. Or perhaps it would indicate the cells are a specific type of leukemia and would suggest a drug known to have efficacy against those cells. I can see the tools for this developing now, and I believe ISAC and Cytometry should play a central leadership role in this growing field. Critical to this future will be continued support for sharing of well-annotated data and the construction of tools that enable integration and analysis across single cell data types and instrument platforms. It will also be vital to train a new generation of cytometry data scientists who can program and who are still in touch with the experimental hypotheses, instrument setup details, and clinical details. As part of the ISAC Council, I will promote this vision of cytometry as a central pillar of basic and clinical cell biology and encourage communication and integration across clinical, methodological, and computational elements of cytometry.