Our projects propose a highly integrated approach to revealing the biology of regulation and differentiation of Tfh CD4 T cells, Th1 CD4 T cells, CTL CD8 T cells, and memory CD8 T cells, making use of high throughput genetic screens of T cell response in mice to multiple viral infections. T cell differentiation into various effector cells,and the capacity to differentiate into memory cells, are important parts of adaptive immunity to pathogens and cancers. Transcription factors are central regulators of these differentiation processes. The identification of key transcription factors (TFs) regulating different pathways of CD4 and CD8 T cell differentiation have been central to understanding the biology of these cells. However, it is abundantly clear that TFs do not act in isolation and many TFs may be important inducers or repressors of a T cell differentiation pathway. The biggest challenge to studying TF network biology is that experimental manipulation of more than 1 factor at a time under controlled conditions has not been generally feasible, particularly in primary cells in vivo. Therefore, the focus on 1 gene at a time has been an experimental necessity for decades, and the large majority of analyses of TF networks have been correlative or computational. The generation of double and triple knockout mice is excessively time consuming. Furthermore, the compelling FANTOM study highlights the importance of moderate changes in TF expression for most cellular differentiation processes, not complete on-off switches. That has always been a clear limitation of knockout mice, and it continues to bias our perception of lymphocyte differentiation and function. Current experimental approaches are insufficient to dramatically advance our understanding of CD4 and CD8 T cell differentiation and function, and lymphocyte biology in general, due to conceptual, time, and monetary limitations. Therefore, our approach to this serious problem has been focused on generating an experimental approach whereby we can modulate and test 100 genes in parallel for their roles in antiviral T cell responses in vivo, using a new shRNAmir vector based approach. We have established this system, and are now able to perform genetic screens, in vivo, in primary CD4 or CDS T cells, probing differentiation and function. The three Projects vigorously pursue an understanding of antiviral CD4 and CD8 T cells, linked by the theme: what transcription factors regulate these cells and how do they do so?

Public Health Relevance

Vaccines are one of the most cost effective and extraordinarily successful medical intervention. While immunology has been an incredibly successful field of research, particularly in the second half of the 20th century, immunology has not turned vaccinology into a field of rational vaccine development. We should be able to do much better in the future. We will pursue an in depth knowledge of the transcription factor regulation of protective antiviral CD4 and CD8 T cell responses to facilitate an understanding of Tfh cells and CTLs for rationale vaccine design.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Program--Cooperative Agreements (U19)
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Special Emphasis Panel (ZAI1-ZL-I (J1))
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Miller, Lara R
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La Jolla Institute
La Jolla
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Chen, Runqiang; BĂ©langer, Simon; Frederick, Megan A et al. (2014) In vivo RNA interference screens identify regulators of antiviral CD4(+) and CD8(+) T cell differentiation. Immunity 41:325-38
Crotty, Shane (2014) T follicular helper cell differentiation, function, and roles in disease. Immunity 41:529-42