Basic Mechanisms of T Cell Exhaustion

To develop truly novel approaches for immunotherapy to reverse immune dysfunction.

It is critical to understand the basic molecular mechanisms of this process.  Here we will use well-established mouse models of T cell exhaustion to interrogate pathways that initiate and sustain T cell exhaustion including signaling, metabolic and transcriptional circuits.


  • Cellular mechanism of inhibitory receptor function and synergy
  • Checkpoint blockade screens in vivo using CRISPR
  • Metabolomics of T cell exhaustion
  • Transcription factor circuitry in exhaustion
  • Epigenetics and enhancer engineering


  • Identified dysregulated metabolism as a hallmark of exhausted T cells. Published
  • Epigenetics of T cell exhaustion defined and changes upon checkpoint blockade interrogated
  • Preliminary data confirms key observations from the mouse model of exhaustion (LCMV)– validating these protocols and approaches
  • Through transcription factor (TF) network modeling we identified Tox as a candidate central regulator T cell exhaustion. Preliminary data indicate Tox regulates multiple aspects of T cell exhaustion
  • New data implicate Tox in modulation of calcium signaling in exhausted T cells.
  • CRISPR/Cas9 library targeting known epigenetic modulators has been established. Multiple inhibitors show promise in improving exhausted T cell function, survival and potency
  • Preliminary data indicate LAG-3 and PD-1 regulate distinct CD8 T cell differentiation programs
  • Testing the functional role of one of the targets, ZC3H12C, in vitro and in vivo, using retroviral overexpression and CRISPR KO approaches
  • Established quadruple adoptive transfer approach to evaluate WT, PD1 KO, LAG3 KO, PD1+LAG3 dKO T cell exhaustion. Preliminary data suggest LAG3 deficiency induces decrease persistence even in the absence of PD1. However, the addition of LAG3 deficiency does not alter the cytokine or TF profile of PD1 KO T cells
  • Preliminary data suggest prolonged PD1 blockade may reduce antigen specific T cell persistence
  • Demonstrated that IL-7 administration with anti-PD-L1 in clone 13 infection (mice) increases the number of viral specific CD8 T cells and results in an increased number of polyfunctional T cells
  • Identified Tox as a key regulator of T cell exhaustion. Found Tox to be required for induction and maintenance of the antigen specific T cell pool in chronic infection by regulating cytokine produccation, TF expression and IR expression

Scharping et al Immunity 2016

Pauken et al Science 2016

Project Participants:  John Wherry, Josephine Giles, Shin Ngiow, Omar Khan, Zeyu Chen, Junwei Shi, Jean-Christophe Beltra