# Phenotypic, Functional and Transcriptional Heterogeneity in T Cell Exhaustion

> **NIH NIH R01** · NORTHWESTERN UNIVERSITY · 2023 · $400,000

## Abstract

ABSTRACT
T cell exhaustion is a differentiation state that is marked by the loss of effector function and increased
expression of inhibitory receptors such as PD-1. Although virus-specific CD8 T cells are commonly considered
as a homogeneous population that gradually become exhausted over time, recent research has clearly
demonstrated that a CXCR5hi TCF-1hi subset is serving as a self-renewing progenitor population that can give
rise to a more terminally exhausted CXCR5lo TCF-1lo subset. To better dissect the heterogeneity of “exhausted”
CD8 T cells, the lab applied single cell RNA-seq (scRNA-seq) to the chronic LCMV infection and identified
three major subsets of virus-specific CD8 T cells that are phenotypically, functionally and transcriptionally
distinct. Not only had the lab validated the existence of these subsets of T cells experimentally by flow
cytometry, more advanced computational analyses were also performed to further predict their core
transcriptional networks and developmental trajectories. Collectively, the findings reveal that a TCF-1hi
progenitor subset can give rise to either a truly exhausted PD-1hi subset or a newly identified functional effector
population that is named CX3CR1hi subset. This discovery laid a solid framework that allows testing of how
extracellular signals and intrinsic genetic circuits regulate the formation and function of these three subsets of
CD8 T cells. More importantly, it provides unprecedented opportunities to explore the possibility of generating
more functional CX3CR1hi cells from TCF-1hi progenitors to overcome T cell exhaustion. This conceptual
breakthrough is obviously applicable to control over chronic viral infection as well as cancer. Intriguingly, the
preliminary study has also demonstrated that CD4 helper T cells, possibly through producing IL-21, are critical
for TCF-1hi  CX3CR1hi transition. This led to the hypothesis that inflammatory cytokines (such as CD4-
derived IL-21) modulate the cellular, functional and transcriptional diversity of virus-specific CD8 T cells during
chronic LCMV infection. Blocking antibodies, RNA interference and genetic deletion models will be used to
further dissect how inflammatory cytokines and transcriptional networks regulate heterogeneity in T cell
exhaustion. Furthermore, the lab proposes to redirect CD8 T cell differentiation away from “exhaustion” by
providing additional “CD4 help”, either alone or in combination with PD-1 blockade. The lab will test if providing
IL-21 producing CD4 T cells through adoptive transfer could drive TCF-1hi progenitor cell differentiation into
functional CX3CR1hi effector cells. Overall, knowledge gained from this research will provide mechanistic
insights into how to redirect the formation of functional effector T cells and simultaneously limit T cell
exhaustion for improved viral control over chronic infection.

## Key facts

- **NIH application ID:** 10743327
- **Project number:** 7R01AI148403-04
- **Recipient organization:** NORTHWESTERN UNIVERSITY
- **Principal Investigator:** WEIGUO CUI
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $400,000
- **Award type:** 7
- **Project period:** 2022-11-18 → 2024-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10743327

## Citation

> US National Institutes of Health, RePORTER application 10743327, Phenotypic, Functional and Transcriptional Heterogeneity in T Cell Exhaustion (7R01AI148403-04). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10743327. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*