2005-02-27 イェール大学
<関連情報>
- https://medicine.yale.edu/news-article/the-rules-of-immunity-what-decides-t-cell-fate/
- https://www.science.org/doi/10.1126/science.adn2337
KLF2はLCMV急性感染症において系統忠実性を維持し、CD8 T細胞の消耗を抑制する KLF2 maintains lineage fidelity and suppresses CD8 T cell exhaustion during acute LCMV infection
Eric Fagerberg, John Attanasio, Christine Dien, Jaiveer Singh, […], and Nikhil S. Joshi
Science Published:14 Feb 2025
Editor’s summary
CD8 T cells within a population responding to signs of disease can form several discrete states with distinct functional properties. Fagerberg et al. combined CRISPR/Cas9-gene editing with single-cell RNA sequencing to examine how the deletion of genes in mouse T cells affected the formation of these different states during immune responses. The transcription factor KLF2 was required to maintain the availability of cells with the potential to form functional effectors and suppressed cells from acquiring an exhausted phenotype after infection with acute lymphocytic choriomeningitis virus. In the context of tumors, KLF2 expression was linked to maintaining stem-like T cells and limiting terminal dysfunction. — Sarah H. Ross
Structured Abstract
INTRODUCTION
Naïve CD8 T cells have the potential to differentiate into a variety of effector and memory CD8 T cell states during an immune response. These states reflect the cells’ functional potential to fight infection, respond to immunotherapies, or cause immunopathology. Acute T cell responses are associated with highly functional effector and memory states. Conversely, chronic antigen environments, as seen in tumors and chronic infection, drive dysfunctional T cell fate decisions, termed generally as T cell exhaustion.
RATIONALE
Despite recent insights into how these divergent T cell differentiation states determine physiological outcomes, it remains uncertain how fate decisions are made and what mechanisms exist to suppress differentiation towards alternative fates and maintain lineage fidelity. High-dimensional single-cell studies have enabled deep inquiry into the spectrum of T cell differentiation states across different immune challenges, and, from this, efforts have been made to infer differentiation trajectories and their underlying transcriptional regulation. Yet, testing these predictions has traditionally been accomplished through lower-throughput knock-out and/or lineage-tracing experiments. PerturbSEQ is a technique that couples CRISPR perturbations of target genes with single-cell RNA sequencing (scRNA-seq) and enables mechanistic dissection of differentiation processes. In this study, we used perturbSEQ with the goal of understanding factors that regulate fate decisions and preserve T cell lineage fidelity.
RESULTS
We generated a differentiation space map (DSM) of the spectrum of CD8 T cell states in acute and chronic lymphocytic choriomeningitis virus (LCMV) infection across time points using scRNA-seq. Analyses across four time points revealed a linear differentiation trajectory in acute infection, whereas a bifurcation between effector and exhausted trajectories was observed in chronic infection. We then performed in vivo perturbSEQ in LCMV-specific CD8 T cells for a library of ~40 genes [largely transcription factors (TFs) and epigenetic modulators] in the context of acute LCMV infection. This experiment identified proteins that could regulate the extent to which cells differentiated along an expected memory to effector trajectory, thereby highlighting their role as a suppressor or promoter of specific T cell functions. Moreover, it elucidated KLF2 as a transcription factor that maintains effector lineage fidelity. KLF2 knockout (KO) T cells aberrantly acquired distinct features of exhaustion during acute LCMV infection. This included impaired effector and memory differentiation and function during both primary and secondary viral challenge. Epigenetic changes, both at sites of KLF2 binding and globally throughout the genome, overlapped with loci accessibility changes seen in chronic infection. Mechanistic studies showed that KLF2 was downregulated upon T cell receptor stimulation and was intrinsically required for suppression of the exhaustion-defining TF, TOX. Epistasis experiments revealed that KLF2 was also critical for enabling the function of the effector-defining TF, TBET. Investigation in tumor models pointed to a role for KLF2 in the early bifurcation of effector and exhausted differentiation trajectories as KLF2 was required to maintain a polyfunctional TCF1+ CD62L+ precursor state. KO cells less potently controlled tumors and exhibited enhanced differentiation with features of exhaustion and residence. Overexpression of KLF2 was sufficient to rescue this precursor state in tumor-draining lymph nodes as well as suppress features of exhaustion and induce effector differentiation in acute and chronic viral infection.
CONCLUSION
Our study highlighted the role of many TFs in regulating the extent to which CD8 T cells differentiate along a defined linear trajectory and revealed KLF2’s distinct role in enabling cells to remain on this effector lineage. This adds to our mechanistic understanding of T cell fate decisions and demonstrates that differentiation toward the exhaustion lineage is suppressed in acute infection. It additionally opens new questions regarding maintenance of lineage fidelity across immune contexts, where little is still known. Further, modulation of KLF2 proved useful in driving or suppressing distinct T cell functional states with potential implications for immunotherapy.
KLF2 prevents aberrant CD8 T cell differentiation in acute LCMV infection.
Naïve CD8 T cells undergo functional effector differentiation in acute LCMV infection. This effector differentiation involves KLF2-dependent TBET activity. KLF2 KO in this setting results in aberrant CD8 T cell differentiation to a TOX+ exhausted-like state. This is characterized by an epigenetic and transcriptional signature resembling hallmark features of CD8 T cells in chronic infection and results in reduced cytolytic potential and memory recall capacity. [Figure created with BioRender.com]
Abstract
Naïve CD8 T cells have the potential to differentiate into a spectrum of functional states during an immune response. How these developmental decisions are made and what mechanisms exist to suppress differentiation toward alternative fates remains unclear. We employed in vivo CRISPR-Cas9–based perturbation sequencing to assess the role of ~40 transcription factors (TFs) and epigenetic modulators in T cell fate decisions. Unexpectedly, we found that knockout of the TF Klf2 resulted in aberrant differentiation to exhausted-like CD8 T cells during acute infection. KLF2 was required to suppress the exhaustion-promoting TF TOX and to enable the TF TBET to drive effector differentiation. KLF2 was also necessary to maintain a polyfunctional tumor-specific progenitor state. Thus, KLF2 provides effector CD8 T cell lineage fidelity and suppresses the exhaustion program.
