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ID3 and c-Kit define the stem-like potential of T cells and their response to chronic infection and cancer

ABSTRACT: Memory CD8+ T cells and precursors of exhausted T (Tpex) cells are important therapeutic targets due to their stem-like potential that allows them to self-renew while also giving rise to large numbers of effector T cells that can provide protection from infection or uncontrolled tumor growth. Identifying T cells with stem-like potential and understanding their molecular regulation is therefore critical to improve a wide range of T cell-focused therapies ranging from vaccination to checkpoint inhibitor and chimeric antigen receptor T cell therapies. Here, we identify memory T cells based on expression of the transcriptional regulator ID3 while lacking expression of the chemokine receptor CXCR6 with superior stem-like potential to sustain T cell responses during chronic infection. Mechanistically, ID3 regulated a transcriptional network including Myb, Sell and cKit that promoted T cell stemness that was specifically required during ongoing T cell receptor stimulation. T cells lacking ID3 were unable to sustain a long-term response to chronic infection but capable of efficiently responding to acute infection. Overall, we identify a critical role for ID3 in promoting functional and long-lasting T cell responses specifically to chronic infections and highlight ID3-expressing stem-like memory T cells as a promising immunotherapeutic target to improve immune responses in chronic infections or tumors.

ORGANISM(S): Mus musculus

PROVIDER: GSE226030 | GEO | 2024/12/13

REPOSITORIES: GEO

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ID3 defines T cells with stem-like potential and sustains their response to chronic infection

Project description:Memory CD8+ T cells and precursors of exhausted T (Tpex) cells are important therapeutic targets due to their stem-like potential that allows them to self-renew while also giving rise to large numbers of effector T cells that can provide protection from infection or uncontrolled tumor growth. Identifying T cells with stem-like potential and understanding their molecular regulation is therefore critical to improve a wide range of T cell-focused therapies ranging from vaccination to checkpoint inhibitor and chimeric antigen receptor T cell therapies. Here, we identify memory T cells based on expression of the transcriptional regulator ID3 while lacking expression of the chemokine receptor CXCR6 with superior stem-like potential to sustain T cell responses during chronic infection. Mechanistically, ID3 regulated a transcriptional network including Myb, Sell and cKit that promoted T cell stemness that was specifically required during ongoing T cell receptor stimulation. T cells lacking ID3 were unable to sustain a long-term response to chronic infection but capable of efficiently responding to acute infection. Overall, we identify a critical role for ID3 in promoting functional and long-lasting T cell responses specifically to chronic infections and highlight ID3-expressing stem-like memory T cells as a promising immunotherapeutic target to improve immune responses in chronic infections or tumors.

2024-12-14 | GSE224367 | GEO

Stem-like potential of T cells in infection and cancer is regulated by ID3

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Epigenetic signature of PD-1+ TCF1+ CD8 T cells thatact as resource cells during chronic viral infectionand respond to PD-1 blockade

Project description:We have recently defined a novel population of PD-1+TCF1+virus-specific CD8 T cells that function as resource cells during chronic LCMV infection and provide the proliferative burst seen after PD-1 blockade. Such CD8 T cells have been found in other chronic infections and also in cancer in mice and humans. These CD8 T cells exhibit stem-like properties undergoing self-renewal and also giving rise to the terminally differentiated (exhausted) CD8 T cells. Here we compared the epigenetic signature of stem-like CD8 T cells with exhausted CD8 T cells. ATAC-seq analysis showed that stem-like CD8 T cells had a unique signature implicating activity of TCF (HMG family) and NF-κB (RHD family) members. In addition, transcription factor networks including Tcf7, Id3, and Bach2 were enriched in stem-like CD8 T cells. In contrast,exhausted CD8 T cells enriched accessible sites for ETS and Runx motifs in addition to a network encompassing Prdm1 and Il10. We also compared the epigenetic signatures of the two CD8 T-cellsubsets from chronically infected mice with effector and memory CD8 T cells generated after an acute LCMV infection. Both CD8T-cell subsets generated during chronic infection were strikingly different from CD8 T-cell subsets from acute infection. Interestingly, the stem-like CD8 T-cell subset from chronic infection, despite sharing key functional properties with memory CD8 T cells,had a very distinct epigenetic program. These results show that the chronic stem-like CD8 T-cell program represents a specific adaptation of the T-cell response to persistent antigenic stimulation.

2019-06-15 | GSE132110 | GEO

The role of IFN-I and IL-27 in the expansion of virus-specific CD8+ T cell subtypes during persistent infection

Project description:Chronic infection and cancer are associated with suppressed T cell responses in the presence of activating antigen. Recent work identified memory-like CD8+ T cells termed follicular cytotoxic T cells (TFC) which sustain T cell responses during persistent infection and are essential for the T-cell proliferative burst following PD1 blockade. Approaches to expand these cells are sought. We show that blockade of interferon type 1 (IFN-I) receptor leads to TFC expansion in an IL-27-and STAT1-dependent manner. IFNAR1 blockade promoted accelerated cell division and retention of TCF1 in virus-specific CD8+ T cells. We found that CD8+ T cell-intrinsic IL-27 signaling safeguards the ability of TCF1-high cells to sustain proliferation and prevents premature cell cycle exit and programmed cell death. Transcriptome analysis revealed an IL-27-regulated gene module controlling survival of activated CD8+ T cells which is enhanced in IFNAR-attenuated conditions. We further demonstrated a cell-intrinsic requirement for the IL-27 target IRF1 in TFC expansion through promoting sustained division. These findings reveal that IL-27 opposes IFN-I to uncouple cell division from effector differentiation, and suggest IL-27 signaling could be exploited to augment self-renewing T cell populations in patients with chronic infections.

2019-04-01 | GSE97139 | GEO

Expression data from sorted Id3-GFP hi Id2-YFP int and Id3-GFP lo Id2-YFP hi activated CD8 T cells

Project description:During an immune response, CD8 T cells fall along a gradient of memory potential, but the regulators of these fate decsisions are not well understood. We utlized Id3-GFP and Id2-YFP reporter mice to elucidate the role of Id3 and Id2 during early CD8 T cell differentiation by gene expression. Id3-GFP hi Id2-YFP int or Id3-GFP lo Id2-YFP hi OT-I cells were sorted into trizol at day 6 of VSV-OVA infection and analyzed by microarray

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Primary and secondary CD8 T cells during acute and chronic LCMV infection

Project description:Understanding the response of memory CD8 T cells to persistent antigen re-stimulation and the role of CD4 T cell help is critical to the design of successful vaccines for chronic diseases. However, studies comparing the protective abilities and qualities of memory and naïve cells have been mostly performed in acute infections, and little is known about their roles during chronic infections. Herein, we show that memory cells dominate over naïve cells and are protective when present in large enough numbers to quickly reduce infection. In contrast, when infection is not rapidly reduced, memory cells are quickly lost, unlike naïve cells. This loss of memory cells is due to (i) an early block in cell proliferation, (ii) selective regulation by the inhibitory receptor 2B4, and (iii) increased reliance on CD4 T cell help. These findings have important implications towards the design of T cell vaccines against chronic infections and tumors. 16 samples are analyzed: 3 replicates of secondary effector CD8 P14 T cells at day 8 post-acute lymphocytic choriomeningitis virus (LCMV) infection; 4 replicates of secondary effector CD8 P14 T cells at day 8 post-chronic LCMV infection; 4 replicates of primary effector CD8 P14 T cells at day 8 post-acute LCMV infection; and 5 replicates of primary effector CD8 P14 T cells at day 8 post-chronic LCMV infection.

2011-08-22 | E-GEOD-30962 | biostudies-arrayexpress

Single cell RNA-seq of CD4+ T cell subsets during LCMV-Armstrong infection

Project description:CD4+ memory T cells play a pivatol role in mediating long-term immunity and therefore are an important target in vaccine development. Multiple functionally distinct helper CD4+ T cell subsets can arise in response to a single invading pathogen, complicating the identification of rare memory CD4+ T cells. Here we found that expression of Id3, an inhibitor of E protein transcription factors, identified a population of cells within both the CD4+ Tfh and Th1 helper lineages that exhibited memory potential in response to secondary infection. Notably, a subset of Th1 memory cells expressing Id3 exhibited enhanced expansion upon response to pathogen, generating both Th1 and Tfh secondary effector cell populations, and displayed enrichment of key molecules associated with memory potential when compared to Id3lo Th1 cells. Thus, Id3 expression serves as an important marker of multipotent memory CD4+ T cells.

2022-07-01 | GSE175742 | GEO

RNA-seq of CD4+ Helper T cell subsets (Th1 and Tfh) during LCMV-Armstrong infection

2022-07-01 | GSE175741 | GEO

RNA-seq of memory CD4+ Helper T cell subsets (Th1 and Tfh) during LCMV-Armstrong infection

2022-07-01 | GSE175740 | GEO

The alarmin interleukin-33 promotes the expansion and preserves the stemness of Tcf-1+ CD8 T cells in chronic viral infection (RNA-Seq II)

Project description:T-cell factor 1 (Tcf-1) expressing CD8 T cells exhibit stem-like self-renewing capacity rendering them key for immune defense against chronic viral infection and cancer. Yet, the signals that promote the formation and maintenance of these memory-like CD8 T cell (CD8ML) remain poorly defined. Studying CD8 T cell differentiation in mice with chronic viral infection we identify the alarmin interleukin-33 (IL-33) as pivotal for the expansion and stem-like functioning of CD8ML as well as for virus control. IL-33 receptor- (ST2-) deficient CD8 T cells exhibit biased end-differentiation and premature loss of Tcf-1. Intriguingly, ST2-deficient CD8ML responses are restored by blockade of type I interferon signaling, suggesting that opposing IFN-I and IL-33 effects control CD8ML formation in chronic infection. IL-33 signals broadly augment chromatin accessibility in CD8ML and determine these cells’ re-expansion potential. Our study identifies the IL-33 – ST2 axis as an important CD8ML-promoting pathway in the context of chronic viral infection.

2023-04-06 | GSE210538 | GEO

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