T Cell Heterogeneity and Plasticity

T Cells

Key Questions

  • How does TCR signaling work?

  • How does costimulation work?

  • What does IL-2 do?

  • What are T cell subsets?

  • How do T cell subsets change?

  • How do T cells stay alive and functioning?

  • Why do we care about different types of T cells?

T Cell Heterogeneity

T cells exhibit heterogeneity, meaning they can perform many different functions.

Plasticity and Heterogeneity of T cells

  • T cells display plasticity and heterogeneity, allowing them to adapt from inflammation to healing during an immune response.

  • Cytokine profiles change during the course of infection or disease.

  • Many diseases require multiple types of immune responses, highlighting the importance of T cell adaptability.

Learning Objectives

  • Understand the difference between heterogeneity and plasticity.

  • Discuss the significance of T cell heterogeneity and plasticity in health and disease.

  • Explain the molecular mechanisms controlling T cell subset decisions.

Population Vs Single Cell

  • Example data from Anne Kelso 1999 showcasing cytokine production (IL-2, IL-4, IFN-γ, IL-10) in T cells.

Importance of T Cell Phenotypes

  • T cell phenotypes determine disease progression and patient outcomes.

  • Immune therapies aim to target specific T cell subsets.

  • A limitation is understanding the extent of T cell heterogeneity and polarization.

Inflammatory Bowel Disease

  • Analysis of T cell populations in healthy controls (HC), Crohn's disease (CD), and ankylosing spondylitis (AS).

  • Comparison of monofunctional and polyfunctional T cells within CD4+ T cells.

T Cell Subsets

  • Data showing the diversity of human peripheral Th and T regulatory cells, defined by single-cell mass cytometry.

  • Analysis includes expression of FOXP3, T-bet, GATA3, and RORC2.

  • Characterization of T cell subsets based on surface markers like CXCR5, CXCR3, CCR4, CCR6, CD161, CD25, CD127, and CD45RA.

  • Evaluation of expression of PD-1, TIGIT, CTLA-4, ICOS, CD226, LAG3, CD49B, and CD62L in different T cell subsets.

Colorectal Tumors

  • High-dimensional mass cytometric analysis reveals an increase in effector regulatory T cells as a distinguishing feature of colorectal tumors.

  • Analysis of T cell clusters in tumor samples.

Brad’s PhD Project

  • Analysis of T cell clusters in peripheral blood mononuclear cells (PBMCs), normal tissue adjacent to tumor (NTB), and tumor tissue.

  • Identification of myeloid, T cell, and B cell populations within the clusters.

  • Examination of marker expression (e.g., CD11b, CD56, PD-L1, FoxP3, Blimp-1, CD45RO, TCF1, Siglec-9, Ki67, CD3, CD123, TOX, CD66b, PD-1, CD33, CD14, CD16, CD11c, CD206, Perforin, CD19, CD64, MPO, CD4, CD1c, IDO, CD27, CD68, TIM3, CD163, CCR7, CD25, IgD, ARG-1, CD141, CD127, HLA-DR).

  • Analysis of combined tumor clusters and their marker expression profiles.

T Cell Heterogeneity and Plasticity

  • Heterogeneity: T cells can perform lots of different things.

  • Plasticity: T cells can change what they do.

T Cell Plasticity Definition

  • Plasticity: The ability of a single T cell to take on characteristics of many T cell subsets simultaneously or at different times during the course of its life cycle.

  • T cells are capable of changing their function and phenotype.

Differentiation / Polarization of T Cell Subsets

  • Previously, T cell differentiation was thought to be a terminal process.

  • However, it is now understood to be a reversible maturation process.

  • This allows cells to adopt alternate fates depending on the environment.

Terminal Differentiation

  • T cells differentiate based on early cytokine signals.

  • Master regulator transcription factors enforce the original programming.

  • Examples include:

    • Th1: IFNγ, T-bet, IL-12

    • Th2: IL-4, Gata-3, IL-4

    • Th17: IL-17, RORγt, IL-6

    • Treg: FoxP3, IL-10, TGFβ, IL-2

    • Th9: PU.1, IL-9, TGFβ, IL-4

    • TfH: Bcl-6, IL-21

Role of Other Signals

  • Other signals can reprogram the differentiation of T cells.

TCR, IL-2 and Cytokine Signals

  • TCR and CD28 signaling, along with IL-2, influence T cell proliferation, survival, and growth.

  • Polarizing cytokines determine the type of immune response and the amount of the immune response.

Control of T Cell Subsets

  • Cytokine signaling pathway (JAK-STAT) controls transcription factor activation and cytokine gene expression.

  • Examples:

    • IL-12 activates STAT4, leading to T-bet expression and IFNγ production.

    • IL-4 activates STAT6, leading to GATA3 expression and IL-4 production.

    • IL-6/TGFβ activate STAT3/STAT5 (indirectly), leading to RORγt and FOXP3 expression, and IL-17 production.

Regulation of T Cell Subsets

  1. Cytokine-mediated inhibition.

  2. Transcriptional inhibition of T cell subsets via master regulators.

  3. Epigenetic control of T cell subsets through histone modification and methylation.

  4. TCR signaling.

Cytokine Control of T Cell Subsets

  • Cytokine combinations can drive hybrid T cell phenotypes.

Plasticity Between all T Cell Subsets

  • Naive CD4+ T cells can differentiate into various T cell subsets.

  • Examples include:

    • T Reg cell

    • TR1 cell

    • T2 cell

    • T9 cell

    • TH2/T17 cell

    • T2/FH Cell

    • T2/T1 cell

    • T 17/FH cell

    • T1/T17 FH Cell

    • TH1/T17 cell

    • T1 cell

    • FH cell

Cytokine Inhibition of T Cell Subsets

  • IFNγ inhibits Th2 and Th17 differentiation.

  • IL-4 inhibits Th1 differentiation.

  • IL-17 inhibits Th1 differentiation.

Transcriptional Control of T Cell Subsets

  • During T cell differentiation toward one lineage, the other lineage fates are usually suppressed.

  • Mutual exclusivity among master transcription factors.

  • Cross-regulation through repression of transcription factors.

“Master Regulators” of T Cell Subsets

  • APC presents antigen, activating the TCR and CD28.

  • Polarizing cytokines activate JAK-STAT pathways.

  • STATs induce the expression of master transcription factors.

  • Examples:

    • Tbet – Th1

    • GATA3 – Th2

    • RORγc – Th17

    • FOXP3 - Treg

Type of Transcriptional Regulation

  1. Pioneer – initial polarizing signal (+) e.g. STATs that coordinate a cytokine signal to get transcription of more cytokines

  2. Antagonism – transcription factors competing for binding sites (-)

  3. Synergy – transcription factors finding friends to help them bind (+)

  4. Competition – transcription factors fighting over their friends (-)

  5. Redistribution – transcription factors move to new places (+, -)

  6. Modulation – transcription factors change activity of other molecules (+)

Epigenetic Control of T Cell Subsets

  • Epigenetics control activation and repression of genes.

  • Differentiated T cells divide and daughter cells keep the same differentiation program by:

    • self-reinforcing transcription factor networks

    • epigenetic mechanisms = stable and heritable program but with the ability to change

Mechanisms of Epigenetic Control

  • Two major substrates:

    • methylation of DNA (usually repressive = gene silencing)

    • chromatin/histone remodeling (activation or repression)

Evidence for Epigenetic Involvement

  • Inhibiting histone modification and observing the effects.

  • Inhibiting DNA methylation and observing the effects.

Epigenetic Control of T Cells - Histone Modifications

  • Histone modifications influence T cell differentiation.

Histone Modifications in Th1 Differentiation

  • Loss of repressive histone modifications leads to IFNγ expression in Th1 cells.

Histone Modifications in Th2 Differentiation

  • Loss of permissive histone modification prevents IFNγ expression in Th2 cells.

Epigenetic Control of T Cells - Methylation

  • Methylation typically silences gene expression.

  • Lack of methylation allows gene expression.

T Cell Receptor Signalling Strength

  • TCR affinity generates different signalling strength pathways in the cell.

  • Can lead to activation of different transcription factors and therefore different cytokine genes.

  • Tuning the receptiveness of a cell to different cytokines.

  • Inducing the expression of specific cytokine receptors.

  • Impinging directly on the activation of specific STATs.

Overview of T Cell Differentiation

  • Phase 1: Priming - TCR and costimulation in naive CD4+ T cells.

  • Phase 2: Reinforcement/terminal differentiation - Cytokines drive T helper subset decision (e.g., Th1 or Th2).

  • Signals downstream of cytokine receptors influence T helper subset decision

Summary II

  • T cells are polarized by exposure to cytokines.

  • T cell polarization is enforced by transcription factors.

  • T cell re-polarization is a normal response to a changing infection.

  • T cell re-polarization results in hybrid populations = plasticity.

  • T cell plasticity is mediated by cytokines and TCR signal strength.

Plasticity Between all T Cell Subsets

  • Overlapping signalling pathways in T cell subsets.

Summary III

  • T cell subsets are controlled at multiple levels:

    1. Cytokines

    2. Transcription factors

    3. Epigenetic mechanisms

  • How might T cell subsets be manipulated?

  • Why are T cell subsets plastic?

  • What does this mean for your lab work?

Learning Objectives

  • Understand the difference between heterogeneity and plasticity.

  • Discuss the significance of T cell heterogeneity and plasticity in health and disease.

  • Explain the molecular mechanisms controlling T cell subset decisions.

Exam Questions

  • Discuss the mechanisms of transcriptional control of T cell subsets