Understanding the complex networks behind a functional adaptive immune system

How does a T cell know that it is a T cell? How does it know what to do to protect the body from infection and disease? The answers are through a complex network of signals and interactions that scientists are teasing apart in the laboratories at St. Jude.

T cells are specialized cells of the adaptive immune system, the part of the immune system that responds to, and learns from, infection and disease. T cells are formed and educated in an organ called the thymus. Educated T cells are then released into the rest of the body to patrol and survey for viral, bacterial or tumor-derived antigens. Antigens are fragments of protein that T cells use to identify a foreign invader or diseased cell. For example, if a T cell recognized a piece of virus on a cell, it will activate and ramp up the immune response.

Problems with T cells can therefore cause major diseases. If they do not activate enough, simple viral or bacterial infections can overwhelm the immune system. If they activate too much, the T cell and its offspring will cause autoimmune issues. T cells need to activate to an appropriate amount – not too much, not too little, but at just the right level. They also need to activate against the correct antigens, making sure it is foreign invaders or diseased cells, not healthy, ‘self’ proteins.  

T-cell development and education form the basis of ensuring that the immune system will function properly. The development and function of T cells are driven by a complex system of signals that come from outside of the T cell itself. This network is comprised of many elements. Some are cell-to-cell interactions and factors, such as signaling molecules called cytokines. Another set of elements are nutrients from the environment. Altogether, the network rewires signaling and metabolic pathways inside of the T cell. These signals dictate how T cells develop and subsequently mount appropriate immune responses to infections or tumors.

Research by St. Jude scientists has unraveled the complex networks shaping T-cell development and identity in response to infections and tumors. These studies establish the framework for developing future therapies for these and other diseases.  

Charting the networks for innate-like T-cell development

When T cells develop in the thymus, they mature into different cell types (lineages). These lineages include conventional and innate-like T cells, which recognize distinct antigens and have discrete functions. When innate-like T cells detect an antigen, they rapidly produce an inflammatory response to start the immune attack against the pathogen or tumor. However, when these cells go awry, they can also trigger autoimmunity or other inflammatory diseases.

An important component of innate-like T-cell development is the T cell receptor (TCR). The TCR is a protein on all T cells, which allows them to recognize antigens. TCR signaling guides innate-like T cell development, when these cells acquire specific functions. How TCR signals in the thymus imprint cells with unique functional fates remains unclear, but may lead to new treatments for diseases caused by imperfections in this process.

Research led by Hongbo Chi, PhD, St. Jude Department of Immunology, revealed that the protein PTEN acts as a brake for the formation of certain innate-like T cells. Specifically, PTEN puts a brake on the production of cells that produce the cytokine IL-17 (called type-17 cells).

The St. Jude group’s work showed that TCR signals trigger decreased PTEN expression in immature immune cells present in the thymus. When PTEN was specifically deleted in developing T cells, more type-17 cells were generated. Mechanistically, PTEN restrained expression of receptors for a different cytokine, IL-23, on immature T-cells (precursors). Deletion of IL-23, or its downstream signaling target STAT3, prevented type-17 cell generation  when PTEN was removed, reversing the result of the earlier deletion experiment.

Chi’s team then explored the possible connections to several of the many PTEN-associated diseases in mouse models. They found that deleting the IL-17 receptor or IL-23 improved the survival of certain mouse models. These models can be used to study a spectrum of disorders called PTEN Hamartoma Tumor Syndrome (PHTS), which arise due to inherited mutations in the PTEN gene.

This work, published in Nature Cell Biology, reveals a two-step process for type-17-cell development, and highlights that immunotherapies targeting type-17 cells or IL-23- or IL-17-mediated signaling may benefit PHTS patients.

T-cell fate decisions are driven by metabolic signaling

Immunometabolism is the interplay between cellular metabolism and the immune system. St. Jude scientists are uncovering the impacts of bidirectional communication between metabolism and the immune system

For example, in the same Nature Cell Biology, Chi’s group established that type-17-cell development was associated with dynamic changes in cellular metabolism. Blocking two key proteins involved in metabolic regulation (mTORC1 or mTORC2) stopped metabolic reprogramming in developing immune cells and type-17-cells triggered by PTEN deletion. The work shows a clear connection between T cell development and immunometabolism.

Immunometabolism also provides an answer to a long-standing question in immunology: why does a T cell become a short-lived effector cell (Teff) versus a long-lived memory cell (Tmem)?

Teff cells are the frontline combatants against an infection. However, they burn out quickly. Tmem cells serve as the body’s strategists. They are the long-term memory used to fight against previous infections. However, if the body only produces Tmem cells, then there will be no frontline fighters against infection. Uncovering mechanisms for regulation of Tmem versus Teff  cell fate may reveal new ways to modulate T-cell responses in various diseases.

Immunometabolism guides Tmem or Teff development. When a T cell recognizes an antigen, it divides into two daughter cells. Those daughter cells then rapidly divide, proliferating to amplify the immune response against the detected antigen. How does one cell produce cells that become two different lineages of cells (Tmem or Teff)?

St. Jude researchers found nutrients and cellular metabolism regulate whether a T cell becomes a pro-inflammatory, Teff or a long-lived, Tmem. A transcription factor called c-Myc is key and shapes the metabolic state of conventional T cells.

Metabolic signaling hubs set the stage for asymmetric cell division

To facilitate Teff or Tmem generation, c-Myc becomes concentrated on one side of the cell. If the cell is like a cookie, c-Myc is like chocolate chips all placed on one half. Then the cell divides at the center – like a knife through the center of the cookie. One daughter cell has most of the chocolate chips (c-Myc). The other has almost none. This process, where a protein is concentrated in one part of the cell before it splits into two daughter cells, is essential for ‘asymmetric cell division.’ After the cell splits, one cell contains more c-Myc and becomes a Teff. The other cell has less c-Myc and differentiates into a Tmem.

Scientists led by Douglas Green, PhD, St. Jude Department of Immunology chair, defined the events preceding asymmetric cell division. They found the metabolic signaling network that concentrated c-Myc on one side of the cell.

Green’s group used super-resolution microscopy techniques to show that a protein complex involved in nutrient-dependent signaling and metabolic regulation, mTORC1, interacts with another protein that controls if c-Myc is made within the cells (eukaryotic initiation factor 4F, eIF4F).

The complex of mTORC1 and eIF4F is required for c-Myc protein synthesis. In essence, mTORC1 checks if the cell has the enough of and the correct components to make c-Myc. Upon T-cell activation, mTORC1 interacts with eIF4F. This mTORC1–eIF4F complex moves toward the immune synapse (where antigen recognition occurs), followed by additional cellular machinery that is required to make c-Myc.

Green’s group found that inhibiting eIF4F prevented the asymmetric distribution of c-Myc. Further, inhibiting eIF4F also promoted Tmem generation. This work, published in Molecular Cell, suggests that where proteins are located in the cell and their interactions with metabolic signaling molecules like mTORC1 and c-Myc dictate T-cell fate decisions.

Together, these studies establish new mechanisms underlying how metabolism-associated signaling specifies T-cell fate decisions.

Boosting T-cell-mediated immunity to infections and cancer

Immunotherapy is now a frontline approach for cancer treatment. Current immunotherapies include infusing patients with tumor-reactive T cells or checkpoint blockade therapies that can reprogram dysfunctional T cells into better tumor-killing cells. St. Jude scientists are uncovering new ways to improve the ability of T cells to combat tumors.

In their recent collaboration published in Nature, researchers in Green and Chi’s groups showed that c-Myc co-segregates with a protein complex called c-BAF during asymmetric cell division.  The c-BAF complex is a molecular platform – a sort of docking station for other proteins.

Using a technique to systematically knockdown the expression of genes called a CRISPR screen, the researchers showed that loss of c-BAF complex components or its transient inhibition increased the generation of Tmem cells. These findings establish a role for c-BAF in Teff or Tmem fate.

T cells that are deficient in c-BAF complex provide better protection from bacterial reinfection. This observation makes sense because Tmem cells provide long-lived protection from pathogen reinfection and serve important roles in vaccine effectiveness. Tumor-reactive T cells with Tmem-like properties can also better persist in tumors to help destroy them. The researchers showed that transient inhibition of c-BAF dramatically boosted tumor killing in mouse models.

This study uncovers a molecular pathway in T cells whose targeting may improve vaccine efficacy and cancer therapy.

Altogether, this work reveals how different cellular and molecular networks orchestrate T-cell fate and function in diverse contexts. These findings represent significant advancements in understanding how the cells that help us battle infectious diseases and cancer are generated and how to treat different diseases.