Tracing virus-specific CD8+ T cell clonotype zonation and function in humans

Project Information

TRACE

Grant agreement ID: 101041484

DOI

10.3030/101041484

EC signature date 18 February 2022

Start date 1 June 2022

End date 31 May 2027

Funded under

• European Research Council (ERC)

Total cost

€ 1 499 932,50

EU contribution

€ 1 499 932,00

Coordinated by

KAROLINSKA INSTITUTET
Sweden

Periodic Reporting for period 1 - TRACE (Tracing virus-specific CD8+ T cell clonotype zonation and function in humans)

Reporting period: 2022-06-01 to 2024-11-30

Summary of the context and overall objectives of the project

The COVID-19 pandemic has shown how important it is to understand how our immune system fights off viruses. One key player in this battle is a type of immune cell called the CD8+ T cell, also known as a "killer" T cell. These cells are crucial because they can directly destroy cells infected by viruses. However, most of what we know about these cells comes from studying blood samples, which doesn't give us the full picture of how they work in the tissues where viruses usually spread. This project aims to fill that gap by studying these cells in different parts of the human body.

Our research will create a detailed map of CD8+ T cells that target various viruses in different tissues. Our project has three main aims. The first aim is to generate a comprehensive reference map of virus-specific CD8+ T cells across different human tissues. The second aim is to identify if different types of these T cells have unique functions in various tissues. The third aim is to determine how the environment in different tissues shapes the genetic and functional properties of these T cells. Using advanced single-cell technologies and data analysis tools, we will track individual T cell clones in organ samples from human donors. This will help us understand how these cells are spread out and how they work in different tissues, giving us important insights into their role in fighting viruses. We will also look at the genetic and functional characteristics of these tissue-resident memory T cells (TRMs) to see how their local environment affects their behavior and effectiveness.

A big part of this project focuses on SARS-CoV-2, the virus that causes COVID-19. By studying how CD8+ T cells respond to this virus in different tissues and blood, both after infection and vaccination, we hope to find ways to improve vaccines and long-term protection. Our research will also look at how existing immunity influences responses to new infections and vaccines, which is crucial for dealing with new viral threats. Besides SARS-CoV-2, we will also study immune responses to other common viruses like CMV, EBV, and the flu. This wide-ranging approach will help us build a detailed map of how CD8+ T cells respond to viruses throughout the body. The findings from this project will not only enhance our understanding of these important immune cells but also help improve vaccine design and antiviral treatments.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The goal of our project is to improve our understanding of antiviral human memory T cells, particularly how they are distributed and function in different tissues. We have made significant progress in our research.

First, we aimed to create a detailed map of virus-specific CD8+ T cells throughout the human body. To do this, we developed advanced single-cell technologies and data analysis tools. We also set up a program to collect and study paired organ samples from well-characterized donors, allowing us to trace individual T cell clones across various tissues. This effort has given us a detailed view of where these cells are located and how they function.

We have further developed methods to detect memory T cell responses to 32 different viruses from a single sample. We identified a set of viral targets and are producing special reagents to identify these for single-cell sequencing. We have recruited nearly 50 organ donors and collected a wide range of tissue samples. Our technical processes for analyzing these samples are fully operational. A pilot study focusing on T cell responses to viruses like CMV, EBV, flu, and SARS-CoV-2 has provided significant insights into the diversity and behavior of these antiviral T cells. Notably, we have published findings on T cell immunity to SARS-CoV-2, including how these T cells recognize viral variants and form unique functional characteristics after vaccination versus infection.

Second, we focused on understanding if different types of virus-specific CD8+ T cells have unique functions in various tissues. Our preliminary data showed that tissue-resident memory T cells (TRMs) can be categorized based on specific markers like CD127. We found that CD8+ T cell killing ability varies by tissue location and viral target. Using various models, we demonstrated that certain environmental cues could influence the expression of killing molecules in these cells.

Finally, we are investigating how the local tissue environment shapes the genetic and functional properties of these T cells. We have started developing organoid models and single-cell techniques to initiate studies of the genetic landscape of these T cells. These organoid models help us understand how the local environment influences T cell behavior.

Overall, we have made substantial progress in setting up the technical infrastructure, recruiting organ donors, and analyzing the collected data. Our work continues to refine methods and expand analyses, aiming to achieve the project's goals and contribute significantly to understanding human immunity.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

This project aims to significantly improve our understanding of CD8+ T cells and their role in fighting viruses. Most previous studies have focused on CD8+ T cells in blood, which doesn't fully capture how these cells work in the tissues where viruses actually replicate.
Our project will go beyond state-of-the-art by collecting and studying paired tissue samples from well-characterized human organ donors, helping us trace individual T cell clones across various tissues. This will give us a complete view of where these cells are located and how they function, helping us understand how different tissues affect T cell behavior.

By using single-cell sequencing and advanced data analysis, we will create a detailed map of CD8+ T cell responses to multiple viruses, including SARS-CoV-2. We expect to find important differences in how these cells work in different tissues, which will help us improve vaccines and develop better treatments for viral infections. We will also study how existing immunity influences responses to new infections and vaccinations. By comparing immune responses in people with different histories of viral exposure, we will learn how memory T cells reactivate and adapt to new viruses. This will help us design more effective vaccines that offer long-lasting protection. Our research will also look at the genetic and functional characteristics of tissue-resident memory T cells (TRMs) to see how they are shaped by their local environment. Understanding these processes will help us enhance the protective functions of TRMs and develop new therapies for persistent and emerging viral infections.

In summary, this project aims to provide a comprehensive and detailed understanding of CD8+ T cell responses across different tissues. By the end of the project, we expect to have created a valuable resource of data and methods that will benefit the broader scientific community and lead to new advancements in vaccine development and antiviral treatments.