Understanding T Cell Phenotype and Persistence in Human Disease through TCR Sequences


CD8+ T cells, also known as cytotoxic T cells, are a type of white blood cell that play a crucial role in the immune system. They are one of the two main types of T cells, the other being CD4+ T cells (helper T cells).  CD8+ T cells primarily target cells in the body that are infected by viruses or sometimes bacteria. They recognize infected cells through their T-cell receptors, which bind to specific antigens presented on the surface of these cells. Once they recognize and bind to an infected cell, CD8+ T cells release toxic substances that can kill the infected cell. This process is crucial in controlling and eliminating infections. They are also important in identifying and destroying cancer cells. They can recognize tumor antigens presented on the surface of cancer cells and contribute to the immune system’s anti-tumor response. After an infection, some CD8+ T cells become memory cells. These cells remain in the body and can quickly respond to the same antigen if it appears again, providing a faster and more effective response to subsequent infections by the same pathogen. While CD8+ T cells are essential for immune defense, they can also play a role in autoimmune diseases, where they may attack the body’s own cells. In organ transplants, CD8+ T cells can contribute to the rejection of the transplanted organ. Due to their ability to kill infected or cancerous cells, CD8+ T cells are a key target in various immunotherapies. Strategies to enhance their function are being explored in cancer treatment and in the control of chronic infections.

In a new study published in Cell Reports, Professor James Heath and his team at the Institute for Systems Biology conducted a detailed examination of CD8+ T cells, focusing on how T Cell Receptor (TCR) sequences and environmental factors influence the phenotype and persistence of these cells in the context of human disease. The authors analyzed 679 CD8+ T cell clonotypes from 68 COVID-19 patients. These patients were selected for their expression of the HLA-A*02:01 allele, a common allele in humans. The study was longitudinal, with data collected at diagnosis (T1), several days post-infection (T2), and during convalescence (2–3 months post-infection, T3). The TCR sequences of these cells were scrutinized to understand their role in determining T cell phenotype. These T cells were specific to antigens from SARS-CoV-2, CMV, and influenza, each associated with different immune responses during COVID-19. The team highlighted the diversity of phenotypes within CD8+ T cells targeting the same antigen, underscoring the influence of TCR sequences.

The authors used tools like GLIPH2 and TCRdist to match TCR sequences from the dataset with known pMHC-TCR pairs and to compare TCR gene usage and amino acid sequence information. The team conducted multi-omics analyses, including transcriptomics, to gain insights into the functional differences between TCR sequence-derived clusters. One of the main findings was that TCR sequences had a greater impact on T cell phenotype than environmental factors. They observed that T cells with similar TCR sequences exhibited similar phenotypes, even when targeting the same antigen.  The study also showed that TCR sequences influenced the persistence of antigen-specific CD8+ T cells post-infection. The research compared the influence of TCR sequences with other environmental factors, such as cytokines and dendritic cell interactions.

They also examined bystander-activated T cells, finding that TCR sequences were still primary in determining phenotype, with environmental factors playing a secondary role.  The study integrated various data types and validated findings with existing literature, ensuring robustness in their conclusions.  The team quantitatively compared the relative importance of TCR sequences and environmental factors in shaping T cell phenotype. This assertion is supported by the observation that TCR sequence similarity correlates with phenotype similarity among CD8+ T cells. By examining T cells specific to SARS-CoV-2, CMV, and influenza antigens, the research highlights the significance of TCR sequences in shaping diverse phenotypic landscapes, even among T cells targeting the same antigen. The data suggest that TCR sequences play a critical role in defining T cell behavior, including their persistence during and after infection. While the study emphasizes the dominance of TCR sequences in shaping T cell phenotype, it does not completely discount environmental influences. The research meticulously compares TCR sequences with various environmental factors, such as cytokines and MHC class I presentation. This comparison reveals a nuanced picture: while TCR sequences are more influential, environmental factors still play a role, albeit a secondary one, in determining T cell phenotype.

In the case of bystander-activated T cells during SARS-CoV-2 infection, the study finds that TCR sequences remain the primary influencer of phenotype. However, environmental cytokine signals, particularly inflammatory cytokines like IL-18, also significantly impact these cells. This finding underscores the complexity of the immune response, where both intrinsic (TCR sequences) and extrinsic (environmental signals) factors interweave to determine T cell behavior.

The study’s findings have profound implications for our understanding of immune responses in human diseases. It suggests that the TCR sequence can be a crucial determinant of a T cell’s fate, influencing its effectiveness in combating infections and its role in immune-related disorders. This insight opens new avenues for therapeutic interventions, where manipulating TCR sequences or modulating environmental factors could enhance immune responses against pathogens and tumors.

While the study is comprehensive, it acknowledges limitations, such as the focus on specific viral antigens and one HLA allele. Future research expanding the scope to include diverse antigens and HLA alleles is necessary for a more generalized understanding. Furthermore, the study sets a foundation for exploring the mechanistic aspects of how TCR sequences influence T cell phenotype and behavior, which could be crucial for developing targeted immunotherapies. In summary, the study by Professor James Heath and his team represents a comprehensive and detailed exploration into the roles of TCR sequences in shaping the behavior of CD8+ T cells in human disease, particularly in the context of COVID-19. Their findings have significant implications for understanding immune responses and developing targeted therapies in various diseases.

Understanding T Cell Phenotype and Persistence in Human Disease through TCR Sequences - Medicine Innovates
Image Credit: Cell Reports 2023;42(11):113279.

About the author

James R. Heath, PhD
President & Professor
Institute for Systems Biology

Dr. James R. Heath is President and Professor at Institute for Systems Biology in Seattle. Heath also has Affiliate Faculty appointments at the University of Washington Bioengineering, Physics and Chemistry departments. Formerly, he was the Elizabeth W. Gilloon Professor of Chemistry at Caltech, Professor of Molecular and Medical Pharmacology at UCLA, and served as co-director of the Parker Institute for Cancer Immunotherapy at UCLA.


Chen DG, Xie J, Su Y, Heath JR. T cell receptor sequences are the dominant factor contributing to the phenotype of CD8+ T cells with specificities against immunogenic viral antigens. Cell Rep. 2023;42(11):113279. doi: 10.1016/j.celrep.2023.113279.

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