T cells – the Unsung Heroes of the Anti-SARS-CoV-2 Immune Response?
T cells are critical for immunity against viruses and understanding their response to SARS-CoV-2 will be critical for scientists to design effective vaccines. However, recent attention has focused on antibodies – the other arm of the adaptive immune response. This week, we will shine a spotlight on how researchers are using a diverse set of computational, immunological, and single-cell tools to decipher the role of SARS-CoV-2 specific T cells. Could T cells be the key to defeating COVID-19?
Bioinformatics Predict Targets for SARS-CoV-2-Specific T Cells
Early in the pandemic when data on the immune response to SARS-CoV-2 was scarce, researchers relied on bioinformatics to predict potential SARS-CoV-2 T cell epitopes – which are short viral peptides recognized by the T cell receptor.
A study in Cell Host and Microbe used two independent computational methods to find SARS-CoV-2 peptides with a high likelihood of being targeted by T cells. First, the authors mined existing data for original SARS-CoV peptides known to be recognized by T cells from SARS patients. Alignment of these peptides’ sequences to the SARS-CoV-2 genome identified their SARS-CoV-2 equivalents or best matches. For the second approach, the authors used algorithms to scan the SARS-CoV-2 genome and predict peptide sequences with the highest potential as T cell targets. In the end, both methods – sequence alignment and algorithm prediction – led to the identification of the same peptides. These peptides are now synthesized and used for various research applications.
Viral peptides are commonly used to identify virus-specific T cells through tetramer staining. Tetramers loaded with SARS-CoV-2 peptides can bind to T cell receptors that recognize those peptides. Since the tetramers are labeled with a fluorescent marker, they allow researchers to detect virus-specific T cells by flow cytometry.
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Multiplex Immunoassays Classify the T Cell Response in COVID-19 Patients
In addition to tetramer staining, peptides can also be used to stimulate virus-specific T cells. When T cells with immunological memory of SARS-CoV-2 are presented again with the same viral peptides, they will express specific activation markers. Two studies published in Cell and Science Immunology examined the blood of SARS-CoV-2-infected individuals, and they looked for T cells expressing these activation markers following SARS-CoV-2 peptide stimulation. Out of the combined 30 people analyzed, almost all of them had SARS-CoV-2 peptide-reactive CD4+ and CD8+ T cells. Disease in the patients studied ranged from mild to severe, suggesting most people infected with SARS-CoV-2 – even those with light symptoms – generate a virus-specific T cell response to some degree.
Though activation markers reveal the presence of virus-specific T cells, these markers don’t tell us how the cells respond. One way to characterize the functional response of peptide-stimulated CD4+ T helper cells is to measure their cytokine production. In both of these studies, the researchers utilized BioLegend’s LEGENDplex™ T Helper Cytokine Panel to simultaneously measure 12 cytokines released by T cells from patient blood. They discovered that the cytokines produced by virus-specific CD4+ T cells were predominantly of the Th1 type – such as IFN-γ and IL-2. Though cytokines of other T helper types were also detected, they were produced at relatively low levels and only observed in T cells from patients with more severe disease.
Grifoni et al. discovered the presence of T cells specific for multiple SARS-CoV-2 proteins in 70-100% of infected individuals. Image source: Grifoni et al. 2020 Cell, DOI: https://doi.org/10.1016/j.cell.2020.05.015
Using these two “read-outs” – activation markers and cytokines – the researchers made two more notable discoveries about SARS-CoV-2-specific T cells.
First, T cells from COVID-19 patients recognized multiple SARS-CoV-2 proteins, and they did not show a strong preference for the spike as they do for other coronaviral infections. The researchers detected T cells reactive to at least 6 out of the 25 proteins encoded by SARS-CoV-2 in patient blood. Based on this data, the authors concluded that vaccines eliciting T cells against multiple viral proteins may be more effective than vaccines eliciting T cells against just a single target.
Second, up to 60% of the SARS-CoV-2-negative people analyzed also had SARS-CoV-2-specific T cells. This suggests that people who have been previously infected with other coronaviruses – such as ones causing common colds – can develop cross-reactive T cells against SARS-CoV-2. Though unproven, the researchers speculate that these cross-reactive T cells may offer some level of protection against SARS-CoV-2. In support of this hypothesis, influenza studies have shown T cells responding to the seasonal flu could cross-react with the pandemic H1N1 strain, and people who had these cross-reactive T cells suffered less severe H1N1 disease. More research is needed to know whether cross-reactive T cells are protective against COVID-19.
Learn more about how you can characterize T cell responses, cytokine storm, or other immune markers during SARS-CoV-2 infection with our LEGENDplex™ multiplex immunoassays.
Single-Cell Sequencing Finds Expanded CD8+ T Cells in SARS-CoV-2-Infected Lungs
Another approach for evaluating the T cell response to SARS-CoV-2 is to phenotype individual cells from patient samples. A study published in Nature Medicine used single-cell transcriptome sequencing to characterize lung T cells from nine COVID-19 patients. By looking at the T cell receptor gene transcripts in single T cells, the researchers tracked how many T cells were derived from a single clone in each patient. Severe COVID-19 was associated with less clonal expansion and more heterogeneity of CD8+ T cells when compared with moderate cases. Though the sample size was small, the authors suggest their observations help us understand T cell phenotypes associated with recovery from COVID-19.
Future single-cell studies will help to pinpoint protective T cell clones, and the exact viral peptides they recognize. This would better inform the design of effective vaccines, especially since recent research has shown correlations between SARS-CoV-2-specific T cell numbers and neutralizing antibody titers.
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- Grifoni A et al. A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2. Cell Host and Microbe (2020). DOI: 10.1016/j.chom.2020.03.002
- Grifoni A et al. Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals. Cell (2020). DOI: 10.1016/j.cell.2020.05.015
- Weiskopf D et al. Phenotype and kinetics of SARS-CoV-2–specific T cells in COVID-19 patients with acute respiratory distress syndrome. Science Immunology (2020). DOI: 10.1126/sciimmunol.abd2071
- Liao M et al. Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19. Nature Medicine (2020). DOI: 10.1038/s41591-020-0901-9
- Ni L et al. Detection of SARS-CoV-2-Specific Humoral and Cellular Immunity in COVID-19 Convalescent Individuals. Immunity (2020). DOI: 10.1016/j.immuni.2020.04.023