Summary of CMS Seminar Club presentation on Friday, April 22, 2022.
Title: COVID-19-specific T cells in infection and vaccination
Speaker: Dr. Nina Le Bert, Senior Research Fellow in the Program in Emerging Infectious Diseases at Duke-NUS Medical School, Singapore.
On Friday, April 22, Dr. Le Bert gave a presentation at Fujita Health University. She showed us the importance of T cell immunity for fighting COVID-19.
Recording: For members of Fujita University, a recording of the meeting (without the discussion part) will be available at our Manabi system. Unfortunately, we cannot open the recording for a wider audience.
There were 36 participants who enjoyed the meeting. Several of them sent me e-mails, from which I am allowed to quote here:
Dr. Akihiko Nishikimi wrote: “Thank you for organizing an excellent seminar. As we are also investigating the prevalence of SARS-CoV-2 and protective immunity after vaccination among workers of our institute, her talk was highly suggestive.”
Prof. Jim Kaufman, who very recently had COVID and therefore is an immune “hybrid”—a term used by Dr. Le Bert for people who got immunity from vaccines as well as natural infection—wrote: “Thanks again, for setting up such an extremely interesting talk (unusually personal for me). I have been overwhelmed with the sheer amount of information about the immune response to COVID, to the point where I just didn’t read any more. Nina did a great job of presenting data with clear points which I could follow and understand the importance of, so please thank her again for me.”
Prof. Teruyuki Nakanishi wrote: “I enjoyed her talk and learned a lot about the importance of T cell immunity in COVID-19 virus infection because the importance of T cell immunity including nasal mucosa in COVID-19 virus infection has not been reported so much when compared to antibody responses in mass media. Particularly, I was happy to learn that they used IFNγ-ELISA Spot assay to evaluate the involvement of IFNγ-secreting T cells because our group has recently established the technique to evaluate the importance of CMI via T cells in fish immune response.”
I also found it an excellent speech, as she showed in a logical way how her group has proceeded in addressing some of the major questions in COVID-19 T cell immunity. I was especially amazed to find how they recently pushed their COVID-19 T cell research to yet another level by being able to analyze nasal T cell immunity from only nasal swabs (!!). Furthermore, Dr. Le Bert’s vivid descriptions of how they investigated the progression of (asymptomatic) COIVID-19 infections and immunity in large communities of young male migrant workers living in close quarters, provided insights that a written text cannot easily convey.
I was especially pleased about how honest, down-to-earth, and unbiased her answers to our questions were. If something is not known yet, she simply stated that. As for the question of whether, by new mutations, COVID-19 virus (SARS-CoV-2) might escape the immunity by Spike-only vaccines (as are commonly used in Japan), she said that there are no strong indications that this will happen at a large scale but that it probably wouldn’t hurt to reduce such risk by adding also better-conserved parts of the virus to the vaccine. She also mentioned that even now in some individuals the vaccines do not induce detectable T cell immunity, and showed that the local T cell immunity in some COVID-19 convalescent patients is not directed against Spike but against other proteins of the virus.
A take-home message of her presentation was that T cell immunity is strongly associated with anti-COVID-19 protection. Given that, by mutations, the virus definitely seems to be on its way to escape antibody immunity (for which it needs to make far fewer changes than for escaping T cell immunity) (e.g., Cao et al. 2022, Cele et al. 2022, and Kaleta et al. 2022), her talk was extremely important. Having such a well-spoken expert giving us a presentation on such an urgent topic was a treat.
THE CONTENTS OF THE PRESENTATION
The below summarizes large (but not all) parts of Dr. Le Bert’s presentation. In some instances, I added some extra information. Unfortunately, I could not include her work on nasal immunity, which formed a big part of her talk but has not been published yet. To members of Fujita Health University, I recommend seeing the recording, as these data on nasal T cell immunity are truly exciting and Dr. Le Bert explained them very well.
Some background information
Basic T cell immunology
Dr. Bert’s presentation was about TCRαβ T cells (from here, just “T cells”), which play a pivotal role in adaptive immunity and therefore immune memory. It depends on the type of virus whether B cells (that make antibodies) or cytotoxic T cells (which can kill virus-infected cells) are more important, and some viral diseases require both responses to be efficient.
The TCRαβ heterodimer receptors are expressed from genes that underwent random recombination during T cell development in the thymus (from which the letter “T” is derived) (Figs. 1A and 1B). This leads to individual T cells expressing unique TCRαβ receptors with which they can only screen peptide antigens if those are presented within the groove of an MHC (major histocompatibility complex) molecule (Fig. 1C). For more information on MHC molecules see the summary of a previous presentation to our CMS Seminar Club by Prof. Jim Kaufman.
B and T cell development generate a wide variety of cells with different B cell receptors (antibodies) and TCRs, respectively. Therefore, of each specific B cell clone or T cell clone there are only very few, and their proliferation (“clonal expansion”) after specific stimulation is necessary for mounting a detectable immune response. Therefore, during a first infection with a pathogen, it takes a week or so before they can play an important role, but, because the proliferation also leads to the generation of multiple long-lived memory B and T cells, they can play a bigger and more-immediate role during a later, second infection with that pathogen (which is the principle of vaccination).
There are CD4+ T cells (Fig. 3), which are important for screening peptides that are derived from extracellular (exogenous) antigens and are presented by MHC class II on professional immune cells (Figs. 2 and 3). By expressing additional surface markers and releasing cytokines, these cells can enhance (or reduce) and direct the responses of other immune cells, for example, B cells or CD8+ T cells (Fig. 3). Like the TCR molecules, CD4 also binds to (is a co-receptor for) the MHC class II molecules.
There are also CD8+ T cells (Fig. 3), which are important for screening peptides that are derived from intracellular (endogenous) antigens and are presented by MHC class I on professional immune cells as well as on most other cell types (Figs. 2 and 3). Activated CD8+ T cells can kill virus-infected cells and thereby block virus replication (Fig. 3). Like the TCR molecules, CD8 also binds to (is a co-receptor for) the MHC class I molecules.
How to Measure T cell specificity
T cell specificities are determined by the MHC+peptide combination that is bound by the TCRs on the respective T cell clone. Typically employed assays for measuring these specificities are (1) staining or stimulation with peptide/MHC tetramers or pentamers, (2) ELISpot, or (3) intracellular cytokine analysis (Hobeika et al. 2005).
Arguably, the gold standard for proving and identifying T cell specificities is to label or stimulate them with purified, recombinant multimeric (usually tetrameric or pentameric) complexes of MHC molecules plus peptide (Fig. 4). Disadvantages of this method are that it is laborious and that the MHC molecules should match (because different people have different allelic versions of the polymorphic MHC molecules). Furthermore, the method is not the most sensitive one and may fail to detect low-frequency T cell clones (e.g., Rius et al. 2018). It is also not clear to which extent the requirements for in vitro peptide/MHC-TCR binding reflect the stringencies of T cell selection in vivo.
The ELISpot method is essentially an ELISA method in which the reactive spots are counted, and its principles are explained in Fig. 5. For measuring T cell activation, the wells of an ELISA plate are coated with an antibody against a cytokine of choice that is released by activated T cells. In the ELISpot experiments that Dr. Le Bert described to us, she used antibodies against interferon-gamma (IFNγ), because this cytokine is highly expressed under conditions that promote cell-mediated cytotoxicity (when CD8+ T cells kill virus-infected cells). A layer of cells, which in the case of Dr. Le Bert’s experiments were PBMC (peripheral blood mononuclear cells), are then put in these wells and stimulated or not with an agent for a certain time period (e.g., for 18 hours). The stimulatory agents used in Dr. Le Bert’s experiments were sets of ⁓40 overlapping SARS-CoV-2 peptides of 15 amino acids long (“15-mers”), together covering some but not all SARS-CoV-2 proteins (for the principle see Fig. 6). These peptides are believed, through some not well-understood processing, to be loaded onto both MHC class I and class II molecules of antigen presenting cells, so that neighboring T cells can be stimulated. Stimulated T cells secrete cytokines, and these are bound by the antibodies coated to the ELISA plate. The cells are then washed away, and labeling for detection of the cytokines reveals spots where the cytokine-secreting cells had been located (Fig. 5); the number of the reactive spots, minus the number of spots in a control well, are considered to represent the number of activated T cells (including both CD4+ and CD8+ cells). This method is very sensitive and relatively easy to perform, and if pools of overlapping peptides are used it needs little adjustment per MHC allele of the cell donor (as most MHC alleles may pick a matching peptide sequence from the mix). The disadvantage is that it is an indirect method, and that, in the case of IFNγ analysis, not only activated CD8+ T cells and Th1 CD4+ T cells secrete IFNγ but this cytokine can also be secreted by NK (natural killer) cells and TCRγδ T cells. Most peptides won’t stimulate other cell types than their specific T cells, but this is not necessarily always the case. So, arguably, while IFNγ-ELISpot analysis is ideal for handling many samples and detecting very small numbers of T cells, important findings of the method may need some confirmation by other methods.
The intracellular cytokine analysis method for checking T cells is usually performed in a manner similar to the above-described ELISpot method in the sense that a mix of cells (e.g., PBMC) is incubated with peptides. However, this method does not include ELISA plates, and the cells themselves are analyzed by flow cytometry for cytokine expression (after intracellular staining of permeabilized cells). The advantage of this method is that the cytokine-expressing cell types can be determined. By using this method, Dr. Le Bert identified IFNγ-positive SARS-CoV-2-peptide specific CD4+ T cells as well as CD8+ T cells, and could also exclude the possibility that NK cells secreted IFNγ (Le Bert et al. 2020; Le Bert et al. 2021). However, also in this method, there remains a theoretical possibility that a stimulatory effect does not involve peptide/MHC-TCR interaction and therefore does not represent T cell specificity.
All in all, T cell analysis is difficult because the frequencies among T cells of the relevant specific T cells are very small (often <0.1%). Furthermore, as in all research, each assay method has some potential background problems, requiring the inclusion of proper control experiments. Nevertheless, the combined analysis of several research groups including that of Dr. Le Bert, using a variety of methods, has provided solid evidence for the importance of T cells in fighting COVID-19.
Tissue-specificity of T cell responses
The (major) sites of SARS-CoV-2 replication are the upper respiratory tract (nose and throat) and lower respiratory tract, each with different conditions for virus replication and a different version of mucosal (local) immunity. However, because of accessibility, most information on immune responses in COVID-19 patients and vaccinated people derives from blood analysis, representing “systemic” immunity. The systemic immune system and the local immune systems are in communication with each other but are not perfect reflections of each other. Therefore, there now is a development to focus more on the respiratory tract for analyzing immune responses or as sites of vaccination. Dr. Le Bert’s group plays an important role in that development by now being able to analyze T cells in nasal swabs. Unfortunately, I cannot show those data here as they have not been published yet, and here only summarize the data of their group based on T cell analysis using blood samples.
Indications that T cells are important for fighting COVID-19
Dr. Le Bert referred, as an example of direct evidence for the importance of CD8+ T cells as part of an immune memory response against SARS-CoV-2, to a study in macaques by McMahan et al., 2020. If in these monkeys the CD8+ T cells were depleted by anti-CD8, a re-infection with SARS-CoV-2 resulted in much higher replication of the virus (Fig. 7).
Dr. Le Bert and coworkers obtained indirect evidence for the importance of T cells in acute COVID-19 by showing that both the early onset and abundance of SARS-CoV-2-specific T cells correlate with mild disease and rapid clearance (Fig. 8) (Tan et al. 2021). This contrasted with the antibody responses, which were somewhat delayed compared to the T cell responses and on average were slightly higher in more severe cases (Fig. 8) (Tan et al. 2021). An early T cell response in mild COVID-19 disease, and a later onset of the antibody response, were later confirmed by another research group (Chandran et al. 2022).
Furthermore, Dr. Le Bert and coworkers, 2020, provided evidence for the longevity of anti-coronavirus T cell memory. Namely, they detected T cells in people who suffered SARS infection (with SARS-CoV-1) 17 years earlier that could be activated by peptides shared between SARS-CoV-1 and SARS-CoV-2. A previous study by another group had already reported that in most individuals who had recovered from SARS, SARS-CoV-1-specific memory CD8+ T cells persisted for up to 6 years after infection whereas memory B cells and antivirus antibodies generally became undetectable (Tang et al. 2011).
Dr. Le Bert also mentioned that her group found anti-SARS-CoV-2 T cell responses in vaccinated people suffering from genetic disorders that inhibit (proper) B cell (antibody) responses, which is consistent with a study by Van Leeuwen et al., 2022. The literature is still incomplete and vague on the level of COVID-19 protection that vaccination induces in such patients with B cell deficiencies, but the protection seems to be significant and may resemble that in healthy people, implying the importance of T cell memory for protection (because the specific immune memory induced by vaccines only resides in B and T cells).
T cells induced by vaccination
The Pfizer RNA vaccine (BNT162b2) induces protection from 12 days after injection of dose 1 (Fig. 9) (Polack et al. 2020). Dr. Le Bert and coworkers investigated the immune responses in people injected with this vaccine, and found that (as with natural COVID-19 infection, see Fig. 8) the T cell responses were faster than the antibody responses after dose 1 (Fig. 10) (Kalimuddin et al. 2021). At day 10, neutralizing antibodies (antibodies that do not only bind to virus proteins but also block virus infection) were still absent, but the Kalimuddin et al. 2021 study does report the ability of the day 10 antibodies to induce antibody-dependence cell-mediated cytotoxicity (ADCC, which involves killing by NK cells of SARS-CoV-2-infected cells that are bound [opsonized] by antibodies directed at viral proteins expressed at the cell membrane). So, the early protection induced by the vaccine from day 12 is more readily explained by T cells than by antibodies, but antibodies may play a role.
T cells in asymptomatic COVID-19 patients
Dr. Le Bert and coworkers were the first to show, in 2021, that asymptomatic COVID-19 “patients” have a considerable number of SARS-CoV-2-specific T cells.
They could find these completely asymptomatic patients because they monitored a large group of about 500 young male migrant workers, mostly from Bangladesh or India, who lived together in a COVID-19-affected dormitory complex. These volunteers had blood samples taken at day 0, and at 2 and 6 weeks (Fig. 11), and in this period their temperatures and oxygen concentrations were measured twice a day. Among the volunteers, there were 281 that did not show or report any COVID-19 symptoms but were seropositive (had antibodies against SARS-CoV-2) at some point during the assay period (Fig. 12A); depending on the time-point at which they were found seropositive, different groups of volunteers were selected for further analysis of their samples taken at 6 weeks (Fig. 12B).
Quantification of SARS-CoV-2-specific T cells at 6 weeks by IFNγ-ELISpot showed that these were, on average, the most abundant in the asymptomatic patients that had only recently been infected (the color red in Figs. 12B and 13 represent the same group of patients). Furthermore, also in four of the 13 investigated volunteers that were persistently serumnegative (color green in Figs. 9 and 10), T cell responses were found (Fig. 13); this may or may not relate to the cells having been isolated at an early timepoint after infection at which only T cell and not B cell responses had yet been induced to detectable levels.
Then, in the same study, Le Bert and coworkers also compared quantities of SARS-CoV-2–specific T cells between asymptomatic and symptomatic patients up to 3 months after infection, by using IFNγ-ELISpot assay, and found similar numbers of reactive T cells (Fig. 14). They also found some T cells reacting in samples from some individuals that certainly had not been previously infected with SARS-CoV-2 (group “unexposed”) as the samples had been isolated prior to 2019. Although this does not reduce the reliability and importance of finding a similar frequency of SARS-CoV-2 specific T cells in asymptomatic and symptomatic patients, my personal estimation is that most of the observed responses in unexposed individuals are not caused by common coronavirus-induced specific (cross-)TCR-pMHC memory but represent something else (“background”; Dijkstra et al. 2021).
Le Bert and coworkers, 2021, also evaluated, in both symptomatic and asymptomatic individuals at several time points after infection, the functional profile of SARS-CoV-2–specific T cells. Therefore, they quantified the cytokines IL-2 (T cell activation), IFNγ and IL-12p70 (type 1 immunity promoting CD8+ T cell function), IL-4 (type 2 immunity promoting IgA- and IgE -type antibody production), IL-1β, IL-6, and TNFα (inflammation), and IL-10 (regulatory/suppressive immunity), in an experiment as shown in Fig. 14A. Basically, they stimulated whole blood samples overnight with pools of SARS-CoV-2-derived peptides and then isolated the sera for determining their different cytokine contents by Ella machine immunoassay. A very important finding of theirs, shown in Fig. 14B, is that distinctively different cytokine profiles were found in individuals within the first four weeks after viral clearance (in case of mild or severe disease) or within four weeks after becoming seropositive (in case of asymptomatic patients), depending on them being asymptomatic or having mild or severe symptoms. The data (Fig. 14B) suggest that IFNγ and IL-2 may confer protection, possibly through activation of Th1 CD4+ T cells and CD8+ T cells, and that inflammatory cytokines like IL-1β, IL-6, and TNFα increase the severity of the disease. Dr. Le Bert also believes that the higher expression in asymptomatic patients of IL-10, which tends to have immunosuppressive functions, may be important for a well-balanced immune response against SARS-CoV-2. Thus, as we discussed before during the presentation of Dr. Wolfgang Leitner, it is not only important that an immune response is induced, but the direction of that immune response is also very critical. The finding by Dr. Le Bert that IL-6 is associated with detrimental immune responses is consistent with other COVID-19 literature (e.g., Cruz et al. 2021), although it is not so easy to explain how peptide pools can stimulate IL-6 since Dr. Le Bert found this expression to be by monocytes (Le Bert et al. 2021). The role of IFNγ is more controversial as it has been reported as being associated with both protective and detrimental responses. The finding by Dr. Le Bert of high IFNγ levels in asymptomatic patients is an extremely important argument for underlining that, at least under some conditions, IFNγ can be protective against COVID-19.
Figure 15 shows the slide in which Dr. Le Bert summarized the major findings of this important study of hers. She concludes that the combined data strongly suggest that highly functional T cells (that secrete IL-2 and IFNγ) are critical for fighting COVID-19, not only against renewed infections (in which cells of the adaptive immune system have an increased importance) but also in naïve people who had not been vaccinated or infected before.