Spheromers reveal robust T cell responses to the Pfizer/BioNTech vaccine and attenuated peripheral CD8+ T cell responses post SARS-CoV-2 infection

doi:10.1016/j.immuni.2023.03.005

. 2023 Apr 11;56(4):864-878.e4.

doi: 10.1016/j.immuni.2023.03.005. Epub 2023 Mar 16.

Spheromers reveal robust T cell responses to the Pfizer/BioNTech vaccine and attenuated peripheral CD8⁺ T cell responses post SARS-CoV-2 infection

Fei Gao¹, Vamsee Mallajosyula¹, Prabhu S Arunachalam¹, Kattria van der Ploeg², Monali Manohar³, Katharina Röltgen⁴, Fan Yang⁴, Oliver Wirz⁴, Ramona Hoh⁴, Emily Haraguchi⁴, Ji-Yeun Lee⁴, Richard Willis⁵, Vasanthi Ramachandiran⁵, Jiefu Li¹, Karan Raj Kathuria¹, Chunfeng Li¹, Alexandra S Lee³, Mihir M Shah³, Sayantani B Sindher³, Joseph Gonzalez⁶, John D Altman⁷, Taia T Wang⁸, Scott D Boyd⁹, Bali Pulendran¹⁰, Prasanna Jagannathan⁸, Kari C Nadeau¹¹, Mark M Davis¹²

Affiliations

¹ Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA.
² Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA.
³ Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA.
⁴ Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
⁵ Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA.
⁶ Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
⁷ Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA.
⁸ Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
⁹ Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
¹⁰ Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
¹¹ Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA; Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard, MA, USA.
¹² Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA. Electronic address: mmdavis@stanford.edu.

PMID: 36996809
PMCID: PMC10017386
DOI: 10.1016/j.immuni.2023.03.005

Spheromers reveal robust T cell responses to the Pfizer/BioNTech vaccine and attenuated peripheral CD8⁺ T cell responses post SARS-CoV-2 infection

Fei Gao et al. Immunity. 2023.

. 2023 Apr 11;56(4):864-878.e4.

doi: 10.1016/j.immuni.2023.03.005. Epub 2023 Mar 16.

Authors

Affiliations

¹ Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA.
² Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA.
³ Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA.
⁴ Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
⁵ Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA.
⁶ Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
⁷ Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA.
⁸ Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
⁹ Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
¹⁰ Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
¹¹ Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA; Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard, MA, USA.
¹² Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA. Electronic address: mmdavis@stanford.edu.

PMID: 36996809
PMCID: PMC10017386
DOI: 10.1016/j.immuni.2023.03.005

Abstract

T cells are a critical component of the response to SARS-CoV-2, but their kinetics after infection and vaccination are insufficiently understood. Using "spheromer" peptide-MHC multimer reagents, we analyzed healthy subjects receiving two doses of the Pfizer/BioNTech BNT162b2 vaccine. Vaccination resulted in robust spike-specific T cell responses for the dominant CD4⁺ (HLA-DRB1^∗15:01/S191) and CD8⁺ (HLA-A^∗02/S691) T cell epitopes. Antigen-specific CD4⁺ and CD8⁺ T cell responses were asynchronous, with the peak CD4⁺ T cell responses occurring 1 week post the second vaccination (boost), whereas CD8⁺ T cells peaked 2 weeks later. These peripheral T cell responses were elevated compared with COVID-19 patients. We also found that previous SARS-CoV-2 infection resulted in decreased CD8⁺ T cell activation and expansion, suggesting that previous infection can influence the T cell response to vaccination.

Keywords: COVID-19; Pfizer/BioNTech mRNA vaccine; SARS-CoV-2; SARS-CoV-2 variants of concern; antigen-specific T cell responses; peptide-MHC multimer; peripheral CD4(+) T cell responses; peripheral CD8(+) T cell responses; spheromer.

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Conflict of interest statement

Declaration of interests V.M. and M.M.D. are inventors on a patent application (PCT/US2021/064378) on the spheromer technology described in this work.

Figures

**Figure 1**
Vaccine elicited spike-specific CD8⁺ T cell responses (A) The experimental design to evaluate the CD8⁺ T cell response to BNT162b2 vaccination. Timeline showing sequential blood draws post vaccination (first dose [day 0] and second dose [day 21]) in HLA-A^∗02:01 and HLA-B^∗40:01 donors. The number of donors (n), age, and sex are indicated. (B–F) (B) Fourteen CD8⁺ T cell epitopes from SARS-CoV-2 spike protein were evaluated. The magnitude of CD8⁺ T cell responses to distinct SARS-CoV-2 spike epitopes in (C) HLA-A^∗02:01 and (D) HLA-B^∗40:01 vaccinees. Baseline for each epitope is shown by a dotted line, determined using pre-pandemic samples (n = 5). Each donor is represented by a dot. Fold-change in the CD8⁺ T cell response to (E) the spike protein and to (F) the dominant epitope (S691) in HLA-A^∗02:01 restricted vaccinees. (G–I) (G) Correlation between spike-specific CD8⁺ T cell response at day 42 and age in HLA-A^∗02:01 donors. The CD8⁺ T cell response dynamics to (H) the spike protein and to (I) the dominant epitope (S1016) in HLA-B^∗40:01 restrictecinees. (J) Correlation between spike-specific CD8⁺ T cell response (day 42) and age in HLA-B^∗40:01 donors. (K and M) Fraction of cytokine producing CD8⁺ T cells within (K) S691/A^∗02:01 and (M) S1016/B^∗40:01 specific CD8⁺ T cells at peak after peptide stimulation. (L and N) Fraction of cells expressing activation-induced markers (AIM) within (L) S691/A^∗02:01 and (N) S1016/B^∗40:01 specific CD8⁺ T cells at peak after peptide stimulation. Data are presented as mean ± range. The Pearson correlation coefficient and statistical significance are noted in (G) and (J). See also Figures S1 and S2.

**Figure 2**
Vaccine elicited spike-specific CD4⁺ T cell response (A) The experimental design to evaluate the epitope-specific CD4⁺ T cell response to BNT162b2 vaccine in longitudinal samples. The number of donors (n), age and sex are indicated. (B–E) (B) Five CD4⁺ T cell epitopes from SARS-CoV-2 spike protein were evaluated. The magnitude of CD4⁺ T cell responses to SARS-CoV-2 epitopes in (C) HLA-DRB^∗15:01 vaccinees. Baseline for each epitope is shown (dotted line), determined using pre-pandemic samples (n = 5). Each donor is represented by a dot. Fold-change in the CD4⁺ T cell response to (D) the spike protein and to (E) the dominant epitope (S191). (F) Correlation between spike-specific CD4⁺ T cell response (day 28) and age. The Pearson correlation coefficient and statistical significance are given. (G) Pearson correlation between the kinetics of vaccine elicited spike-specific IgG response, total spike-specific CD4⁺ T cell response (left) and DRB^∗15:01/S191 specific CD4⁺ T cell response (right). (H) Fraction of cytokine producing cells within S191/DRB^∗15:01 specific CD4⁺ T cells (day 28) after peptide stimulation. (I) Fraction of AIM+ CD4⁺ T cells within S191/DRB^∗15:01 specific CD4⁺ T cells (day 28) after peptide (S191) stimulation. Data are presented as mean ± range. See also Figures S1 and S2.

**Figure 3**
BNT162b2 vaccination and SARS-CoV-2 infection induce distinct CD8⁺ T cell response (A) The experimental design to compare the epitope-specific CD8⁺ T cell response to BNT162b2 vaccine and SARS-CoV-2 infection. Samples were matched by time points for comparison as shown. The number of subjects (n) is indicated. (B) The twenty-five evaluated CD8⁺ T cell epitopes mapped onto the SARS-CoV-2 genome. (C) The magnitude of CD8⁺ T cell responses to SARS-CoV-2 epitopes in HLA-A^∗02:01 restricted COVID-19 patients. (D) The comparison of spike and non-spike-specific CD8⁺ T cell response in COVID-19 patients. (E) The comparison of antigen-specific CD8⁺ T cell response to BNT162b2 vaccine and SARS-CoV-2 infection. Data in (C)–(E) represented as mean ± range. (F) Fraction of AIM⁺ CD8⁺ T cells in day 42 samples after spike peptide mega pool (spike MP), non-spike peptide mega pool (non-spike MP) or DMSO stimulation. Data presented as mean ± SD. (G) Total memory CD8⁺ T cell counts in vaccinees and patients. Data presented as mean ± range. (H) Antigen-specific memory CD8⁺ T cell distribution in vaccinees and patients. (CM, central memory; EM, effector memory; EMRA effector memory T cells expressing CD45RA). Data presented as mean ± range. p values were determined by Mann-Whitney test with Holm-Šídák method. See also Figures S3 and S4.

**Figure 4**
BNT162b2 vaccination and SARS-CoV-2 infection elicited CD4⁺ T cell response (A) The experimental design to compare the epitope-specific CD4⁺ T cell response with BNT162b2 vaccine and SARS-CoV-2 infection. Samples matched for comparison as shown. The number of subjects (n) is indicated. (B) The eleven evaluated CD4⁺ T cell epitopes are mapped onto the SARS-CoV-2 genome. (C) The magnitude of CD4⁺ T cell responses to SARS-CoV-2 epitopes in COVID-19 patients. (D) The comparison of spike and non-spike-specific CD4⁺ T cell response in COVID-19 patients. (E) The comparison of antigen-specific CD4⁺ T cell response to BNT162b2 vaccine and SARS-CoV-2 infection. Data in (C)–(E) are represented as mean ± range. (F) Fraction of AIM+ CD4⁺ T cells in day 28 samples after spike MP, non-spike MP or DMSO stimulation. Data represented as mean ± SD. (G) Total memory CD4⁺ T cell counts in vaccinees and patients. Data represented as mean ± range. (H) Antigen-specific memory CD4⁺ T cell distribution in vaccinees and patients. Data represented as mean ± range. p values determined by Mann-Whitney test with Holm-Šídák method. See also Figures S3 and S4.

**Figure 5**
Reduced peripheral vaccine-induced CD8⁺ T cell response in recovered COVID-19 patients (A) The experimental design to study the CD8⁺ and CD4⁺ T cell responses to BNT162b2 vaccine in individuals recovered from previous COVID-19 infection. Timeline indicating the collection of sequential blood samples from HLA-A^∗02:01, HLA-B^∗40:01 (days 21 and 42) and HLA-DRB1^∗15:01 (days 21 and 28) recovered vaccinees. The number of donors (n) is indicated. (B) Thirty-eight CD8⁺ T and eleven CD4⁺ T cell epitopes evaluated in this study are mapped onto the SARS-CoV-2 genome. The number of donors (n) is indicated. (C) The magnitude of CD8⁺ T cell responses to SARS-CoV-2 epitopes in HLA-A^∗02:01 (red) and HLA-B^∗40:01 (yellow) donors. (D) The magnitude of CD4⁺ T cell responses to SARS-CoV-2 epitopes in HLA-DRB1^∗15:01 donors. Data in (C) and (D) are represented as mean ± range. (E) The comparison of spike and non-spike-specific HLA-A^∗02:01 (red) and HLA-B^∗40:01 (yellow) CD8⁺ T cell responses. (F) The comparison of HLA-A^∗02:01 (red) and HLA-B^∗40:01 (yellow) CD8⁺ T cell responses to BNT162b2 vaccine in naive and recovered vaccinees. Data represented as mean ± range. (G and H) Fraction of (G) cytokine producing and (H) AIM expressing T cells within S691/A^∗02:01 and S1016/B^∗40:01 specific CD8⁺ T cells (day 42 samples) after peptide stimulation (S691 and S1016, respectively). (I) The comparison of spike and non-spike-specific CD4⁺ T cell response in recovered vaccinees. (J) The comparison of antigen-specific CD4⁺ T cell response to BNT162b2 vaccine in naive and recovered vaccinees. (K and L) Fraction of (K) cytokine producing and (L) AIM expressing T cells within S191/DRB^∗15:01 specific CD4+ T cells (day 28) after peptide stimulation (S191). p values were determined by Mann-Whitney test with Holm-Šídák method. See also Figure S5.

**Figure 6**
T cell epitope conservation across SARS-CoV-2 variants The fractional conservation of all predicted spike-derived T cell epitopes from the SARS-CoV-2 reference Wuhan-1 (Wu-1) strain against the indicated SARS-CoV-2 variant for (A) HLA-A^∗02:01 (B) HLA-B^∗40:01 and (C) HLA-DRB1^∗15:01 are shown. The Pango lineage for each SARS-CoV-2 variant is also mentioned. The fraction of spike epitopes from Wu-1 strain that are fully conserved in each SARS-CoV-2 variant is listed. The logograms show the conservation of all spike-derived T cell epitopes tested in this study for (D) HLA-A^∗02:01, (E) HLA-B^∗40:01, and (F) HLA-DRB1^∗15:01. The mutated residues are colored and labeled accordingly. An amino acid deletion is marked as “-.”

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References

1. Chakraborty S., Mallajosyula V., Tato C.M., Tan G.S., Wang T.T. SARS-CoV-2 vaccines in advanced clinical trials: where do we stand? Adv. Drug Deliv. Rev. 2021;172:314–338. doi: 10.1016/j.addr.2021.01.014. - DOI - PMC - PubMed
1. Polack F.P., Thomas S.J., Kitchin N., Absalon J., Gurtman A., Lockhart S., Perez J.L., Pérez Marc G., Moreira E.D., Zerbini C., et al. Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine. N. Engl. J. Med. 2020;383:2603–2615. doi: 10.1056/NEJMoa2034577. - DOI - PMC - PubMed
1. Arunachalam P.S., Scott M.K.D., Hagan T., Li C., Feng Y., Wimmers F., Grigoryan L., Trisal M., Edara V.V., Lai L., et al. Systems vaccinology of the BNT162b2 mRNA vaccine in humans. Nature. 2021;596:410–416. doi: 10.1038/s41586-021-03791-x. - DOI - PMC - PubMed
1. Goel R.R., Painter M.M., Apostolidis S.A., Mathew D., Meng W., Rosenfeld A.M., Lundgreen K.A., Reynaldi A., Khoury D.S., Pattekar A., et al. mRNA vaccines induce durable immune memory to SARS-CoV-2 and variants of concern. Science. 2021;374:abm0829. doi: 10.1126/science.abm0829. - DOI - PMC - PubMed
1. Röltgen K., Nielsen S.C.A., Silva O., Younes S.F., Zaslavsky M., Costales C., Yang F., Wirz O.F., Solis D., Hoh R.A., et al. Immune imprinting, breadth of variant recognition, and germinal center response in human SARS-CoV-2 infection and vaccination. Cell. 2022;185 doi: 10.1016/j.cell.2022.01.018. 1025–1040.e14. - DOI - PMC - PubMed

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[1] Chakraborty S., Mallajosyula V., Tato C.M., Tan G.S., Wang T.T. SARS-CoV-2 vaccines in advanced clinical trials: where do we stand? Adv. Drug Deliv. Rev. 2021;172:314–338. doi: 10.1016/j.addr.2021.01.014. - DOI - PMC - PubMed

[2] Chakraborty S., Mallajosyula V., Tato C.M., Tan G.S., Wang T.T. SARS-CoV-2 vaccines in advanced clinical trials: where do we stand? Adv. Drug Deliv. Rev. 2021;172:314–338. doi: 10.1016/j.addr.2021.01.014. - DOI - PMC - PubMed

[3] Polack F.P., Thomas S.J., Kitchin N., Absalon J., Gurtman A., Lockhart S., Perez J.L., Pérez Marc G., Moreira E.D., Zerbini C., et al. Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine. N. Engl. J. Med. 2020;383:2603–2615. doi: 10.1056/NEJMoa2034577. - DOI - PMC - PubMed

[4] Polack F.P., Thomas S.J., Kitchin N., Absalon J., Gurtman A., Lockhart S., Perez J.L., Pérez Marc G., Moreira E.D., Zerbini C., et al. Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine. N. Engl. J. Med. 2020;383:2603–2615. doi: 10.1056/NEJMoa2034577. - DOI - PMC - PubMed

[5] Arunachalam P.S., Scott M.K.D., Hagan T., Li C., Feng Y., Wimmers F., Grigoryan L., Trisal M., Edara V.V., Lai L., et al. Systems vaccinology of the BNT162b2 mRNA vaccine in humans. Nature. 2021;596:410–416. doi: 10.1038/s41586-021-03791-x. - DOI - PMC - PubMed

[6] Arunachalam P.S., Scott M.K.D., Hagan T., Li C., Feng Y., Wimmers F., Grigoryan L., Trisal M., Edara V.V., Lai L., et al. Systems vaccinology of the BNT162b2 mRNA vaccine in humans. Nature. 2021;596:410–416. doi: 10.1038/s41586-021-03791-x. - DOI - PMC - PubMed

[7] Goel R.R., Painter M.M., Apostolidis S.A., Mathew D., Meng W., Rosenfeld A.M., Lundgreen K.A., Reynaldi A., Khoury D.S., Pattekar A., et al. mRNA vaccines induce durable immune memory to SARS-CoV-2 and variants of concern. Science. 2021;374:abm0829. doi: 10.1126/science.abm0829. - DOI - PMC - PubMed

[8] Goel R.R., Painter M.M., Apostolidis S.A., Mathew D., Meng W., Rosenfeld A.M., Lundgreen K.A., Reynaldi A., Khoury D.S., Pattekar A., et al. mRNA vaccines induce durable immune memory to SARS-CoV-2 and variants of concern. Science. 2021;374:abm0829. doi: 10.1126/science.abm0829. - DOI - PMC - PubMed

[9] Röltgen K., Nielsen S.C.A., Silva O., Younes S.F., Zaslavsky M., Costales C., Yang F., Wirz O.F., Solis D., Hoh R.A., et al. Immune imprinting, breadth of variant recognition, and germinal center response in human SARS-CoV-2 infection and vaccination. Cell. 2022;185 doi: 10.1016/j.cell.2022.01.018. 1025–1040.e14. - DOI - PMC - PubMed

[10] Röltgen K., Nielsen S.C.A., Silva O., Younes S.F., Zaslavsky M., Costales C., Yang F., Wirz O.F., Solis D., Hoh R.A., et al. Immune imprinting, breadth of variant recognition, and germinal center response in human SARS-CoV-2 infection and vaccination. Cell. 2022;185 doi: 10.1016/j.cell.2022.01.018. 1025–1040.e14. - DOI - PMC - PubMed

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Spheromers reveal robust T cell responses to the Pfizer/BioNTech vaccine and attenuated peripheral CD8⁺ T cell responses post SARS-CoV-2 infection

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Spheromers reveal robust T cell responses to the Pfizer/BioNTech vaccine and attenuated peripheral CD8⁺ T cell responses post SARS-CoV-2 infection

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