Assessing Predictive Value of SARS-CoV-2 Epitope-Specific CD8+ T-Cell Response in Patients with Severe Symptoms
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Cohorts
2.2. PBMC Isolation and Serum Samples
2.3. HLA Typing
2.4. SARS-CoV-2 Epitope Selection and MHC I Dextramer Reagents
2.5. Flow Cytometry Assays
2.6. In Vitro Expansion of SARS-CoV-2-Specific T CD8+ Cells
2.7. Detection of SARS-CoV-2 Spike-Specific Antibodies
2.8. Statistical Analysis
3. Results
3.1. Ex Vivo Detection of SARS-CoV-2 Epitope-Specific CD8+ T-Cell Response during Acute Infection and Recovery
3.2. Functionality of SARS-CoV-2-Specific CD8+ T Cells during the Convalescent Phase
3.3. COVID-19 Vaccination Elicited a Higher CD8+ T Cell-Mediated Immune Response Than Severe Infection
3.4. The Initial Cellular Response Provides Evidence of Post-Acute Sequelae to SARS-CoV-2 Infection
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Chen, N.; Zhou, M.; Dong, X.; Qu, J.; Gong, F.; Han, Y.; Qiu, Y.; Wang, J.; Liu, Y.; Wei, Y.; et al. Epidemiological and Clinical Characteristics of 99 Cases of 2019 Novel Coronavirus Pneumonia in Wuhan, China: A Descriptive Study. Lancet 2020, 395, 507–513. [Google Scholar] [CrossRef] [PubMed]
- Vigón, L.; Fuertes, D.; García-Pérez, J.; Torres, M.; Rodríguez-Mora, S.; Mateos, E.; Corona, M.; Saez-Marín, A.J.; Malo, R.; Navarro, C.; et al. Impaired Cytotoxic Response in PBMCs From Patients With COVID-19 Admitted to the ICU: Biomarkers to Predict Disease Severity. Front. Immunol. 2021, 12, 665329. [Google Scholar] [CrossRef] [PubMed]
- Oronsky, B.; Larson, C.; Hammond, T.C.; Oronsky, A.; Kesari, S.; Lybeck MReid, T.R. A Review of Persistent Post-COVID Syndrome (PPCS). Clin. Rev. Allergy Immunol. 2021, 64, 66–74. [Google Scholar] [CrossRef] [PubMed]
- Ruan, Q.; Yang, K.; Wang, W.; Jiang, L.; Song, J. Clinical Predictors of Mortality Due to COVID-19 Based on an Analysis of Data of 150 Patients From Wuhan, China. Intensive Care Med. 2020, 46, 846–848. [Google Scholar] [CrossRef] [PubMed]
- Alwan, N.A. A Negative COVID-19 Test Does Not Mean Recovery. Nature 2020, 584, 170. [Google Scholar] [CrossRef] [PubMed]
- Rydyznski Moderbacher, C.; Ramirez, S.I.; Dan, J.M.; Grifoni, A.; Hastie, K.M.; Weiskopf, D.; Belanger, S.; Abbott, R.K.; Kim, C.; Choi, J.; et al. Antigen-Specific Adaptive Immunity to SARS-CoV-2 in Acute COVID-19 and Associations with Age and Disease Severity. Cell 2020, 183, 996–1012.e19. [Google Scholar] [CrossRef] [PubMed]
- Shahbaz, S.; Xu, L.; Sligl, W.; Osman, M.; Bozorgmehr, N.; Mashhouri, S.; Redmond, D.; Rosero, E.P.; Walker, J.; Elahi, S. The Quality of SARS-CoV-2-Specific T Cell Functions Differs in Patients with Mild/Moderate versus Severe Disease, and T Cells Expressing Coinhibitory Receptors Are Highly Activated. J. Immunol. 2021, 207, 1099–1111. [Google Scholar] [CrossRef] [PubMed]
- Grifoni, A.; Weiskopf, D.; Ramirez, S.I.; Mateus, J.; Dan, J.M.; Moderbacher, C.R.; Rawlings, S.A.; Sutherland, A.; Premkumar, L.; Jadi, R.S.; et al. Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals. Cell 2020, 181, 1489–1501.e15. [Google Scholar] [CrossRef]
- Le Bert, N.; Tan, A.T.; Kunasegaran, K.; Tham, C.Y.L.; Hafezi, M.; Chia, A.; Chng, M.H.Y.; Lin, M.; Tan, N.; Linster, M.; et al. SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature 2020, 584, 457–462. [Google Scholar] [CrossRef]
- Sekine, T.; Perez-Potti, A.; Rivera-Ballesteros, O.; Strålin, K.; Gorin, J.-B.; Olsson, A.; Llewellyn-Lacey, S.; Kamal, H.; Bogdanovic, G.; Muschiol, S.; et al. Robust T Cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19. Cell 2020, 183, 158–168.e14. [Google Scholar] [CrossRef]
- Sureshchandra, S.; Lewis, S.A.; Doratt, B.M.; Jankeel, A.; Coimbra Ibraim, I.; Messaoudi, I. Single-cell profiling of T and B cell repertoires following SARS-CoV-2 mRNA vaccine. JCI Insight 2021, 6, e153201. [Google Scholar] [CrossRef] [PubMed]
- Salgado Del Riego, E.; Saiz, M.L.; Corte-Iglesias, V.; Gordillo, B.L.; Martin-Martin, C.; Rodríguez-Pérez, M.; Escudero, D.; Lopez-Larrea, C.; Suarez-Alvarez, B. Divergent SARS-CoV-2-specific T cell responses in intensive care unit workers following mRNA COVID-19 vaccination. Front. Immunol. 2022, 13, 942192. [Google Scholar] [CrossRef] [PubMed]
- Long, Q.X.; Liu, B.Z.; Deng, H.J.; Wu, G.C.; Deng, K.; Chen, Y.K.; Liao, P.; Qiu, J.F.; Lin, Y.; Cai, X.F.; et al. Antibody responses to SARS-CoV-2 in patients with COVID-19. Nat. Med. 2020, 26, 845–848. [Google Scholar] [CrossRef] [PubMed]
- Jurtz, V.; Paul, S.; Andreatta, M.; Marcatili, P.; Peters, B.; Nielsen, M. NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data. J. Immunol. 2017, 199, 3360–3368. [Google Scholar] [CrossRef] [PubMed]
- Song, C.Y.; Xu, J.; He, J.Q.; Lu, Y.Q. Immune dysfunction following COVID-19, especially in severe patients. Sci. Rep. 2020, 10, 15838. [Google Scholar] [CrossRef] [PubMed]
- Rha, M.S.; Shin, E.C. Activation or exhaustion of CD8+ T cells in patients with COVID-19. Cell Mol. Immunol. 2021, 18, 2325–2333. [Google Scholar] [CrossRef] [PubMed]
- Heim, K.; Neumann-Haefelin, C.; Thimme, R.; Hofmann, M. Heterogeneity of HBV-Specific CD8+ T-Cell Failure: Implications for Immunotherapy. Front. Immunol. 2019, 10, 2240. [Google Scholar] [CrossRef]
- McKinney, E.F.; Lee, J.C.; Jayne, D.R.; Lyons, P.A.; Smith, K.G. T-cell exhaustion, co-stimulation and clinical outcome in autoimmunity and infection. Nature 2015, 523, 612–616. [Google Scholar] [CrossRef] [PubMed]
- Radziewicz, H.; Ibegbu, C.C.; Fernandez, M.L.; Workowski, K.A.; Obideen, K.; Wehbi, M.; Hanson, H.L.; Steinberg, J.P.; Masopust, D.; Wherry, E.J.; et al. Liver-infiltrating lymphocytes in chronic human hepatitis C virus infection display an exhausted phenotype with high levels of PD-1 and low levels of CD127 expression. J. Virol. 2007, 81, 2545–2553. [Google Scholar] [CrossRef]
- Takahashi, T.; Ellingson, M.K.; Wong, P.; Israelow, B.; Lucas, C.; Klein, J.; Silva, J.; Mao, T.; Oh, J.E.; Tokuyama, M.; et al. Sex differences in immune responses that underlie COVID-19 disease outcomes. Nature 2020, 588, 315–320. [Google Scholar] [CrossRef]
- Ma, T.; Ryu, H.; McGregor, M.; Babcock, B.; Neidleman, J.; Xie, G.; George, A.F.; Frouard, J.; Murray, V.; Gill, G.; et al. Protracted yet Coordinated Differentiation of Long-Lived SARS-CoV-2-Specific CD8+ T Cells during Convalescence. J. Immunol. 2021, 207, 1344–1356. [Google Scholar] [CrossRef] [PubMed]
- Neidleman, J.; Luo, X.; Frouard, J.; Xie, G.; Gill, G.; Stein, E.S.; McGregor, M.; Ma, T.; George, A.F.; Kosters, A.; et al. SARS-CoV-2-Specific T Cells Exhibit Phenotypic Features of Helper Function, Lack of Terminal Differentiation, and High Proliferation Potential. Cell Rep. Med. 2020, 1, 100081. [Google Scholar] [CrossRef] [PubMed]
- Neidleman, J.; Luo, X.; George, A.F.; McGregor, M.; Yang, J.; Yun, C.; Murray, V.; Gill, G.; Greene, W.C.; Vasquez, J.; et al. Distinctive features of SARS-CoV-2-specific T cells predict recovery from severe COVID-19. Cell Rep. 2021, 36, 109414. [Google Scholar] [CrossRef] [PubMed]
- Santopaolo, M.; Gregorova, M.; Hamilton, F.; Arnold, D.; Long, A.; Lacey, A.; Oliver, E.; Halliday, A.; Baum, H.; Hamilton, K.; et al. Prolonged T-cell activation and long COVID symptoms independently associate with severe COVID-19 at 3 months. eLife 2023, 12, e85009. [Google Scholar] [CrossRef] [PubMed]
- Cruz, T.; Mendoza, N.; Lledó, G.M.; Perea, L.; Albacar, N.; Agustí, A.; Sellares, J.; Sibila, O.; Faner, R. Persistence of a SARS-CoV-2 T-cell response in patients with long COVID and lung sequelae after COVID-19. ERJ Open Res. 2023, 9, 00020-2023. [Google Scholar] [CrossRef] [PubMed]
- Phetsouphanh, C.; Zaunders, J.; Kelleher, A. Detecting antigen-specific T cell responses: From bulk populations to single cells. Int. J. Mol. Sci. 2015, 16, 18878–18893. [Google Scholar] [CrossRef] [PubMed]
- Ji, N.; Forsthuber, T.G. ELISPOT techniques. Methods Mol. Biol. 2016, 1304, 63–71. [Google Scholar] [CrossRef] [PubMed]
- Gangaev, A.; Ketelaars, S.L.C.; Isaeva, O.I.; Patiwael, S.; Dopler, A.; Hoefakker, K.; De Biasi, S.; Gibellini, L.; Mussini, C.; Guaraldi, G.; et al. Identification and characterization of a SARS-CoV-2 specific CD8+ T cell response with immunodominant features. Nat. Commun. 2021, 12, 2593. [Google Scholar] [CrossRef] [PubMed]
- Saini, S.K.; Hersby, D.S.; Tamhane, T.; Povlsen, H.R.; Hernandez, S.P.A.; Nielsen, M.; Gang, A.O.; Hadrup, S.R. SARS-CoV-2 genome-wide T cell epitope mapping reveals immunodominance and substantial CD8 + T cell activation in COVID-19 patients. Sci. Immunol. 2021, 6, eabf7550. [Google Scholar] [CrossRef]
- Rowntree, L.C.; Nguyen, T.H.O.; Kedzierski, L.; Neeland, M.R.; Petersen, J.; Crawford, J.C.; Allen, L.F.; Clemens, E.B.; Chua, B.; McQuilten, H.A.; et al. SARS-CoV-2-specific T cell memory with common TCRαβ motifs is established in unvaccinated children who seroconvert after infection. Immunity 2022, 55, 1299–1315.e4. [Google Scholar] [CrossRef]
- Yang, G.; Wang, J.; Sun, P.; Qin, J.; Yang, X.; Chen, D.; Zhang, Y.; Zhong, N.; Wang, Z. SARS-CoV-2 epitope-specific T cells: Immunity response feature, TCR repertoire characteristics and cross-reactivity. Front. Immunol. 2023, 14, 1146196. [Google Scholar] [CrossRef] [PubMed]
- Kuhlmann, C.; Mayer, C.K.; Claassen, M.; Maponga, T.; Burgers, W.A.; Keeton, R.; Riou, C.; Sutherland, A.D.; Suliman, T.; Shaw, M.L.; et al. Breakthrough infections with SARS-CoV-2 omicron despite mRNA vaccine booster dose. Lancet 2022, 399, 625–626. [Google Scholar] [CrossRef] [PubMed]
- Rha, M.-S.; Jeong, H.W.; Ko, J.-H.; Choi, S.J.; Seo, I.-H.; Lee, J.S.; Sa, M.; Kim, A.R.; Joo, E.-J.; Ahn, J.Y.; et al. PD-1-Expressing SARS-CoV-2-Specific CD8+ T Cells Are Not Exhausted, but Functional in Patients with COVID-19. Immunity 2021, 54, 44–52.e3. [Google Scholar] [CrossRef] [PubMed]
- Wei, J.; Pouwels, K.B.; Stoesser, N.; Matthews, P.C.; Diamond, I.; Studley, R.; Rourke, E.; Cook, D.; Bell, J.I.; Newton, J.N.; et al. Antibody responses and correlates of protection in the general population after two doses of the ChAdOx1 or BNT162b2 vaccines. Nat. Med. 2022, 28, 1072–1082. [Google Scholar] [CrossRef] [PubMed]
- Röltgen, K.; Nielsen, S.C.; 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, 1025–1040.e14. [Google Scholar] [CrossRef] [PubMed]
- Peluso, M.J.; Deitchman, A.N.; Torres, L.; Iyer, N.S.; Munter, S.E.; Nixon, C.C.; Donatelli, J.; Thanh, C.; Takahashi, S.; Hakim, J.; et al. Long-term SARS-CoV-2-specific immune and inflammatory responses in individuals recovering from COVID-19 with and without post-acute symptoms. Cell Rep. 2021, 36, 109518. [Google Scholar] [CrossRef]
- Kundura, L.; Cezar, R.; André, S.; Campos-Mora, M.; Lozano, C.; Vincent, T.; Muller, L.; Lefrant, J.-Y.; Roger, C.; Claret, P.-G.; et al. Low perforin expression in CD8+ T lymphocytes during the acute phase of severe SARS-CoV-2 infection predicts long COVID. Front. Immunol. 2022, 13, 1029006. [Google Scholar] [CrossRef]
Infection Cohort | Vaccination Cohort | |
---|---|---|
N° of individuals; n | 26 | 32 |
Male/Female; n | 25/1 | 8/24 |
Age; mean (range); y | 67.1 (56–78) | 40.4 (26–66) |
SARS-CoV-2 infection by RT-PCR, n (%) | 26 (100%) | 0 |
First sample collection; mean (range); d | 21.6 (8–36) | 43.5 (36–57) |
Comorbidities, n (%) | ||
Hypertension | 14 (53.8%) | 0 |
Diabetes mellitus | 4 (15.4%) | 1 (3.1%) |
Dyslipidemia | 9 (34.6%) | 3 (9.4%) |
Cancer | 0 | 0 |
Pulmonary disease | 3 | 0 |
Treatment, n (%) | ||
Statins | 7/26.9%) | 3(9.4%) |
ARA II | 14 (53.8%) | 0 |
Immunosuppressant | 0 | 0 |
HLA Restriction | Sequence | Protein | Epitope Abbreviation |
---|---|---|---|
A*01:01 | TTDPSFLGRY | ORF1ab | ORF1ab1637 |
LTDEMIAQY | S | S865 | |
FTSDYYQLY | ORF3a | ORF3a207 | |
A*02:01 | ILFTRFFYV | ORF1ab | ORF1ab1637 |
LLYDANYFL | ORF3a | ORF3a139 | |
YLQPRTFLL | S | S269 | |
FLHVTYVPA | S | S1062 | |
RLITGRLQSL | S | S995 | |
LLLLDRLNQL | N | N221 | |
ALWEIQQVV | ORF1ab | ORF1ab4094 | |
A*03:01 | VVYRGTTTYK | ORF1ab | ORF1ab 5538 |
KTFPPTEPK | N | N362 | |
KCYGVSPTK | S | S378 | |
A*11:01 | ATEGALNTPK | N | N134 |
STFNVPMEK | ORF1ab | ORF1ab2600 | |
ATSRTLSYYK | M | M171 | |
KTFPPTEPK | N | N361 | |
A*24:02 | VYIGDPAQL | ORF1ab | ORF1ab 5840 |
QYIKWPWYI | S | S1208 | |
B*07:02 | SPRWYFYYL | N | N105 |
SPRRARSVA | S | S680 | |
RPDTRYVL | ORF1ab | ORF1ab2949 | |
B*08:01 | DLKGKYVQI | ORF1ab | ORF1ab4344 |
B*35:01 | TPSGTWLTY | N | N325 |
QFAPSASAF | N | N305 | |
B*44:03 | SEFSSLPSY | ORF1ab | ORF1ab3946 |
PASC | Recovered | p | |
---|---|---|---|
N° of individuals; n | 10 | 16 | |
Age; mean (range); y | 68.6 (58–76) | 66.4 (56–78) | 0.527 |
Male / Female; n | 10/0 | 15/1 | 1 |
BMI (kg/m2); mean (range) | 28.9 (24.2–33.8) | 29.1 (27.7–33.4) | 0.9222 |
Duration of stay in ICU; d (range) | 35.7 (8–85) | 22.5 (6–58) | 0.1621 |
Comorbidities, n (%) | |||
Hypertension | 5 (50%) | 9 (56.3%) | 0.6785 |
Diabetes mellitus | 1 (10%) | 3 (18.8%) | 1 |
Dyslipidemia | 4 (40%) | 5 (31.3%) | 0.6924 |
Cancer | 0 | 0 | 1 |
Pulmonary disease | 0 | 3 (18.8%) | 0.2615 |
Laboratory data (admission) | |||
D-dimer (ng/mL), mean (range) | 1752 (1174–2126) | 1373 (852.3–6054) | 0.8557 |
Ferritin (ng/mL), mean (range) | 1529 (897.8–3792) | 1459 (1345–2524) | 0.9636 |
IL6 (pg/mL), mean (range) | 136 (74–1487) | 77.5 (44.5–302.8) | 0.1663 |
Treatment during ICU stay | |||
Hydroxychloroquine | 6 (60%) | 14 (87.5%) | 0.1627 |
Azythromycin | 6 (60%) | 13 (81.2%) | 0.3692 |
Tocilizumab | 6 (60%) | 8 (50%) | 0.7015 |
Corticosteroids | 6 (60%) | 11 (68.8%) | 0.6924 |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Martín-Martín, C.; del Riego, E.S.; Castiñeira, J.R.V.; Zapico-Gonzalez, M.S.; Rodríguez-Pérez, M.; Corte-Iglesias, V.; Saiz, M.L.; Diaz-Bulnes, P.; Escudero, D.; Suárez-Alvarez, B.; et al. Assessing Predictive Value of SARS-CoV-2 Epitope-Specific CD8+ T-Cell Response in Patients with Severe Symptoms. Vaccines 2024, 12, 679. https://doi.org/10.3390/vaccines12060679
Martín-Martín C, del Riego ES, Castiñeira JRV, Zapico-Gonzalez MS, Rodríguez-Pérez M, Corte-Iglesias V, Saiz ML, Diaz-Bulnes P, Escudero D, Suárez-Alvarez B, et al. Assessing Predictive Value of SARS-CoV-2 Epitope-Specific CD8+ T-Cell Response in Patients with Severe Symptoms. Vaccines. 2024; 12(6):679. https://doi.org/10.3390/vaccines12060679
Chicago/Turabian StyleMartín-Martín, Cristina, Estefanía Salgado del Riego, Jose R. Vidal Castiñeira, Maria Soledad Zapico-Gonzalez, Mercedes Rodríguez-Pérez, Viviana Corte-Iglesias, Maria Laura Saiz, Paula Diaz-Bulnes, Dolores Escudero, Beatriz Suárez-Alvarez, and et al. 2024. "Assessing Predictive Value of SARS-CoV-2 Epitope-Specific CD8+ T-Cell Response in Patients with Severe Symptoms" Vaccines 12, no. 6: 679. https://doi.org/10.3390/vaccines12060679