Distinctive evolution of alveolar T cell responses is associated with clinical outcomes in unvaccinated patients with SARS-CoV-2 pneumonia

Budinger, G. R. S., Misharin, A. V., Ridge, K. M., Singer, B. D. & Wunderink, R. G. Distinctive features of severe SARS-CoV-2 pneumonia. J. Clin. Invest. 131, e149412 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gao, C. A. et al. Machine learning links unresolving secondary pneumonia to mortality in patients with severe pneumonia, including COVID-19. J. Clin. Invest. 133, e170682 (2023).

Article  PubMed  PubMed Central  Google Scholar 

Grant, R. A. et al. Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia. Nature 590, 635–641 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rydyznski Moderbacher, C. et al. Antigen-specific adaptive immunity to SARS-CoV-2 in acute COVID-19 and associations with age and disease severity. Cell 183, 996–1012 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Markov, N. S. et al. SCRIPT CarpeDiem dataset: demographics, outcomes, and per-day clinical parameters for critically ill patients with suspected pneumonia (version 1.1.0). PhysioNet https://doi.org/10.13026/5phr-4r89 (2023).

Pickens, C. O. et al. Bacterial superinfection pneumonia in patients mechanically ventilated for COVID-19 pneumonia. Am. J. Respir. Crit. Care Med. 204, 921–932 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Grant, R. A. et al. Prolonged exposure to lung-derived cytokines is associated with activation of microglia in patients with COVID-19. JCI Insight 9, e178859 (2024).

PubMed  PubMed Central  Google Scholar 

Pickens, C. I. et al. An adjudication protocol for severe pneumonia. Open Forum Infect. Dis. 10, ofad336 (2023).

Article  PubMed  PubMed Central  Google Scholar 

Recovery Collaborative Group et al. Dexamethasone in hospitalized patients with COVID-19. N. Engl. J. Med. 384, 693–704 (2021).

Article  Google Scholar 

Wu, H., Harder, C. & Culley, C. The 2016 clinical practice guidelines for management of hospital-acquired and ventilator-associated pneumonia. Can. J. Hosp. Pharm. 70, 251–252 (2017).

PubMed  PubMed Central  Google Scholar 

Szabo, P. A. et al. Longitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19. Immunity 54, 797–814 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bergamaschi, L. et al. Longitudinal analysis reveals that delayed bystander CD8+ T cell activation and early immune pathology distinguish severe COVID-19 from mild disease. Immunity 54, 1257–1275 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Neidleman, J. et al. Distinctive features of SARS-CoV-2-specific T cells predict recovery from severe COVID-19. Cell Rep. 36, 109414 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mathew, D. et al. Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications. Science 369, eabc8511 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jovisic, M., Mambetsariev, N., Singer, B. D. & Morales-Nebreda, L. Differential roles of regulatory T cells in acute respiratory infections. J. Clin. Invest. 133, e170505 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhao, J. et al. Airway memory CD4+ T cells mediate protective immunity against emerging respiratory coronaviruses. Immunity 44, 1379–1391 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Woodland, D. L. & Blackman, M. A. Immunity and age: living in the past? Trends Immunol. 27, 303–307 (2006).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Goronzy, J. J., Fang, F., Cavanagh, M. M., Qi, Q. & Weyand, C. M. Naive T cell maintenance and function in human aging. J. Immunol. 194, 4073–4080 (2015).

Article  CAS  PubMed  Google Scholar 

Goronzy, J. J. & Weyand, C. M. Successful and maladaptive T cell aging. Immunity 46, 364–378 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huang, H., Wang, C., Rubelt, F., Scriba, T. J. & Davis, M. M. Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening. Nat. Biotechnol. 38, 1194–1202 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lineburg, K. E. et al. CD8+ T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope cross-react with selective seasonal coronaviruses. Immunity 54, 1055–1065 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pogorelyy, M. V. et al. Resolving SARS-CoV-2 CD4+ T cell specificity via reverse epitope discovery. Cell Rep. Med. 3, 100697 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nolan, S. et al. A large-scale database of T-cell receptor β (TCRβ) sequences and binding associations from natural and synthetic exposure to SARS-CoV-2. Preprint at Res. Sq. https://doi.org/10.21203/rs.3.rs-51964/v1 (2020).

Moutaftsi, M. et al. Uncovering the interplay between CD8, CD4 and antibody responses to complex pathogens. Future Microbiol. 5, 221–239 (2010).

Article  CAS  PubMed  Google Scholar 

Orenbuch, R. et al. arcasHLA: high-resolution HLA typing from RNAseq. Bioinformatics 36, 33–40 (2020).

Article  CAS  PubMed  Google Scholar 

Reynisson, B., Alvarez, B., Paul, S., Peters, B. & Nielsen, M. NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Res. 48, W449–W454 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gonzalez-Galarza, F. F. et al. Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools. Nucleic Acids Res. 48, D783–D788 (2020).

CAS  PubMed  Google Scholar 

Chi, H., Pepper, M. & Thomas, P. G. Principles and therapeutic applications of adaptive immunity. Cell 187, 2052–2078 (2024).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schultheiss, C. et al. Next-generation sequencing of T and B cell receptor repertoires from COVID-19 patients showed signatures associated with severity of disease. Immunity 53, 442–455 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nguyen, T. H. O. et al. CD8+ T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope display high naive precursor frequency and TCR promiscuity. Immunity 54, 1066–1082 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Le Bert, N. et al. SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature 584, 457–462 (2020).

Article 

Comments (0)

No login
gif