Recruitment of highly functional SARS-CoV-2-specific CD8 + T cell receptors mediating cytotoxicity of virus-infected target cells in non-severe COVID-19
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Abstract
T cell immunity is crucial for the control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and has been widely characterized on a quantitative level. In contrast, the quality of such T cell responses has been poorly investigated, in particular in the case of CD8 + T cells. Here, we explored the quality of SARS-CoV-2-specific CD8 + T cell responses in individuals who recovered from mild symptomatic infections, through which protective immunity should develop, by functional characterization of their T cell receptor (TCR) repertoire. CD8 + T cell responses specific for SARS-CoV-2-derived epitopes were low in frequency but could be detected robustly early as well as late - up to twelve months - after infection. A pool of immunodominant epitopes, which accurately identified previous SARS-CoV-2 infections, was used to isolate TCRs specific for epitopes restricted by common HLA class I molecules. TCR-engineered T cells showed heterogeneous functional avidity and cytotoxicity towards virus-infected target cells. High TCR functionality correlated with gene signatures of T cell function and activation that, remarkably, could be retrieved for each epitope:HLA combination and patient analyzed. Overall, our data demonstrate that highly functional HLA class I TCRs are recruited and maintained upon mild SARS-CoV-2 infection. Such validated epitopes and TCRs could become valuable tools for the development of diagnostic tests determining the quality of SARS-CoV-2-specific CD8 + T cell immunity, and thereby investigating correlates of protection, as well as to restore functional immunity through therapeutic transfer of TCR-engineered T cells.
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SciScore for 10.1101/2021.07.20.21260845: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: All participants provided informed written consent.
IRB: Approval for the study design and sample collection was obtained within the framework of study “Establishment and validation of epitope-specific SARS-CoV-2 blood-based testing methods” (EPI-SARS) by the ethics committee of the Technical University of Munich (reference number 182/20) and the Institutional Ethics Committee of the University Medicine Mannheim (reference number 2020-556N).Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources After incubation, cells were stained with EMA … SciScore for 10.1101/2021.07.20.21260845: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: All participants provided informed written consent.
IRB: Approval for the study design and sample collection was obtained within the framework of study “Establishment and validation of epitope-specific SARS-CoV-2 blood-based testing methods” (EPI-SARS) by the ethics committee of the Technical University of Munich (reference number 182/20) and the Institutional Ethics Committee of the University Medicine Mannheim (reference number 2020-556N).Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources After incubation, cells were stained with EMA solution (1:1000) for live/dead discrimination and subsequently with surface antibodies: CD19-ECD (1:100), CD8-PE (1:200), CD3-BV421 (1:100) and murine TCR β-chain-APC/Fire750 (1:100). CD19-ECDsuggested: NoneCD8-PEsuggested: NoneCD3-BV421suggested: NoneHLA type for asymptomatic seropositive and seronegative donors was determined via surface antibody staining using commercially available antibodies targeting HLA-A*02-FITC (1:200,), HLA-A*03-APC (1:200), HLA-B*07-PE (1:100), HLA-B*08-APCVio770 (1:200). HLA-A*03-APCsuggested: NoneHLA-B*07-PEsuggested: NoneHLA-B*08-APCVio770suggested: NoneExperimental Models: Cell Lines Sentences Resources A549-ACE2 RFP+ cells were then retrovirally transduced with plasmids encoding HLA-A*01:01 or HLA-A*03:01. A549-ACE2 RFP+suggested: NoneFor the production of retroviral particles, RD114 cells were transfected with pMP71 expression vector (containing the HLA heavy chain construct, gag/pol and amphotropic envelope) by calcium phosphate precipitation. RD114suggested: ATCC Cat# PTA-4440, RRID:CVCL_1J88)1*105 A549 ACE2 RFP+ cells were then transduced via spinoculation on virus-coated plates. A549suggested: NCI-DTP Cat# A549, RRID:CVCL_0023)For the Incucyte killing assay, 5*103 A549-ACE2+ RFP+ HLA-A*01 or A549-ACE2+ RFP+ HLA-A*03 cells were seeded 24 h prior infection with SARS-CoV-2 GFP virus (MOI 5). HLA-A*03suggested: NoneRecombinant DNA Sentences Resources For the production of retroviral particles, RD114 cells were transfected with pMP71 expression vector (containing the HLA heavy chain construct, gag/pol and amphotropic envelope) by calcium phosphate precipitation. pMP71suggested: RRID:Addgene_141355)Software and Algorithms Sentences Resources After import of sequence raw data in the uType software, the sequences were analyzed for HLA type creation by aligning to recent IMGT HLA allele uTypesuggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:A limitation of our study is the use of an in vitro expansion step prior T cell analyses, which may bias the relative abundance of clonotypes and may favor outgrowing of some clones at the expense of others. However, this approach of peptide stimulation offered the possibility of exploiting signatures of recent activation to discriminate epitope-specific and functional TCRs66. Indeed, we identified signatures of T cell function and recent activation correlating with TCR functionality, which allowed a broad in silico investigation of the functional landscape of entire TCR repertoires, otherwise unfeasible by conventional experimental validation. Remarkably, we predicted highly functional TCRs for each of the eleven immunodominant SARS-CoV-2 epitopes analyzed, despite a certain degree of functional heterogeneity. Together with the observed polyclonality, our data indicate that functional and diverse CD8+ T cell immunity should normally establish in non-severe SARS-CoV-2 infections. Polyclonality and high functionality are hallmarks of a protective TCR repertoire67, thus strongly supporting a similar role also in the context of SARS-CoV-2 infections. Nevertheless, the extension of TCR repertoire analyses to settings of severe infections remains a fundamental next step to assign CD8+ T cell responses a role as correlates of protection. Overall, our data provide first evidence that SARS-CoV-2-specific CD8+ T cells persists up to 12 months after infection and are composed of a poly...
Results from TrialIdentifier: No clinical trial numbers were referenced.
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Results from scite Reference Check: We found no unreliable references.
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