HLA-E Restricted SARS-CoV-2 Specific T Cells from Convalescent COVID19 Patients Suppress Virus Replication Despite HLA Class Ia Downregulation

Description

Raw sequencing data (FASTQ files) of the HLA-E-restricted, SARS-CoV-2-specific T cells reported in Yang et al (2023) "HLA-E Restricted SARS-CoV-2 Specific T Cells from Convalescent COVID19 Patients Suppress Virus Replication Despite HLA Class Ia Downregulation" Science Immunology, In press ABSTRACT Pathogen specific CD8+ T cell responses restricted by the non-polymorphic non-classical class Ib molecule HLA-E are rarely reported in viral infections. The natural HLA-E ligand is a signal peptide derived from classical class Ia HLA molecules that interacts with the NKG2/CD94 receptors to regulate natural killer (NK) cell functions – but pathogen-derived peptides can also be presented by HLA-E. Here we describe five peptides from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that elicited HLA-E restricted CD8+ T cell responses in COVID-19 convalescent patients. These T cell responses were present in the blood at frequencies similar to those reported for classical HLA-Ia-restricted anti-SARS-CoV-2 CD8+ T cells. HLA-E-peptide specific CD8+ T cell clones, which expressed diverse T cell receptors, suppressed SARS-CoV-2 replication in Calu-3 human lung epithelial cells. SARS-CoV-2 infection markedly downregulated classical HLA class I expression in Calu-3 cells and primary reconstituted human airway epithelia cells whereas HLA-E expression was not affected, enabling T cell recognition. Thus HLA-E restricted T cells could contribute to the control of SARS-CoV-2 infection alongside classical T cells. METHODS Total RNA of CD8 clones was extracted using a RNeasy Plus Mini Kit (Qiagen). TCR libraries using 100ng RNA were prepared using a SMARTer Human TCR a/b Profiling Kit (Takara Bio) according to the manufacturer instructions. Full length TCR alpha and beta chains were sequenced using a Miseq Reagent Kit v3 (600-cycle) on an Miseq sequencer (Illumina). Raw BCL files were converted to FASTQ format using bcl2fastq (v2.20.0.422). TCR sequences were reconstructed using MiXCR (v3.0.13) 57, using the mixcr analyze amplicon command, and only productive TCRs were included. MiXCR output files were parsed into R (v4.0.1) using tcR (v2.3.2). TCRs were filtered based on clone counts to retain only 1α1β or 2α1β paired TCRs for each clone. Clonality was confirmed by the uniqueness of TCR sequences, where each clone showed only one TCR β chain NOTE: Data files are named by Patient ID, Clone ID, and whether the data is alpha or beta chain. Fastq format, compressed by GZIP.

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