Genomics

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5a9f4bd6-d795-47e9-9690-979bf5b1df6b - samples

ABSTRACT: The data contains single-cell gene sequencing data (10x Genomics) from FACS-purified CD8 T lymphocytes from two Austrian patients. The cells were stimulated with one MHC class I peptides obtained from a common (wild type) variant and an emerging mutant variant of the SARS-Cov-2 virus. Then the samples were multiplexed using hashtag oligos. We provide the raw and aligned sequence data for: i. The single-cell experiments ii. The PCR-amplified samples for enrichment of the hashtag oligo multiplexing barcodes iii. The PCR-amplified samples for enrichment of the T Cell Receptor (TCR) VDJ region for immuno-profiling. The samples and libraries were processed and obtained in collaboration between St. Anna Children's Cancer Research Institute (CCRI), CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, and the Medical University of Vienna. The cell barcodes and processed data has been submitted to the GEO database with GEO accession GSE166651.

PROVIDER: EGAD00001006995 | EGA |

REPOSITORIES: EGA

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SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8<sup>+</sup> T cell responses.

Agerer Benedikt B   Koblischke Maximilian M   Gudipati Venugopal V   Montaño-Gutierrez Luis Fernando LF   Smyth Mark M   Popa Alexandra A   Genger Jakob-Wendelin JW   Endler Lukas L   Florian David M DM   Mühlgrabner Vanessa V   Graninger Marianne M   Aberle Stephan W SW   Husa Anna-Maria AM   Shaw Lisa Ellen LE   Lercher Alexander A   Gattinger Pia P   Torralba-Gombau Ricard R   Trapin Doris D   Penz Thomas T   Barreca Daniele D   Fae Ingrid I   Wenda Sabine S   Traugott Marianna M   Walder Gernot G   Pickl Winfried F WF   Thiel Volker V   Allerberger Franz F   Stockinger Hannes H   Puchhammer-Stöckl Elisabeth E   Weninger Wolfgang W   Fischer Gottfried G   Hoepler Wolfgang W   Pawelka Erich E   Zoufaly Alexander A   Valenta Rudolf R   Bock Christoph C   Paster Wolfgang W   Geyeregger René R   Farlik Matthias M   Halbritter Florian F   Huppa Johannes B JB   Aberle Judith H JH   Bergthaler Andreas A  

Science immunology 20210301 57

CD8<sup>+</sup> T cell immunity to SARS-CoV-2 has been implicated in COVID-19 severity and virus control. Here, we identified nonsynonymous mutations in MHC-I-restricted CD8<sup>+</sup> T cell epitopes after deep sequencing of 747 SARS-CoV-2 virus isolates. Mutant peptides exhibited diminished or abrogated MHC-I binding in a cell-free in vitro assay. Reduced MHC-I binding of mutant peptides was associated with decreased proliferation, IFN-γ production and cytotoxic activity of CD8<sup>+</sup> T  ...[more]

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