Dataset Information

The landscape of the SARS-CoV-2 HLA-peptidome

ABSTRACT: The human leukocyte antigen (HLA)-bound-viral antigens, serve as an immunological signature that can be selectively recognized by T cells. As viruses evolve by acquiring mutations, it is essential to identify a range of viral presented antigens. Utilizing HLA-peptidomics we Identified SARS-CoV-2-derived peptides presented by highly prevalent HLA Class-I (HLA-I) molecules using infected cells as well as overexpression of SARS-CoV-2 genes. We found 26 HLA-I peptides and 36 HLA class-II (HLA-II) peptides, which are estimated to be presented by at least one HLA allele in 99% of the world population. Among the identified peptides were recurrently presented HLA-I peptides, peptides derived from out-of-frame-ORFs and presentation-hotspots. Seven of these peptides were previously shown to be immunogenic, and we identified two novel immuno-reactive peptides using HLA-multimer staining. These results may aid the development of the next generation of SARS-CoV-2 vaccines based on viral-specific-presented antigens that span several of the viral genes.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Prof. Yardena Samuels

PROVIDER: MSV000088298 | MassIVE | Mon Nov 01 10:09:00 GMT 2021

SECONDARY ACCESSION(S): PXD023614

REPOSITORIES: MassIVE

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Publications

Identification of presented SARS-CoV-2 HLA class I and HLA class II peptides using HLA peptidomics.

Nagler Adi A Kalaora Shelly S Barbolin Chaya C Gangaev Anastasia A Ketelaars Steven L C SLC Alon Michal M Pai Joy J Benedek Gil G Yahalom-Ronen Yfat Y Erez Noam N Greenberg Polina P Yagel Gal G Peri Aviyah A Levin Yishai Y Satpathy Ansuman T AT Bar-Haim Erez E Paran Nir N Kvistborg Pia P Samuels Yardena Y

Cell reports 20210608 13

The human leukocyte antigen (HLA)-bound viral antigens serve as an immunological signature that can be selectively recognized by T cells. As viruses evolve by acquiring mutations, it is essential to identify a range of presented viral antigens. Using HLA peptidomics, we are able to identify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-derived peptides presented by highly prevalent HLA class I (HLA-I) molecules by using infected cells as well as overexpression of SARS-CoV-2 genes. ...[more]

PMID: 34166618

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Project description:Treatment of cancer cells with anti-cancer drugs often fails to achieve complete remission. Yet, such drug treatments may induce alteration in the tumorâs gene expression patterns, including those of Cancer/Testis Antigens (CTA). The degradation products of such antigens can be presented as HLA peptides on the surface of the tumor cells and be developed into anti-cancer immunotherapeutics. For example, the DNA methyl transferase inhibitor, 5-aza-2'-deoxycytidine (Decitabine) has limited anti-tumor efficacy, yet it induces the expression of many genes, including CTAs that are normally silenced in the healthy adult tissues. In this study, the presentation of many new HLA peptides derived from CTAs and induced by Decitabine was demonstrated in three human Glioblastoma cell lines. Such presentation of CTA-derived HLA peptides can be exploited for development of new treatment modalities, combining drug treatment with anti-CTA targeted immunotherapy. The Decitabine-induced HLA peptidomes include many CTAs that are not normally detected in healthy tissues or in cancer cells, unless treated with the drug. In addition, the study included large-scale analyses of the simultaneous effects of Decitabine on the transcriptomes, proteomes and HLA peptidomes of the human Glioblastoma cells. It demonstrates the poor correlations between these three levels of gene expression, both in their total levels and in their response to the drug. The transcriptomes, proteomes and HLA peptidomes of the U-87, T98G and LNT-229 GBM human cell lines were analyzed before and after treatment with Decitabine. Overall, the RNA-Seq transcriptome analyses resulted in the identification of above 26000 transcripts, the proteome analyses identified about 7500 proteins and the HLA class I peptidome analyses resulted in above 25000 identified HLA peptides. Two biological repetitions of the transcriptome, three of the proteome and three of the HLA peptidome were performed with each of the cell lines and treatment, resulting in highly reproducible datasets.

Dataset Information

The landscape of the SARS-CoV-2 HLA-peptidome

Publications

Identification of presented SARS-CoV-2 HLA class I and HLA class II peptides using HLA peptidomics.

Similar Datasets

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