GSE159191

SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs

Submitted by Shira Weingarten-Gabbay (Weizmann Institute Of Science, Israel) on Oct 07 2020

Platform: ngs – NextSeq 550 (Homo sapiens)

Pubmed: None listed

Summary T cell-mediated immunity seems to play a critical role against SARS-CoV-2 infection and establishing protective memory. Yet the repertoire of viral epitopes responsible for activation of T cell responses remains mostly unknown. Identification and characterization of viral peptides presented on class I human leukocyte antigen (HLA-I) will reveal the viral signatures as seen by cytotoxic T cells that can then be harnessed for the development of effective vaccines. Here, we report the first HLA-I immunopeptidome of SARS-CoV-2 in two human cell lines at different times post-infection using mass spectrometry. We found HLA-I peptides derived not only from canonical ORFs, but also from internal out-of-frame ORFs in Spike and Nucleoprotein not currently captured by vaccine approaches. Whole proteome analysis revealed that expression of ubiquitination pathway proteins, and the proteasome maturation protein, POMP, were significantly altered in infected cells. Retrospective analysis of computational predictions highlighted shortcomings of in silico-only approaches in recovering the observed viral epitopes. Finally, given the experimental evidence for endogenous processing and presentation of the viral peptides we detected, we estimated that at least one HLA-A, -B, or -C allele is covered by at least one peptide for 99% of the population. These biological insights and the list of naturally presented SARS-CoV-2 peptides will facilitate data-driven selection of peptides for immune monitoring and vaccine development.

16 Samples

ID	Title	Cell Type	Timepoint	Reported Virus	Virus Species
GSM4822344	A549 non-infecetd	non-small cell lung adenocarcinoma cell line [A-549 ]		non-infected	Uninfected
GSM4822345	A549 12h post infection	non-small cell lung adenocarcinoma cell line [A-549 ]	12 hrs	SARS-CoV-2	Severe acute respiratory syndrome-related coronavirus
GSM4822346	A549 18h post infection	non-small cell lung adenocarcinoma cell line [A-549 ]	18 hrs	SARS-CoV-2	Severe acute respiratory syndrome-related coronavirus
GSM4822347	A549 24h post infection	non-small cell lung adenocarcinoma cell line [A-549 ]	24 hrs	SARS-CoV-2	Severe acute respiratory syndrome-related coronavirus
GSM4822348	HEK293T non-infecetd Rep1	embryonic kidney cell line [HEK293T ]		non-infected	Uninfected
GSM4822349	HEK293T non-infecetd Rep2	embryonic kidney cell line [HEK293T ]		non-infected	Uninfected
GSM4822350	HEK293T non-infecetd Rep3	embryonic kidney cell line [HEK293T ]		non-infected	Uninfected
GSM4822351	HEK293T 12h post infection Rep1	embryonic kidney cell line [HEK293T ]	12 hrs	SARS-CoV-2	Severe acute respiratory syndrome-related coronavirus
GSM4822352	HEK293T 12h post infection Rep2	embryonic kidney cell line [HEK293T ]	12 hrs	SARS-CoV-2	Severe acute respiratory syndrome-related coronavirus
GSM4822353	HEK293T 12h post infection Rep3	embryonic kidney cell line [HEK293T ]	12 hrs	SARS-CoV-2	Severe acute respiratory syndrome-related coronavirus
GSM4822354	HEK293T 18h post infection Rep1	embryonic kidney cell line [HEK293T ]	18 hrs	SARS-CoV-2	Severe acute respiratory syndrome-related coronavirus
GSM4822355	HEK293T 18h post infection Rep2	embryonic kidney cell line [HEK293T ]	18 hrs	SARS-CoV-2	Severe acute respiratory syndrome-related coronavirus
GSM4822356	HEK293T 18h post infection Rep3	embryonic kidney cell line [HEK293T ]	18 hrs	SARS-CoV-2	Severe acute respiratory syndrome-related coronavirus
GSM4822357	HEK293T 24h post infection Rep1	embryonic kidney cell line [HEK293T ]	24 hrs	SARS-CoV-2	Severe acute respiratory syndrome-related coronavirus
GSM4822358	HEK293T 24h post infection Rep2	embryonic kidney cell line [HEK293T ]	24 hrs	SARS-CoV-2	Severe acute respiratory syndrome-related coronavirus
GSM4822359	HEK293T 24h post infection Rep3	embryonic kidney cell line [HEK293T ]	24 hrs	SARS-CoV-2	Severe acute respiratory syndrome-related coronavirus