PMID- 33024965
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20230407
DP  - 2020 Oct 26
TI  - SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame 
      ORFs.
LID - 2020.10.02.324145 [pii]
LID - 10.1101/2020.10.02.324145 [doi]
AB  - T cell-mediated immunity may play a critical role in controlling and establishing 
      protective immunity against SARS-CoV-2 infection; yet the repertoire of viral 
      epitopes responsible for T cell response activation remains mostly unknown. 
      Identification of viral peptides presented on class I human leukocyte antigen 
      (HLA-I) can reveal epitopes for recognition by cytotoxic T cells and potential 
      incorporation into 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 captured by 
      current vaccines. Proteomics analyses of infected cells revealed that SARS-CoV-2 
      may interfere with antigen processing and immune signaling pathways. Based on the 
      endogenously processed and presented viral peptides that we identified, we 
      estimate that a pool of 24 peptides would provide one or more peptides for 
      presentation by at least one HLA allele in 99% of the human 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.
FAU - Weingarten-Gabbay, Shira
AU  - Weingarten-Gabbay S
AUID- ORCID: 0000-0001-7579-0236
FAU - Klaeger, Susan
AU  - Klaeger S
AUID- ORCID: 0000-0002-0074-5163
FAU - Sarkizova, Siranush
AU  - Sarkizova S
AUID- ORCID: 0000-0003-2530-8610
FAU - Pearlman, Leah R
AU  - Pearlman LR
FAU - Chen, Da-Yuan
AU  - Chen DY
FAU - Bauer, Matthew R
AU  - Bauer MR
FAU - Taylor, Hannah B
AU  - Taylor HB
FAU - Conway, Hasahn L
AU  - Conway HL
FAU - Tomkins-Tinch, Christopher H
AU  - Tomkins-Tinch CH
FAU - Finkel, Yaara
AU  - Finkel Y
AUID- ORCID: 0000-0002-3843-2357
FAU - Nachshon, Aharon
AU  - Nachshon A
AUID- ORCID: 0000-0003-2283-5220
FAU - Gentili, Matteo
AU  - Gentili M
FAU - Rivera, Keith D
AU  - Rivera KD
FAU - Keskin, Derin B
AU  - Keskin DB
AUID- ORCID: 0000-0002-8496-6181
FAU - Rice, Charles M
AU  - Rice CM
FAU - Clauser, Karl R
AU  - Clauser KR
AUID- ORCID: 0000-0002-1052-9456
FAU - Hacohen, Nir
AU  - Hacohen N
AUID- ORCID: 0000-0002-2349-2656
FAU - Carr, Steven A
AU  - Carr SA
AUID- ORCID: 0000-0002-7203-4299
FAU - Abelin, Jennifer G
AU  - Abelin JG
AUID- ORCID: 0000-0001-5262-7241
FAU - Saeed, Mohsan
AU  - Saeed M
AUID- ORCID: 0000-0002-9843-1890
FAU - Sabeti, Pardis C
AU  - Sabeti PC
LA  - eng
GR  - U24 CA210986/CA/NCI NIH HHS/United States
GR  - T32 HG002295/HG/NHGRI NIH HHS/United States
GR  - U24 CA270823/CA/NCI NIH HHS/United States
GR  - U24 CA210979/CA/NCI NIH HHS/United States
GR  - U01 CA214125/CA/NCI NIH HHS/United States
PT  - Preprint
DEP - 20201026
PL  - United States
TA  - bioRxiv
JT  - bioRxiv : the preprint server for biology
JID - 101680187
PMC - PMC7536868
EDAT- 2020/10/08 06:00
MHDA- 2020/10/08 06:01
PMCR- 2020/11/09
CRDT- 2020/10/07 05:52
PHST- 2020/10/08 06:00 [pubmed]
PHST- 2020/10/08 06:01 [medline]
PHST- 2020/10/07 05:52 [entrez]
PHST- 2020/11/09 00:00 [pmc-release]
AID - 2020.10.02.324145 [pii]
AID - 10.1101/2020.10.02.324145 [doi]
PST - epublish
SO  - bioRxiv [Preprint]. 2020 Oct 26:2020.10.02.324145. doi: 
      10.1101/2020.10.02.324145.