PMID- 37709257
OWN - NLM
STAT- Publisher
LR  - 20231021
IS  - 1535-9484 (Electronic)
IS  - 1535-9476 (Print)
IS  - 1535-9476 (Linking)
VI  - 22
IP  - 10
DP  - 2023 Oct
TI  - Integrated Immunopeptidomics and Proteomics Study of SARS-CoV-2-Infected Calu-3 
      Cells Reveals Dynamic Changes in Allele-specific HLA Abundance and Antigen 
      Presentation.
PG  - 100645
LID - S1535-9476(23)00156-1 [pii]
LID - 10.1016/j.mcpro.2023.100645 [doi]
LID - 100645
AB  - We present an integrated immunopeptidomics and proteomics study of severe acute 
      respiratory syndrome coronavirus 2 (SARS-CoV-2) infection to comprehensively 
      decipher the changes in host cells in response to viral infection. 
      Immunopeptidomics analysis identified viral antigens presented by host cells 
      through both class I and class II MHC system for recognition by the adaptive 
      immune system. The host proteome changes were characterized by quantitative 
      proteomics and glycoproteomics and from these data, the activation of toll-like 
      receptor 3-interferon pathway was identified. Glycosylation analysis of human 
      leukocyte antigen (HLA) proteins from the elution and flow-through of 
      immunoprecipitation revealed that SARS-CoV-2 infection changed the glycosylation 
      pattern of certain HLA alleles with different HLA alleles, showing distinct 
      dynamic changes in relative abundance. The difference in the glycosylation and 
      abundance of HLA alleles changed the number of strong binding antigens each 
      allele presented, suggesting the impact of SARS-CoV-2 infection on antigen 
      presentation is allele-specific. These results could be further exploited to 
      explain the imbalanced response from innate and adaptive immune system in 
      coronavirus disease 2019 cases, which would be helpful for the development of 
      therapeutics and vaccine for coronavirus disease 2019 and preparation for future 
      pandemic.
CI  - Crown Copyright (c) 2023. Published by Elsevier Inc. All rights reserved.
FAU - Chen, Rui
AU  - Chen R
AD  - Human Health Therapeutics Research Centre, National Research Council Canada, 
      Ottawa, Ontario, Canada. Electronic address: Rui.Chen@nrc-cnrc.gc.ca.
FAU - Fulton, Kelly M
AU  - Fulton KM
AD  - Human Health Therapeutics Research Centre, National Research Council Canada, 
      Ottawa, Ontario, Canada.
FAU - Tran, Anh
AU  - Tran A
AD  - Human Health Therapeutics Research Centre, National Research Council Canada, 
      Ottawa, Ontario, Canada.
FAU - Duque, Diana
AU  - Duque D
AD  - Human Health Therapeutics Research Centre, National Research Council Canada, 
      Ottawa, Ontario, Canada.
FAU - Kovalchik, Kevin
AU  - Kovalchik K
AD  - CHU Sainte-Justine Research Center, Montreal, Quebec, Canada.
FAU - Caron, Etienne
AU  - Caron E
AD  - CHU Sainte-Justine Research Center, Montreal, Quebec, Canada; Department of 
      Pathology and Cellular Biology, Faculty of Medicine, Universite de Montreal, 
      Quebec, Canada.
FAU - Twine, Susan M
AU  - Twine SM
AD  - Human Health Therapeutics Research Centre, National Research Council Canada, 
      Ottawa, Ontario, Canada.
FAU - Li, Jianjun
AU  - Li J
AD  - Human Health Therapeutics Research Centre, National Research Council Canada, 
      Ottawa, Ontario, Canada. Electronic address: Jianjun.Li@nrc-cnrc.gc.ca.
LA  - eng
PT  - Journal Article
DEP - 20230913
PL  - United States
TA  - Mol Cell Proteomics
JT  - Molecular & cellular proteomics : MCP
JID - 101125647
SB  - IM
PMC - PMC10580047
COIS- Conflict of interest The authors declare no competing interests.
EDAT- 2023/09/15 00:42
MHDA- 2023/09/15 00:42
PMCR- 2023/09/13
CRDT- 2023/09/14 19:19
PHST- 2022/10/04 00:00 [received]
PHST- 2023/08/29 00:00 [revised]
PHST- 2023/09/11 00:00 [accepted]
PHST- 2023/09/15 00:42 [pubmed]
PHST- 2023/09/15 00:42 [medline]
PHST- 2023/09/14 19:19 [entrez]
PHST- 2023/09/13 00:00 [pmc-release]
AID - S1535-9476(23)00156-1 [pii]
AID - 100645 [pii]
AID - 10.1016/j.mcpro.2023.100645 [doi]
PST - ppublish
SO  - Mol Cell Proteomics. 2023 Oct;22(10):100645. doi: 10.1016/j.mcpro.2023.100645. 
      Epub 2023 Sep 13.