PMID- 34509645
OWN - NLM
STAT- MEDLINE
DCOM- 20220324
LR  - 20220324
IS  - 1535-9484 (Electronic)
IS  - 1535-9476 (Print)
IS  - 1535-9476 (Linking)
VI  - 20
DP  - 2021
TI  - Immunopeptidogenomics: Harnessing RNA-Seq to Illuminate the Dark Immunopeptidome.
PG  - 100143
LID - S1535-9476(21)00115-8 [pii]
LID - 10.1016/j.mcpro.2021.100143 [doi]
LID - 100143
AB  - Human leukocyte antigen (HLA) molecules are cell-surface glycoproteins that 
      present peptide antigens on the cell surface for surveillance by T lymphocytes, 
      which contemporaneously seek signs of disease. Mass spectrometric analysis allows 
      us to identify large numbers of these peptides (the immunopeptidome) following 
      affinity purification of solubilized HLA-peptide complexes. However, in recent 
      years, there has been a growing awareness of the "dark side" of the 
      immunopeptidome: unconventional peptide epitopes, including neoepitopes, which 
      elude detection by conventional search methods because their sequences are not 
      present in reference protein databases (DBs). Here, we establish a bioinformatics 
      workflow to aid identification of peptides generated by noncanonical translation 
      of mRNA or by genome variants. The workflow incorporates both standard 
      transcriptomics software and novel computer programs to produce cell 
      line-specific protein DBs based on three-frame translation of the transcriptome. 
      The final protein DB also includes sequences resulting from variants determined 
      by variant calling on the same RNA-Seq data. We then searched our experimental 
      data against both transcriptome-based and standard DBs using PEAKS Studio 
      (Bioinformatics Solutions, Inc). Finally, further novel software helps to compare 
      the various result sets arising for each sample, pinpoint putative genomic 
      origins for unconventional sequences, and highlight potential neoepitopes. We 
      applied the workflow to study the immunopeptidome of the acute myeloid leukemia 
      cell line THP-1, using RNA-Seq and immunopeptidome data. We confidently 
      identified over 14,000 peptides from three replicates of purified HLA peptides 
      derived from THP-1 cells using the conventional UniProt human proteome. Using the 
      transcriptome-based DB generated using our workflow, we recapitulated >85% of 
      these and also identified 1029 unconventional peptides not explained by UniProt, 
      including 16 sequences caused by nonsynonymous variants. Our workflow, which we 
      term "immunopeptidogenomics," can provide DBs, which include pertinent 
      unconventional sequences and allow neoepitope discovery, without becoming too 
      large to search. Immunopeptidogenomics is a step toward unbiased search 
      approaches that are needed to illuminate the dark side of the immunopeptidome.
CI  - Copyright (c) 2021 The Authors. Published by Elsevier Inc. All rights reserved.
FAU - Scull, Katherine E
AU  - Scull KE
AD  - Department of Biochemistry and Molecular Biology and Infection and Immunity 
      Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 
      Victoria, Australia.
FAU - Pandey, Kirti
AU  - Pandey K
AD  - Department of Biochemistry and Molecular Biology and Infection and Immunity 
      Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 
      Victoria, Australia.
FAU - Ramarathinam, Sri H
AU  - Ramarathinam SH
AD  - Department of Biochemistry and Molecular Biology and Infection and Immunity 
      Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 
      Victoria, Australia. Electronic address: sri.ramarathinam@monash.edu.
FAU - Purcell, Anthony W
AU  - Purcell AW
AD  - Department of Biochemistry and Molecular Biology and Infection and Immunity 
      Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 
      Victoria, Australia. Electronic address: anthony.purcell@monash.edu.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20210910
PL  - United States
TA  - Mol Cell Proteomics
JT  - Molecular & cellular proteomics : MCP
JID - 101125647
RN  - 0 (Epitopes)
RN  - 0 (HLA Antigens)
RN  - 0 (Peptides)
RN  - 0 (Proteome)
SB  - IM
MH  - *Databases, Protein
MH  - Epitopes
MH  - Genomics
MH  - HLA Antigens/genetics/*metabolism
MH  - Humans
MH  - Peptides/genetics/*metabolism
MH  - Proteome
MH  - RNA-Seq
MH  - Software
MH  - THP-1 Cells
MH  - Transcriptome
MH  - *Workflow
PMC - PMC8724885
OTO - NOTNLM
OT  - HLA
OT  - antigen presentation
OT  - immunology
OT  - immunopeptidomics
OT  - unconventional antigen
COIS- Conflict of interest The authors declare no competing interests.
EDAT- 2021/09/13 06:00
MHDA- 2022/03/25 06:00
PMCR- 2021/09/10
CRDT- 2021/09/12 20:44
PHST- 2021/03/01 00:00 [received]
PHST- 2021/08/10 00:00 [revised]
PHST- 2021/08/24 00:00 [accepted]
PHST- 2021/09/13 06:00 [pubmed]
PHST- 2022/03/25 06:00 [medline]
PHST- 2021/09/12 20:44 [entrez]
PHST- 2021/09/10 00:00 [pmc-release]
AID - S1535-9476(21)00115-8 [pii]
AID - 100143 [pii]
AID - 10.1016/j.mcpro.2021.100143 [doi]
PST - ppublish
SO  - Mol Cell Proteomics. 2021;20:100143. doi: 10.1016/j.mcpro.2021.100143. Epub 2021 
      Sep 10.