PMID- 33363023
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20201229
IS  - 2234-943X (Print)
IS  - 2234-943X (Electronic)
IS  - 2234-943X (Linking)
VI  - 10
DP  - 2020
TI  - Systematically Characterizing A-to-I RNA Editing Neoantigens in Cancer.
PG  - 593989
LID - 10.3389/fonc.2020.593989 [doi]
LID - 593989
AB  - A-to-I RNA editing can contribute to the transcriptomic and proteomic diversity 
      of many diseases including cancer. It has been reported that peptides generated 
      from RNA editing could be naturally presented by human leukocyte antigen (HLA) 
      molecules and elicit CD8+ T cell activation. However, a systematical 
      characterization of A-to-I RNA editing neoantigens in cancer is still lacking. 
      Here, an integrated RNA-editing based neoantigen identification pipeline PREP 
      (Prioritizing of RNA Editing-based Peptides) was presented. A comprehensive RNA 
      editing neoantigen profile analysis on 12 cancer types from The Cancer Genome 
      Atlas (TCGA) cohorts was performed. PREP was also applied to 14 ovarian tumor 
      samples and two clinical melanoma cohorts treated with immunotherapy. We finally 
      proposed an RNA editing neoantigen immunogenicity score scheme, i.e. REscore, 
      which takes RNA editing level and infiltrating immune cell population into 
      consideration. We reported variant peptide from protein IFI30 in breast cancer 
      which was confirmed expressed and presented in two samples with mass spectrometry 
      data support. We showed that RNA editing neoantigen could be identified from 
      RNA-seq data and could be validated with mass spectrometry data in ovarian tumor 
      samples. Furthermore, we characterized the RNA editing neoantigen profile of 
      clinical melanoma cohorts treated with immunotherapy. Finally, REscore showed 
      significant associations with improved overall survival in melanoma cohorts 
      treated with immunotherapy. These findings provided novel insights of cancer 
      biomarker and enhance our understanding of neoantigen derived from A-to-I RNA 
      editing as well as more types of candidates for personalized cancer vaccines 
      design in the context of cancer immunotherapy.
CI  - Copyright (c) 2020 Zhou, Wei, Zhang, Yang and Liu.
FAU - Zhou, Chi
AU  - Zhou C
AD  - Translational Medical Center for Stem Cell Therapy and Institute for Regenerative 
      Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life 
      Sciences and Technology, Tongji University, Shanghai, China.
FAU - Wei, Zhiting
AU  - Wei Z
AD  - Translational Medical Center for Stem Cell Therapy and Institute for Regenerative 
      Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life 
      Sciences and Technology, Tongji University, Shanghai, China.
FAU - Zhang, Liye
AU  - Zhang L
AD  - School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
FAU - Yang, Zhaoyi
AU  - Yang Z
AD  - Department of Pharmacy, The First Affiliated Hospital of University of Science 
      and Technology of China, Hefei, China.
FAU - Liu, Qi
AU  - Liu Q
AD  - Translational Medical Center for Stem Cell Therapy and Institute for Regenerative 
      Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life 
      Sciences and Technology, Tongji University, Shanghai, China.
LA  - eng
PT  - Journal Article
DEP - 20201210
PL  - Switzerland
TA  - Front Oncol
JT  - Frontiers in oncology
JID - 101568867
PMC - PMC7758481
OTO - NOTNLM
OT  - RNA editing
OT  - cancer immunotherapy
OT  - melanoma
OT  - neoantigen identification
OT  - predictive biomarker
COIS- The authors declare that the research was conducted in the absence of any 
      commercial or financial relationships that could be construed as a potential 
      conflict of interest.
EDAT- 2020/12/29 06:00
MHDA- 2020/12/29 06:01
PMCR- 2020/01/01
CRDT- 2020/12/28 11:57
PHST- 2020/08/12 00:00 [received]
PHST- 2020/11/09 00:00 [accepted]
PHST- 2020/12/28 11:57 [entrez]
PHST- 2020/12/29 06:00 [pubmed]
PHST- 2020/12/29 06:01 [medline]
PHST- 2020/01/01 00:00 [pmc-release]
AID - 10.3389/fonc.2020.593989 [doi]
PST - epublish
SO  - Front Oncol. 2020 Dec 10;10:593989. doi: 10.3389/fonc.2020.593989. eCollection 
      2020.