PMID- 35740681
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20220716
IS  - 2072-6694 (Print)
IS  - 2072-6694 (Electronic)
IS  - 2072-6694 (Linking)
VI  - 14
IP  - 12
DP  - 2022 Jun 19
TI  - A Novel Proteogenomic Integration Strategy Expands the Breadth of Neo-Epitope 
      Sources.
LID - 10.3390/cancers14123016 [doi]
LID - 3016
AB  - Tumor-specific antigens can activate T cell-based antitumor immune responses and 
      are ideal targets for cancer immunotherapy. However, their identification is 
      still challenging. Although mass spectrometry can directly identify human 
      leukocyte antigen (HLA) binding peptides in tumor cells, it focuses on 
      tumor-specific antigens derived from annotated protein-coding regions 
      constituting only 1.5% of the genome. We developed a novel proteogenomic 
      integration strategy to expand the breadth of tumor-specific epitopes derived 
      from all genomic regions. Using the colorectal cancer cell line HCT116 as a 
      model, we accurately identified 10,737 HLA-presented peptides, 1293 of which were 
      non-canonical peptides that traditional database searches could not identify. 
      Moreover, we found eight tumor neo-epitopes derived from somatic mutations, four 
      of which were not previously reported. Our findings suggest that this new 
      proteogenomic approach holds great promise for increasing the number of 
      tumor-specific antigen candidates, potentially enlarging the tumor target pool 
      and improving cancer immunotherapy.
FAU - Xiang, Haitao
AU  - Xiang H
AUID- ORCID: 0000-0001-9971-1715
AD  - College of Life Sciences, University of Chinese Academy of Sciences, Beijing 
      100049, China.
AD  - BGI-Shenzhen, Shenzhen 518103, China.
FAU - Zhang, Le
AU  - Zhang L
AUID- ORCID: 0000-0002-2526-6484
AD  - BGI-GenoImmune, BGI-Shenzhen, Shenzhen 518083, China.
FAU - Bu, Fanyu
AU  - Bu F
AUID- ORCID: 0000-0002-0875-7708
AD  - BGI-Shenzhen, Shenzhen 518103, China.
FAU - Guan, Xiangyu
AU  - Guan X
AD  - College of Life Sciences, University of Chinese Academy of Sciences, Beijing 
      100049, China.
AD  - BGI-Shenzhen, Shenzhen 518103, China.
FAU - Chen, Lei
AU  - Chen L
AD  - BGI-Shenzhen, Shenzhen 518103, China.
FAU - Zhang, Haibo
AU  - Zhang H
AD  - BGI-Shenzhen, Shenzhen 518103, China.
FAU - Zhao, Yuntong
AU  - Zhao Y
AUID- ORCID: 0000-0002-5729-8747
AD  - BGI-Shenzhen, Shenzhen 518103, China.
FAU - Chen, Huanyi
AU  - Chen H
AD  - BGI-Shenzhen, Shenzhen 518103, China.
FAU - Zhang, Weicong
AU  - Zhang W
AD  - College of Life Sciences, University of Chinese Academy of Sciences, Beijing 
      100049, China.
AD  - BGI-Shenzhen, Shenzhen 518103, China.
FAU - Li, Yijian
AU  - Li Y
AD  - College of Life Sciences, University of Chinese Academy of Sciences, Beijing 
      100049, China.
AD  - BGI-Shenzhen, Shenzhen 518103, China.
AD  - Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key 
      Laboratory of Genomics, Shenzhen 518083, China.
FAU - Lee, Leo Jingyu
AU  - Lee LJ
AD  - BGI-GenoImmune, BGI-Shenzhen, Shenzhen 518083, China.
FAU - Mei, Zhanlong
AU  - Mei Z
AD  - BGI, Shenzhen 518083, China.
FAU - Rao, Yuan
AU  - Rao Y
AD  - BGI, Shenzhen 518083, China.
FAU - Gu, Ying
AU  - Gu Y
AD  - BGI-Shenzhen, Shenzhen 518103, China.
AD  - Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120, 
      China.
FAU - Hou, Yong
AU  - Hou Y
AD  - BGI, Shenzhen 518083, China.
FAU - Mu, Feng
AU  - Mu F
AUID- ORCID: 0000-0002-0496-4996
AD  - BGI, Shenzhen 518083, China.
FAU - Dong, Xuan
AU  - Dong X
AD  - BGI-Shenzhen, Shenzhen 518103, China.
AD  - Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key 
      Laboratory of Genomics, Shenzhen 518083, China.
LA  - eng
GR  - JSGG20180508152912700/the Science, Technology and Innovation Commission of 
      Shenzhen Municipality/
GR  - 2020B1212070028/the Guangdong Enterprise Key Laboratory of Human Disease 
      Genomics/
PT  - Journal Article
DEP - 20220619
PL  - Switzerland
TA  - Cancers (Basel)
JT  - Cancers
JID - 101526829
PMC - PMC9220843
OTO - NOTNLM
OT  - immunopeptidome
OT  - immunotherapy
OT  - mass spectrometry
OT  - neo-epitope
COIS- The authors declare no conflict of interest.
EDAT- 2022/06/25 06:00
MHDA- 2022/06/25 06:01
PMCR- 2022/06/19
CRDT- 2022/06/24 01:07
PHST- 2022/05/08 00:00 [received]
PHST- 2022/06/09 00:00 [revised]
PHST- 2022/06/13 00:00 [accepted]
PHST- 2022/06/24 01:07 [entrez]
PHST- 2022/06/25 06:00 [pubmed]
PHST- 2022/06/25 06:01 [medline]
PHST- 2022/06/19 00:00 [pmc-release]
AID - cancers14123016 [pii]
AID - cancers-14-03016 [pii]
AID - 10.3390/cancers14123016 [doi]
PST - epublish
SO  - Cancers (Basel). 2022 Jun 19;14(12):3016. doi: 10.3390/cancers14123016.