PMID- 32523802
OWN - NLM
STAT- MEDLINE
DCOM- 20210728
LR  - 20220531
IS  - 2162-4011 (Print)
IS  - 2162-402X (Electronic)
IS  - 2162-4011 (Linking)
VI  - 9
IP  - 1
DP  - 2020
TI  - HLA class-I and class-II restricted neoantigen loads predict overall survival in 
      breast cancer.
PG  - 1744947
LID - 10.1080/2162402X.2020.1744947 [doi]
LID - 1744947
AB  - Tumors acquire numerous mutations during development and progression. When 
      translated into proteins, these mutations give rise to neoantigens that can be 
      recognized by T cells and generate antibodies, representing an exciting direction 
      of cancer immunotherapy. While neoantigens have been reported in many cancer 
      types, the profiling of neoantigens often focused on the class-I subtype that are 
      presented to CD8 + T cells, and the relationship between neoantigen load and 
      clinical outcomes was often inconsistent among cancer types. In this study, we 
      described an informatics workflow, REAL-neo, for identification, quality control 
      (QC), and prioritization of both class-I and class-II human leukocyte antigen 
      (HLA) bound neoantigens that arise from somatic single nucleotide mutations 
      (SNM), small insertions and deletions (INDEL), and gene fusions. We applied 
      REAL-neo to 835 primary breast tumors in the Cancer Genome Atlas (TCGA) and 
      performed comprehensive profiling and characterization of the detected 
      neoantigens. We found recurrent HLA class-I and class-II restricted neoantigens 
      across breast cancer cases, and uncovered associations between neoantigen load 
      and clinical traits. Both class-I and class-II neoantigen loads from SNM and 
      INDEL were found to predict overall survival independent of tumor mutational 
      burden (TMB), breast cancer subtypes, tumor-infiltrating lymphocyte (TIL) levels, 
      tumor stage, and age at diagnosis. Our study highlighted the importance of 
      accurate and comprehensive neoantigen profiling and QC, and is the first to 
      report the predictive value of neoantigen load for overall survival in breast 
      cancer.
CI  - (c) 2020 The Author(s). Published with license by Taylor & Francis Group, LLC.
FAU - Ren, Yingxue
AU  - Ren Y
AD  - Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA.
FAU - Cherukuri, Yesesri
AU  - Cherukuri Y
AD  - Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA.
FAU - Wickland, Daniel P
AU  - Wickland DP
AD  - Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA.
FAU - Sarangi, Vivekananda
AU  - Sarangi V
AD  - Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.
FAU - Tian, Shulan
AU  - Tian S
AD  - Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.
FAU - Carter, Jodi M
AU  - Carter JM
AD  - Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
FAU - Mansfield, Aaron S
AU  - Mansfield AS
AUID- ORCID: 0000-0002-9483-6903
AD  - Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA.
FAU - Block, Matthew S
AU  - Block MS
AD  - Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA.
FAU - Sherman, Mark E
AU  - Sherman ME
AD  - Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA.
FAU - Knutson, Keith L
AU  - Knutson KL
AD  - Department of Immunology, Mayo Clinic, Jacksonville, FL, USA.
FAU - Lin, Yi
AU  - Lin Y
AD  - Division of Hematology, Mayo Clinic, Rochester, MN, USA.
FAU - Asmann, Yan W
AU  - Asmann YW
AD  - Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20200401
PL  - United States
TA  - Oncoimmunology
JT  - Oncoimmunology
JID - 101570526
RN  - 0 (Antigens, Neoplasm)
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Histocompatibility Antigens Class II)
MH  - *Antigens, Neoplasm/genetics
MH  - *Breast Neoplasms/diagnosis/genetics
MH  - Female
MH  - Histocompatibility Antigens Class I
MH  - Histocompatibility Antigens Class II
MH  - Humans
MH  - Immunotherapy
MH  - Lymphocytes, Tumor-Infiltrating
MH  - Survival Rate
PMC - PMC7255108
OTO - NOTNLM
OT  - Breast cancer
OT  - neoantigen
OT  - overall survival
OT  - tumor mutational burden
EDAT- 2020/06/12 06:00
MHDA- 2020/06/12 06:01
PMCR- 2020/04/01
CRDT- 2020/06/12 06:00
PHST- 2019/11/06 00:00 [received]
PHST- 2020/01/21 00:00 [revised]
PHST- 2020/02/17 00:00 [accepted]
PHST- 2020/06/12 06:00 [entrez]
PHST- 2020/06/12 06:00 [pubmed]
PHST- 2020/06/12 06:01 [medline]
PHST- 2020/04/01 00:00 [pmc-release]
AID - 1744947 [pii]
AID - 10.1080/2162402X.2020.1744947 [doi]
PST - epublish
SO  - Oncoimmunology. 2020 Apr 1;9(1):1744947. doi: 10.1080/2162402X.2020.1744947. 
      eCollection 2020.