PMID- 35675780
OWN - NLM
STAT- MEDLINE
DCOM- 20220610
LR  - 20220912
IS  - 2211-1247 (Electronic)
VI  - 39
IP  - 10
DP  - 2022 Jun 7
TI  - Single-cell RNA-seq-based proteogenomics identifies glioblastoma-specific 
      transposable elements encoding HLA-I-presented peptides.
PG  - 110916
LID - S2211-1247(22)00693-3 [pii]
LID - 10.1016/j.celrep.2022.110916 [doi]
AB  - We analyze transposable elements (TEs) in glioblastoma (GBM) patients using a 
      proteogenomic pipeline that combines single-cell transcriptomics, bulk RNA 
      sequencing (RNA-seq) samples from tumors and healthy-tissue cohorts, and 
      immunopeptidomic samples. We thus identify 370 human leukocyte antigen 
      (HLA)-I-bound peptides encoded by TEs differentially expressed in GBM. Some of 
      the peptides are encoded by repeat sequences from intact open reading frames 
      (ORFs) present in up to several hundred TEs from recent long interspersed nuclear 
      element (LINE)-1, long terminal repeat (LTR), and SVA subfamilies. Other 
      HLA-I-bound peptides are encoded by single copies of TEs from old subfamilies 
      that are expressed recurrently in GBM tumors and not expressed, or very 
      infrequently and at low levels, in healthy tissues (including brain). These 
      peptide-coding, GBM-specific, highly recurrent TEs represent potential 
      tumor-specific targets for cancer immunotherapies.
CI  - Copyright (c) 2022 Institut Curie. Published by Elsevier Inc. All rights reserved.
FAU - Bonte, Pierre-Emmanuel
AU  - Bonte PE
AD  - Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, 
      France.
FAU - Arribas, Yago A
AU  - Arribas YA
AD  - Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, 
      France.
FAU - Merlotti, Antonela
AU  - Merlotti A
AD  - Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, 
      France.
FAU - Carrascal, Montserrat
AU  - Carrascal M
AD  - Biological and Environmental Proteomics, Institut d'Investigacions Biomediques de 
      Barcelona-CSIC, IDIBAPS, Rosello 161, 6a planta, 08036 Barcelona, Spain.
FAU - Zhang, Jiasi Vicky
AU  - Zhang JV
AD  - GBM Translational Center of Excellence, Department of Neurosurgery, Perelman 
      School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
FAU - Zueva, Elina
AU  - Zueva E
AD  - Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, 
      France.
FAU - Binder, Zev A
AU  - Binder ZA
AD  - GBM Translational Center of Excellence, Department of Neurosurgery, Perelman 
      School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
FAU - Alanio, Cecile
AU  - Alanio C
AD  - Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, 
      France; Laboratoire d'Immunologie Clinique, Institut Curie, Paris 75005, France; 
      Parker Institute of Cancer Immunotherapy, San Francisco, CA, USA.
FAU - Goudot, Christel
AU  - Goudot C
AD  - Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, 
      France. Electronic address: christel.goudot@curie.fr.
FAU - Amigorena, Sebastian
AU  - Amigorena S
AD  - Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, 
      France. Electronic address: sebastian.amigorena@curie.fr.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Cell Rep
JT  - Cell reports
JID - 101573691
RN  - 0 (DNA Transposable Elements)
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Peptides)
SB  - IM
MH  - DNA Transposable Elements
MH  - *Glioblastoma/genetics
MH  - *Histocompatibility Antigens Class I/genetics
MH  - Humans
MH  - Peptides/genetics
MH  - *Proteogenomics
MH  - RNA-Seq
OTO - NOTNLM
OT  - HLA-I
OT  - cancer immunotherapy
OT  - endogenous retrovirus
OT  - glioblastoma
OT  - immunopeptidomics
OT  - neoantigen
OT  - non-canonical proteome
OT  - non-coding genome
OT  - single-cell RNA-seq
OT  - transposable elements
COIS- Declaration of interests C.A. is a consultant for Biotherapy Partners. S.A. is 
      shareholder and consultant for Mnemo Therapeutics. P.-E.B., Y.A.A., A.M., E.Z., 
      and C.G. are consultants for Mnemo Therapeutics. A patent related to this work 
      has been deposited under number EP22305355 in European Patent Application.
EDAT- 2022/06/09 06:00
MHDA- 2022/06/11 06:00
CRDT- 2022/06/08 18:23
PHST- 2021/09/21 00:00 [received]
PHST- 2022/03/22 00:00 [revised]
PHST- 2022/05/12 00:00 [accepted]
PHST- 2022/06/08 18:23 [entrez]
PHST- 2022/06/09 06:00 [pubmed]
PHST- 2022/06/11 06:00 [medline]
AID - S2211-1247(22)00693-3 [pii]
AID - 10.1016/j.celrep.2022.110916 [doi]
PST - ppublish
SO  - Cell Rep. 2022 Jun 7;39(10):110916. doi: 10.1016/j.celrep.2022.110916.