PMID- 36060059
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20230228
IS  - 2589-0042 (Electronic)
IS  - 2589-0042 (Linking)
VI  - 25
IP  - 9
DP  - 2022 Sep 16
TI  - The role of antigen expression in shaping the repertoire of HLA presented 
      ligands.
PG  - 104975
LID - 10.1016/j.isci.2022.104975 [doi]
LID - 104975
AB  - Human leukocyte antigen (HLA) presentation of peptides is a prerequisite of 
      T cell immune activation. The understanding of the rules defining this event has 
      large implications for our knowledge of basic immunology and for the rational 
      design of immuno-therapeutics and vaccines. Historically, most of the available 
      prediction methods have been solely focused on the information related to antigen 
      processing and presentation. Recent work has, however, demonstrated that method 
      performance can be boosted by integrating information related to antigen 
      abundance. Here we expand on these later findings and develop an extended version 
      of NetMHCpan, called NetMHCpanExp, integrating information on antigen abundance 
      from RNA-Seq experiments. In line with earlier works, the model demonstrates 
      improved performance for both HLA ligand and cancer neoantigen epitope 
      prediction. Optimal results are obtained by use of sample-specific abundance 
      information but also reference datasets can be applied with a limited performance 
      drop. The developed tool is available at 
      https://services.healthtech.dtu.dk/service.php?NetMHCpanExp-1.0.
CI  - (c) 2022 The Author(s).
FAU - Garcia Alvarez, Heli M
AU  - Garcia Alvarez HM
AD  - Instituto de Investigaciones Biotecnologicas, Universidad Nacional de San Martin, 
      CP 1650 San Martin, Argentina.
FAU - Kosaloglu-Yalcin, Zeynep
AU  - Kosaloglu-Yalcin Z
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology, La Jolla, 92037 CA, USA.
FAU - Peters, Bjoern
AU  - Peters B
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology, La Jolla, 92037 CA, USA.
AD  - Department of Medicine, University of California, San Diego, La Jolla, 92093 CA, 
      USA.
FAU - Nielsen, Morten
AU  - Nielsen M
AD  - Instituto de Investigaciones Biotecnologicas, Universidad Nacional de San Martin, 
      CP 1650 San Martin, Argentina.
AD  - Department of Health Technology, Technical University of Denmark, DK-2800 Lyngby, 
      Denmark.
LA  - eng
GR  - U24 CA248138/CA/NCI NIH HHS/United States
PT  - Journal Article
DEP - 20220817
PL  - United States
TA  - iScience
JT  - iScience
JID - 101724038
PMC - PMC9437844
OTO - NOTNLM
OT  - Immunology
OT  - biocomputational method
OT  - biological sciences tools
OT  - transcriptomics
COIS- The authors declare no competing interests.
EDAT- 2022/09/06 06:00
MHDA- 2022/09/06 06:01
PMCR- 2022/08/17
CRDT- 2022/09/05 03:48
PHST- 2022/04/16 00:00 [received]
PHST- 2022/07/21 00:00 [revised]
PHST- 2022/08/14 00:00 [accepted]
PHST- 2022/09/05 03:48 [entrez]
PHST- 2022/09/06 06:00 [pubmed]
PHST- 2022/09/06 06:01 [medline]
PHST- 2022/08/17 00:00 [pmc-release]
AID - S2589-0042(22)01247-0 [pii]
AID - 104975 [pii]
AID - 10.1016/j.isci.2022.104975 [doi]
PST - epublish
SO  - iScience. 2022 Aug 17;25(9):104975. doi: 10.1016/j.isci.2022.104975. eCollection 
      2022 Sep 16.