PMID- 38000035
OWN - NLM
STAT- MEDLINE
DCOM- 20231127
LR  - 20240210
IS  - 2375-2548 (Electronic)
IS  - 2375-2548 (Linking)
VI  - 9
IP  - 47
DP  - 2023 Nov 24
TI  - Accurate prediction of HLA class II antigen presentation across all loci using 
      tailored data acquisition and refined machine learning.
PG  - eadj6367
LID - 10.1126/sciadv.adj6367 [doi]
LID - eadj6367
AB  - Accurate prediction of antigen presentation by human leukocyte antigen (HLA) 
      class II molecules is crucial for rational development of immunotherapies and 
      vaccines targeting CD4(+) T cell activation. So far, most prediction methods for 
      HLA class II antigen presentation have focused on HLA-DR because of limited 
      availability of immunopeptidomics data for HLA-DQ and HLA-DP while not taking 
      into account alternative peptide binding modes. We present an update to the 
      NetMHCIIpan prediction method, which closes the performance gap between all three 
      HLA class II loci. We accomplish this by first integrating large 
      immunopeptidomics datasets describing the HLA class II specificity space across 
      all loci using a refined machine learning framework that accommodates inverted 
      peptide binders. Next, we apply targeted immunopeptidomics assays to generate 
      data that covers additional HLA-DP specificities. The final method, 
      NetMHCIIpan-4.3, achieves high accuracy and molecular coverage across all HLA 
      class II allotypes.
FAU - Nilsson, Jonas B
AU  - Nilsson JB
AUID- ORCID: 0000-0002-1322-2644
AD  - Department of Health Technology, Technical University of Denmark, DK-2800 Lyngby, 
      Denmark.
FAU - Kaabinejadian, Saghar
AU  - Kaabinejadian S
AUID- ORCID: 0000-0002-8434-8703
AD  - Pure MHC LLC, Oklahoma City, OK, USA.
AD  - Department of Microbiology and Immunology, University of Oklahoma Health Sciences 
      Center, Oklahoma City, OK, USA.
FAU - Yari, Hooman
AU  - Yari H
AUID- ORCID: 0000-0002-8285-7985
AD  - Department of Microbiology and Immunology, University of Oklahoma Health Sciences 
      Center, Oklahoma City, OK, USA.
FAU - Kester, Michel G D
AU  - Kester MGD
AUID- ORCID: 0000-0002-8960-7348
AD  - Department of Hematology, Leiden University Medical Center, Leiden, Netherlands.
FAU - van Balen, Peter
AU  - van Balen P
AUID- ORCID: 0000-0002-9670-4664
AD  - Department of Hematology, Leiden University Medical Center, Leiden, Netherlands.
FAU - Hildebrand, William H
AU  - Hildebrand WH
AUID- ORCID: 0000-0002-7066-4174
AD  - Department of Microbiology and Immunology, University of Oklahoma Health Sciences 
      Center, Oklahoma City, OK, USA.
FAU - Nielsen, Morten
AU  - Nielsen M
AUID- ORCID: 0000-0001-7885-4311
AD  - Department of Health Technology, Technical University of Denmark, DK-2800 Lyngby, 
      Denmark.
LA  - eng
GR  - 75N93019C00001/AI/NIAID NIH HHS/United States
GR  - U24 CA248138/CA/NCI NIH HHS/United States
PT  - Journal Article
DEP - 20231124
PL  - United States
TA  - Sci Adv
JT  - Science advances
JID - 101653440
RN  - 0 (HLA-DR Antigens)
RN  - 0 (HLA-DP Antigens)
RN  - 0 (HLA-DQ Antigens)
RN  - 0 (Peptides)
SB  - IM
MH  - Humans
MH  - *Antigen Presentation
MH  - *HLA-DR Antigens/metabolism
MH  - HLA-DP Antigens/chemistry
MH  - HLA-DQ Antigens/chemistry
MH  - Peptides/chemistry
PMC - PMC10672173
EDAT- 2023/11/24 18:42
MHDA- 2023/11/27 12:43
PMCR- 2023/11/24
CRDT- 2023/11/24 14:03
PHST- 2023/11/27 12:43 [medline]
PHST- 2023/11/24 18:42 [pubmed]
PHST- 2023/11/24 14:03 [entrez]
PHST- 2023/11/24 00:00 [pmc-release]
AID - adj6367 [pii]
AID - 10.1126/sciadv.adj6367 [doi]
PST - ppublish
SO  - Sci Adv. 2023 Nov 24;9(47):eadj6367. doi: 10.1126/sciadv.adj6367. Epub 2023 Nov 
      24.