PMID- 29242379
OWN - NLM
STAT- MEDLINE
DCOM- 20190213
LR  - 20240321
IS  - 1535-9484 (Electronic)
IS  - 1535-9476 (Print)
IS  - 1535-9476 (Linking)
VI  - 17
IP  - 3
DP  - 2018 Mar
TI  - High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound 
      Interferongamma-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome.
PG  - 533-548
LID - 10.1074/mcp.TIR117.000383 [doi]
AB  - Comprehensive knowledge of the human leukocyte antigen (HLA) class-I and class-II 
      peptides presented to T-cells is crucial for designing innovative therapeutics 
      against cancer and other diseases. However methodologies for their purification 
      for mass-spectrometry analysis have been a major limitation. We designed a novel 
      high-throughput, reproducible and sensitive method for sequential immuno-affinity 
      purification of HLA-I and -II peptides from up to 96 samples in a plate format, 
      suitable for both cell lines and tissues. Our methodology drastically reduces 
      sample-handling and can be completed within five hours. We challenged our 
      methodology by extracting HLA peptides from multiple replicates of tissues (n = 
      7) and cell lines (n = 21, 10(8) cells per replicate), which resulted in 
      unprecedented depth, sensitivity and high reproducibility (Pearson correlations 
      up to 0.98 and 0.97 for HLA-I and HLA-II). Because of the method's achieved 
      sensitivity, even single measurements of peptides purified from 10(7) B-cells 
      resulted in the identification of more than 1700 HLA-I and 2200 HLA-II peptides. 
      We demonstrate the feasibility of performing drug-screening by using ovarian 
      cancer cells treated with interferon gamma (IFNgamma). Our analysis revealed an 
      augmented presentation of chymotryptic-like and longer ligands associated with 
      IFNgamma induced changes of the antigen processing and presentation machinery. This 
      straightforward method is applicable for basic and clinical applications.
CI  - (c) 2018 by The American Society for Biochemistry and Molecular Biology, Inc.
FAU - Chong, Chloe
AU  - Chong C
AD  - From the double daggerLudwig Institute for Cancer Research, University of Lausanne, 1066 
      Epalinges, Switzerland.
AD  -  section signDepartment of Oncology, University Hospital of Lausanne, 1011 Lausanne, 
      Switzerland.
FAU - Marino, Fabio
AU  - Marino F
AD  - From the double daggerLudwig Institute for Cancer Research, University of Lausanne, 1066 
      Epalinges, Switzerland.
AD  -  section signDepartment of Oncology, University Hospital of Lausanne, 1011 Lausanne, 
      Switzerland.
FAU - Pak, HuiSong
AU  - Pak H
AD  - From the double daggerLudwig Institute for Cancer Research, University of Lausanne, 1066 
      Epalinges, Switzerland.
AD  -  section signDepartment of Oncology, University Hospital of Lausanne, 1011 Lausanne, 
      Switzerland.
FAU - Racle, Julien
AU  - Racle J
AD  - From the double daggerLudwig Institute for Cancer Research, University of Lausanne, 1066 
      Epalinges, Switzerland.
AD  -  section signDepartment of Oncology, University Hospital of Lausanne, 1011 Lausanne, 
      Switzerland.
AD  - **Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
FAU - Daniel, Roy T
AU  - Daniel RT
AD  -  paragraph signService of Neurosurgery, University Hospital of Lausanne, 1011 Lausanne, 
      Switzerland.
FAU - Muller, Markus
AU  - Muller M
AD  -  ||Vital IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
FAU - Gfeller, David
AU  - Gfeller D
AD  - From the double daggerLudwig Institute for Cancer Research, University of Lausanne, 1066 
      Epalinges, Switzerland.
AD  -  section signDepartment of Oncology, University Hospital of Lausanne, 1011 Lausanne, 
      Switzerland.
AD  - **Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
FAU - Coukos, George
AU  - Coukos G
AD  - From the double daggerLudwig Institute for Cancer Research, University of Lausanne, 1066 
      Epalinges, Switzerland.
AD  -  section signDepartment of Oncology, University Hospital of Lausanne, 1011 Lausanne, 
      Switzerland.
FAU - Bassani-Sternberg, Michal
AU  - Bassani-Sternberg M
AD  - From the double daggerLudwig Institute for Cancer Research, University of Lausanne, 1066 
      Epalinges, Switzerland; Michal.bassani@chuv.ch.
AD  -  section signDepartment of Oncology, University Hospital of Lausanne, 1011 Lausanne, 
      Switzerland.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20171214
PL  - United States
TA  - Mol Cell Proteomics
JT  - Molecular & cellular proteomics : MCP
JID - 101125647
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Histocompatibility Antigens Class II)
RN  - 0 (Ligands)
RN  - 0 (Peptides)
RN  - 82115-62-6 (Interferon-gamma)
SB  - IM
MH  - B-Lymphocytes/metabolism
MH  - Cell Line
MH  - Histocompatibility Antigens Class I/*metabolism
MH  - Histocompatibility Antigens Class II/*metabolism
MH  - Humans
MH  - Interferon-gamma/*pharmacology
MH  - Ligands
MH  - Neoplasms/metabolism
MH  - Peptides/*metabolism
MH  - Proteomics/methods
MH  - T-Lymphocytes/metabolism
PMC - PMC5836376
EDAT- 2017/12/16 06:00
MHDA- 2019/02/14 06:00
PMCR- 2017/12/14
CRDT- 2017/12/16 06:00
PHST- 2017/10/05 00:00 [received]
PHST- 2017/12/12 00:00 [revised]
PHST- 2017/12/16 06:00 [pubmed]
PHST- 2019/02/14 06:00 [medline]
PHST- 2017/12/16 06:00 [entrez]
PHST- 2017/12/14 00:00 [pmc-release]
AID - S1535-9476(20)32260-X [pii]
AID - TIR117.000383 [pii]
AID - 10.1074/mcp.TIR117.000383 [doi]
PST - ppublish
SO  - Mol Cell Proteomics. 2018 Mar;17(3):533-548. doi: 10.1074/mcp.TIR117.000383. Epub 
      2017 Dec 14.