PMID- 27452731
OWN - NLM
STAT- MEDLINE
DCOM- 20170620
LR  - 20210217
IS  - 1535-9484 (Electronic)
IS  - 1535-9476 (Print)
IS  - 1535-9476 (Linking)
VI  - 15
IP  - 9
DP  - 2016 Sep
TI  - Approach for Identifying Human Leukocyte Antigen (HLA)-DR Bound Peptides from 
      Scarce Clinical Samples.
PG  - 3017-29
LID - 10.1074/mcp.M116.060764 [doi]
AB  - Immune-mediated diseases strongly associating with human leukocyte antigen (HLA) 
      alleles are likely linked to specific antigens. These antigens are presented to T 
      cells in the form of peptides bound to HLA molecules on antigen presenting cells, 
      e.g. dendritic cells, macrophages or B cells. The identification of HLA-DR-bound 
      peptides presents a valuable tool to investigate the human immunopeptidome. The 
      lung is likely a key player in the activation of potentially auto-aggressive T 
      cells prior to entering target tissues and inducing autoimmune disease. This 
      makes the lung of exceptional interest and presents an ideal paradigm to study 
      the human immunopeptidome and to identify antigenic peptides.Our previous 
      investigation of HLA-DR peptide presentation in the lung required high numbers of 
      cells (800 x 10(6) bronchoalveolar lavage (BAL) cells). Because BAL from healthy 
      nonsmokers typically contains 10-15 x 10(6) cells, there is a need for a highly 
      sensitive approach to study immunopeptides in the lungs of individual patients 
      and controls.In this work, we analyzed the HLA-DR immunopeptidome in the lung by 
      an optimized methodology to identify HLA-DR-bound peptides from low cell numbers. 
      We used an Epstein-Barr Virus (EBV) immortalized B cell line and bronchoalveolar 
      lavage (BAL) cells obtained from patients with sarcoidosis, an inflammatory T 
      cell driven disease mainly occurring in the lung. Specifically, membrane 
      complexes were isolated prior to immunoprecipitation, eluted peptides were 
      identified by nanoLC-MS/MS and processed using the in-house developed 
      ClusterMHCII software. With the optimized procedure we were able to identify 
      peptides from 10 x 10(6) cells, which on average correspond to 10.9 
      peptides/million cells in EBV-B cells and 9.4 peptides/million cells in BAL 
      cells. This work presents an optimized approach designed to identify HLA-DR-bound 
      peptides from low numbers of cells, enabling the investigation of the BAL 
      immunopeptidome from individual patients and healthy controls in order to 
      identify disease-associated peptides.
CI  - (c) 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
FAU - Heyder, Tina
AU  - Heyder T
AD  - From the double daggerRespiratory Medicine Unit, Department of Medicine and Center for 
      Molecular Medicine, Solna, Karolinska Institutet and Karolinska University 
      Hospital, Stockholm, Sweden;  section signDivision of Physiological Chemistry I, Department 
      of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden;
FAU - Kohler, Maxie
AU  - Kohler M
AD  - From the double daggerRespiratory Medicine Unit, Department of Medicine and Center for 
      Molecular Medicine, Solna, Karolinska Institutet and Karolinska University 
      Hospital, Stockholm, Sweden;
FAU - Tarasova, Nataliya K
AU  - Tarasova NK
AD  -  section signDivision of Physiological Chemistry I, Department of Medical Biochemistry and 
      Biophysics, Karolinska Institutet, Stockholm, Sweden;
FAU - Haag, Sabrina
AU  - Haag S
AD  -  paragraph signDivision of Medical Inflammation Research, Department of Medical Biochemistry 
      and Biophysics, Karolinska Institutet, Stockholm, Sweden;
FAU - Rutishauser, Dorothea
AU  - Rutishauser D
AD  -  section signDivision of Physiological Chemistry I, Department of Medical Biochemistry and 
      Biophysics, Karolinska Institutet, Stockholm, Sweden;
FAU - Rivera, Natalia V
AU  - Rivera NV
AD  - From the double daggerRespiratory Medicine Unit, Department of Medicine and Center for 
      Molecular Medicine, Solna, Karolinska Institutet and Karolinska University 
      Hospital, Stockholm, Sweden;
FAU - Sandin, Charlotta
AU  - Sandin C
AD  -  ||Rheumatology Unit, Department of Medicine, Solna, Karolinska Institutet, 
      Stockholm, Sweden.
FAU - Mia, Sohel
AU  - Mia S
AD  -  ||Rheumatology Unit, Department of Medicine, Solna, Karolinska Institutet, 
      Stockholm, Sweden.
FAU - Malmstrom, Vivianne
AU  - Malmstrom V
AD  -  ||Rheumatology Unit, Department of Medicine, Solna, Karolinska Institutet, 
      Stockholm, Sweden.
FAU - Wheelock, Asa M
AU  - Wheelock AM
AD  - From the double daggerRespiratory Medicine Unit, Department of Medicine and Center for 
      Molecular Medicine, Solna, Karolinska Institutet and Karolinska University 
      Hospital, Stockholm, Sweden;
FAU - Wahlstrom, Jan
AU  - Wahlstrom J
AD  - From the double daggerRespiratory Medicine Unit, Department of Medicine and Center for 
      Molecular Medicine, Solna, Karolinska Institutet and Karolinska University 
      Hospital, Stockholm, Sweden;
FAU - Holmdahl, Rikard
AU  - Holmdahl R
AD  -  paragraph signDivision of Medical Inflammation Research, Department of Medical Biochemistry 
      and Biophysics, Karolinska Institutet, Stockholm, Sweden;
FAU - Eklund, Anders
AU  - Eklund A
AD  - From the double daggerRespiratory Medicine Unit, Department of Medicine and Center for 
      Molecular Medicine, Solna, Karolinska Institutet and Karolinska University 
      Hospital, Stockholm, Sweden;
FAU - Zubarev, Roman A
AU  - Zubarev RA
AD  -  section signDivision of Physiological Chemistry I, Department of Medical Biochemistry and 
      Biophysics, Karolinska Institutet, Stockholm, Sweden;
FAU - Grunewald, Johan
AU  - Grunewald J
AD  - From the double daggerRespiratory Medicine Unit, Department of Medicine and Center for 
      Molecular Medicine, Solna, Karolinska Institutet and Karolinska University 
      Hospital, Stockholm, Sweden;
FAU - Ytterberg, A Jimmy
AU  - Ytterberg AJ
AD  -  section signDivision of Physiological Chemistry I, Department of Medical Biochemistry and 
      Biophysics, Karolinska Institutet, Stockholm, Sweden;  ||Rheumatology Unit, 
      Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden 
      jimmy.ytterberg@ki.se.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20160724
PL  - United States
TA  - Mol Cell Proteomics
JT  - Molecular & cellular proteomics : MCP
JID - 101125647
RN  - 0 (HLA-DR Antigens)
RN  - 0 (Peptides)
SB  - IM
MH  - Adult
MH  - Bronchoalveolar Lavage Fluid/cytology/*immunology
MH  - Cells, Cultured
MH  - Female
MH  - HLA-DR Antigens/*metabolism
MH  - Humans
MH  - Male
MH  - Middle Aged
MH  - Peptides/*analysis/chemistry/immunology
MH  - Protein Binding
MH  - Sarcoidosis/immunology/*therapy
PMC - PMC5013314
EDAT- 2016/07/28 06:00
MHDA- 2017/06/21 06:00
PMCR- 2017/09/01
CRDT- 2016/07/26 06:00
PHST- 2016/05/06 00:00 [received]
PHST- 2016/07/26 06:00 [entrez]
PHST- 2016/07/28 06:00 [pubmed]
PHST- 2017/06/21 06:00 [medline]
PHST- 2017/09/01 00:00 [pmc-release]
AID - S1535-9476(20)33376-4 [pii]
AID - M116.060764 [pii]
AID - 10.1074/mcp.M116.060764 [doi]
PST - ppublish
SO  - Mol Cell Proteomics. 2016 Sep;15(9):3017-29. doi: 10.1074/mcp.M116.060764. Epub 
      2016 Jul 24.