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      The HLA Class II Allele DRB1*1501 Is Over-Represented in Patients with Idiopathic Pulmonary Fibrosis

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          Abstract

          Background

          Idiopathic pulmonary fibrosis (IPF) is a progressive and medically refractory lung disease with a grim prognosis. Although the etiology of IPF remains perplexing, abnormal adaptive immune responses are evident in many afflicted patients. We hypothesized that perturbations of human leukocyte antigen (HLA) allele frequencies, which are often seen among patients with immunologic diseases, may also be present in IPF patients.

          Methods/Principal Findings

          HLA alleles were determined in subpopulations of IPF and normal subjects using molecular typing methods. HLA-DRB1*15 was over-represented in a discovery cohort of 79 Caucasian IPF subjects who had lung transplantations at the University of Pittsburgh (36.7%) compared to normal reference populations. These findings were prospectively replicated in a validation cohort of 196 additional IPF subjects from four other U.S. medical centers that included both ambulatory patients and lung transplantation recipients. High-resolution typing was used to further define specific HLA-DRB1*15 alleles. DRB1*1501 prevalence in IPF subjects was similar among the 143 ambulatory patients and 132 transplant recipients (31.5% and 34.8%, respectively, p = 0.55). The aggregate prevalence of DRB1*1501 in IPF patients was significantly greater than among 285 healthy controls (33.1% vs. 20.0%, respectively, OR 2.0; 95%CI 1.3–2.9, p = 0.0004). IPF patients with DRB1*1501 (n = 91) tended to have decreased diffusing capacities for carbon monoxide (DL CO) compared to the 184 disease subjects who lacked this allele (37.8±1.7% vs. 42.8±1.4%, p = 0.036).

          Conclusions/Significance

          DRB1*1501 is more prevalent among IPF patients than normal subjects, and may be associated with greater impairment of gas exchange. These data are novel evidence that immunogenetic processes can play a role in the susceptibility to and/or manifestations of IPF. Findings here of a disease association at the HLA-DR locus have broad pathogenic implications, illustrate a specific chromosomal area for incremental, targeted genomic study, and may identify a distinct clinical phenotype among patients with this enigmatic, morbid lung disease.

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          Most cited references30

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          How TCRs bind MHCs, peptides, and coreceptors.

          Since the first crystal structure determinations of alphabeta T cell receptors (TCRs) bound to class I MHC-peptide (pMHC) antigens in 1996, a sizable database of 24 class I and class II TCR/pMHC complexes has been accumulated that now defines a substantial degree of structural variability in TCR/pMHC recognition. Recent determination of free and bound gammadelta TCR structures has enabled comparisons of the modes of antigen recognition by alphabeta and gammadelta T cells and antibodies. Crystal structures of TCR accessory (CD4, CD8) and coreceptor molecules (CD3epsilondelta, CD3epsilongamma) have further advanced our structural understanding of most of the components that constitute the TCR signaling complex. Despite all these efforts, the structural basis for MHC restriction and signaling remains elusive as no structural features that define a common binding mode or signaling mechanism have yet been gleaned from the current set of TCR/pMHC complexes. Notwithstanding, the impressive array of self, foreign (microbial), and autoimmune TCR complexes have uncovered the diverse ways in which antigens can be specifically recognized by TCRs.
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            A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC.

            The proteins encoded by the classical HLA class I and class II genes in the major histocompatibility complex (MHC) are highly polymorphic and are essential in self versus non-self immune recognition. HLA variation is a crucial determinant of transplant rejection and susceptibility to a large number of infectious and autoimmune diseases. Yet identification of causal variants is problematic owing to linkage disequilibrium that extends across multiple HLA and non-HLA genes in the MHC. We therefore set out to characterize the linkage disequilibrium patterns between the highly polymorphic HLA genes and background variation by typing the classical HLA genes and >7,500 common SNPs and deletion-insertion polymorphisms across four population samples. The analysis provides informative tag SNPs that capture much of the common variation in the MHC region and that could be used in disease association studies, and it provides new insight into the evolutionary dynamics and ancestral origins of the HLA loci and their haplotypes.
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              Global impairment of CD4+CD25+FOXP3+ regulatory T cells in idiopathic pulmonary fibrosis.

              The implication of T cells in the pathogenesis of idiopathic pulmonary fibrosis (IPF) is controversial. CD4(+)CD25(+)FOXP3(+) regulatory T cells (Tregs) are pivotal in maintaining immune homeostasis, but their role in IPF pathophysiology has not yet been studied. To explore Treg dynamics and function in IPF. Treg levels and dynamics were analyzed by flow cytometry in the peripheral blood (PB) and bronchoalveolar lavage (BAL) of 21 patients with IPF, 35 patients with lung diseases other than IPF (patients without IPF), 20 patients with collagen vascular diseases with pulmonary parenchymal involvement (CVD-IP), and 28 healthy volunteers. The suppression of autologous CD4(+)CD25(-) cell-proliferative responses and cytokine release by magnetic bead-isolated Tregs was evaluated by proliferation assays and cytometric bead array. Correlations of Treg function and levels with lung function parameters were also performed. In patients with IPF, both BAL and PB Tregs were reduced compared with those of healthy volunteers and patients without IPF, although not always significantly. Treg levels were not affected by the administration of low-dose prednisone in four nonresponding patients. The suppressor potential of BAL and PB Tregs was compromised in patients with IPF and patients with CVD-IP, compared with healthy volunteers and patients without IPF. Similarly, the Treg-induced suppression of helper T-cell type 1 and 2 cytokine secretion was impaired in the BAL of patients with IPF and patients with CVD-IP. Moreover, the defective function of BAL Tregs correlated highly with parameters of disease severity. This study provides the first evidence of global Treg impairment in IPF that strongly correlates with disease severity, suggesting a role for Tregs in the fibrotic process.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2011
                23 February 2011
                : 6
                : 2
                : e14715
                Affiliations
                [1 ]Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
                [2 ]Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
                [3 ]Department of Medicine, University of Chicago Medical Center, Chicago, Illinois, United States of America
                [4 ]Advanced Lung Disease Program, Inova Fairfax Hospital, Falls Church, Virginia, United States of America
                [5 ]Department of Medicine, Stanford University Medical Center, Stanford, California, United States of America
                [6 ]Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
                [7 ]Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
                [8 ]Department of Radiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
                [9 ]Department of Oral Biology-Dental Medicine and Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
                [10 ]Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
                [11 ]Department of Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
                Comprehensive Pneumology Center, Germany
                Author notes

                Conceived and designed the experiments: JX IOR VGV YZ SD. Performed the experiments: JX BRG ASA CFB SDN GR IOR SD IO CF MAS SSJ AZ PAM JMP FCS YZ SD. Analyzed the data: BRG ASA CFB IN SDN GR IOR SD IO CF KC MAS SSJ AZ PAM JMP VGV FCS YZ SD. Contributed reagents/materials/analysis tools: BRG ASA CFB IN SDN GR IOR SD IO CF KC MAS SSJ AZ PAM JMP VGV KFG NK FCS YZ SD. Wrote the paper: JX KC PAM KFG SD. Proofed and/or edited paper: JX BG AS CF-B SDN GR SD IO CF KC MAS SSJ AZ JMP VGV KFG NK YZ FCS Performed the brunt of the specimen processing, DNA extraction, HLA assays and validations of same. Assisted with data interpretations and analyses: JX. Identified NIH normal and IPF subjects, recruited them, obtained and processed specimens, and compiled and analyzed relevant clinical and HLA data for this validation cohort: BG. Assisted with specimen collation, DNA purification from same, and with HLA assays: AS. Assisted with HLA typing assays, contributed to experimental design features: CF-B. Identified Inova IPF subjects, enrolled them, obtained and processed specimens, and compiled and analyzed relevant clinical data for a validation cohort: SDN. Identified Stanford IPF subjects, enrolled them, obtained and processed specimens, and compiled and analyzed relevant clinical data for a validation cohort: GR. Performed blinded interpreations of surgical pathology specimens that validated their diagnoses of IPF: SD. In conjunction with Dr. Fuhrman, interpreted and validated chest CT scans of IPF patients: IO. Provided blinded radiographic validations of IPF chest CT scans: CF. Provided information critical for study design, assisted with and validated data analyses: KC. In conjunction with Dr. Nathan, identified Inova subjects, enrolled them, obtained and processed specimens, and compiled and analyzed relevant clinical data for a validation cohort from Inova: MAS. In conjunction with Dr. Rosen, identified Stanford subjects, enrolled them, obtained and processed specimens, and compiled and analyzed relevant clinical data for a validation cohort from Stanford: SSJ. Obtained and processed specimens of the U. Pgh. transplant population, performed HLA analyses of same. Provided additional specimens for high resolution typing as well as technical advice: AZ. Identified control subjects, enrolled them, obtained and processed specimens, performed HLA analyses, and compiled and analyzed relevant clinical data for the initial discovery control cohort. Assisted with data interpretations and manuscript writing: PAM. Identified transplant recipient subjects, enrolled them, obtained and processed specimens, and compiled and analyzed relevant clinical data for the initial IPF discovery cohort. Facilitated or procured specimen acquisitions from same: JMP. Analyzed data, assisted with study design and identifications of collaborators and validation cohorts. Assisted with data analyses. Procured additional data: VGV. Identified ambulatory IPF subjects, recruited them for these studies, obtained and processed specimens, and compiled and analyzed relevant clinical data for this validation cohort: KFG NK. Provided technical assistance and advice. Helped with DNA isolation and analyses: YZ. Identified normal volunteer subjects, enrolled them, obtained and processed specimens, and compiled and analyzed relevant clinical data for a validation control cohort: FCS. Conceived and designed experiments, coordinated specimen acquistion, processing and analyses, collated clinical information provided by colleagues, analyzed the data in conjunction with co-authors, provided financial support of the studies, and wrote the paper: SRD.

                Article
                10-PONE-RA-20923R2
                10.1371/journal.pone.0014715
                3044131
                21373184
                2af9fbab-1303-498f-b086-5b3372bd0861
                This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
                History
                : 11 July 2010
                : 26 January 2011
                Page count
                Pages: 7
                Categories
                Research Article
                Immunology/Genetics of the Immune System
                Immunology/Immune Response
                Respiratory Medicine/Interstitial Lung Diseases

                Uncategorized
                Uncategorized

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