Crystal structure of HLA-DP2 and implications for chronic beryllium disease

Interleukin-1 signaling and CD4+ T cells control B cell recruitment to the lungs in chronic beryllium disease

Chronic beryllium disease (CBD) is a debilitating pulmonary disorder that occurs due to persistent exposure to beryllium (Be) particles in the workplace. Be-exposure causes activation of the innate immune system, resulting in the secretion of interleukins and chemokines that drive the accumulation of B and T cells in the lungs. However, the mechanisms by which innate molecules influence the recruitment of B cells and B cell-mediated protection in CBD are poorly understood. In this study, we employed multiple approaches to examine the role of innate immune signaling and CD4+ T cells in B cell recruitment and function in the lungs. We show that the absence or blocking of IL-1R1 signaling prevents the recruitment of B cells to the lungs of BeO-exposed mice. Additionally, we show that B cell recruitment to the lungs depends on the chemokine receptor, CXCR5, and CD4+ T cells. In BeO-exposed mice, lung B cells down-regulate IgM but showed an increased IgD and CD44 surface expression. Further, RNA sequencing of pulmonary tissue-specific B cells in CBD revealed distinct gene signatures compared to splenic B cells, with increased expression of pathways involved in antigen presentation, tight junction interactions, and interferon signaling. Overall, our study shows that B cell recruitment and aggregate formation during CBD depend on sequential activation of innate and adaptive immune responses.

Population genetic dissection of HLA-DPB1 amino acid polymorphism to infer selection

Although allele frequency data for most HLA loci provide strong evidence for balancing selection at the allele level, the DPB1 locus is a notable exception, with allele frequencies compatible with neutral evolution (genetic drift) or directional selection in most populations. This discrepancy is especially interesting as evidence for balancing selection has been seen at the nucleotide and amino acid (AA) sequence levels for DPB1. We describe methods used to examine the global distribution of DPB1 alleles and their constituent AA sequences. These methods allow investigation of the influence of natural selection in shaping DPβ diversity in a hierarchical fashion for DPB1 alleles, all polymorphic DPB1 exon 2-encoded AA positions, as well as all pairs and trios of these AA positions. In addition, we describe how asymmetric linkage disequilibrium for all DPB1 exon 2-encoded AA pairs can be used to complement other methods. Application of these methods provides strong evidence for the operation of balancing selection on AA positions 56, 85-87, 36, 55 and 84 (listed in decreasing order of the strength of selection), but no evidence for balancing selection on DPB1 alleles.

Natural Selection on HLA-DPB1 Amino Acids Operates Primarily on DP Serologic Categories

The DPB1 locus is notable among the classical HLA loci in that allele frequencies at this locus are consistent with genetic drift, whereas the frequencies of specific DPβ amino acids are consistent with the action of balancing selection. We investigated the influence of natural selection in shaping the diversity of three functional categories of DPB1 diversity defined by specific amino acid motifs, DPB1 T-cell epitopes, DPB1 supertypes and DP1-DP4 serologic categories (SCs), via Ewens-Watterson (EW) selective neutrality and asymmetric Linkage Disequilibrium (ALD) analyses in a worldwide sample of 136 populations. These EW analyses provide strong evidence for the operation of balancing selection on DP SCs, but no evidence for balancing selection on T-cell epitopes or supertypes. We further investigated the global distribution of SCs. Each SC is common in a different region of the world, with the DP1 SC most common in Southeast Asia and Oceania, the DP2 SC in North and South America, the DP3 SC in South America, and the DP4 SC in Europe. The DP2 SC is present in all populations, while 14% of populations are missing at least one DP1, DP3, or DP4 SC. We observed consistent DPA1∼DP SC haplotype associations across 10 populations from five global regions, and found that asymmetric linkage disequilibrium (LD) between the DPB1 locus and the four most-common DPA1 alleles (DPA1*01:03, *02:01, *02:02 and *03:01) is determined by variation at DPβ AA positions 85-87. These positions are in LD with both DPα positions 31 and 50. We conclude from these EW analyses that natural selection is primarily operating to maintain population-level diversity of DP SCs, rather than DPB1 alleles or other functional categories of DPB1 diversity.

Leaching behavior and kinetics of beryllium in beryllium-containing sludge (BCS)

Beryllium-containing sludge (BCS) is a byproduct of the physicochemical treatment of beryllium smelting wastewater. The pollutant element beryllium within BCS is highly unstable and extremely toxic, characterized by its small ionic radius and low charge density, resulting in a high risk of leaching and migration. This study is the first to investigate the leaching behavior, influencing mechanisms, and kinetic processes of beryllium in BCS under various environmental conditions. The results indicate that, under national standard conditions, beryllium exhibits a rapid leaching phase within the first 5 h, which then stabilizes after 10 h, with the total leached content significantly exceeding the leaching toxicity identification standards. Under mildly acidic (pH ≤ 5) or highly alkaline (pH = 14) conditions, beryllium demonstrates pronounced leaching and migration behaviors. Notably, in acidic conditions, the leaching rate exceeds 80% within 5 h. Combining the treatment process of beryllium-containing wastewater with analytical methods such as SEM, XPS, ToF-SIMS, and FTIR, it is revealed that due to the heterogeneous nature of BCS, the particle aggregates dissociate over time under acidic conditions. The particle surfaces become increasingly rough, leading to dissolution and the emergence of more reactive sites, resulting in a high proportion of beryllium leaching. Under these conditions, the gradual reaction of Be(OH)2 in BCS to form soluble Be2+ and its hydrolytic complexes is identified as the primary mechanism for extensive beryllium migration. The process encounters minimal diffusion resistance and is classified as reaction-controlled. In acidic conditions with pH = 4, the leaching rate of beryllium significantly increases with rising temperature. The leaching kinetics equation is [(1-x)-0.44]=e(18.26-53050RT)·t, with an apparent activation energy of 53.05 kJ mol-1.

Non-overlapping epitopes on the gHgL-gp42 complex for the rational design of a triple-antibody cocktail against EBV infection

Epstein-Barr virus (EBV) is closely associated with cancer, multiple sclerosis, and post-acute coronavirus disease 2019 (COVID-19) sequelae. There are currently no approved therapeutics or vaccines against EBV. It is noteworthy that combining multiple EBV glycoproteins can elicit potent neutralizing antibodies (nAbs) against viral infection, suggesting possible synergistic effects. Here, we characterize three nAbs (anti-gp42 5E3, anti-gHgL 6H2, and anti-gHgL 10E4) targeting different glycoproteins of the gHgL-gp42 complex. Two antibody cocktails synergistically neutralize infection in B cells (5E3+6H2+10E4) and epithelial cells (6H2+10E4) in vitro. Moreover, 5E3 alone and the 5E3+6H2+10E4 cocktail confer potent in vivo protection against lethal EBV challenge in humanized mice. The cryo-EM structure of a heptatomic gHgL-gp42 immune complex reveals non-overlapping epitopes of 5E3, 6H2, and 10E4 on the gHgL-gp42 complex. Structural and functional analyses highlight different neutralization mechanisms for each of the three nAbs. In summary, our results provide insight for the rational design of therapeutics or vaccines against EBV infection.

HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery

CD4+ T cell responses are exquisitely antigen specific and directed toward peptide epitopes displayed by human leukocyte antigen class II (HLA-II) on antigen-presenting cells. Underrepresentation of diverse alleles in ligand databases and an incomplete understanding of factors affecting antigen presentation in vivo have limited progress in defining principles of peptide immunogenicity. Here, we employed monoallelic immunopeptidomics to identify 358,024 HLA-II binders, with a particular focus on HLA-DQ and HLA-DP. We uncovered peptide-binding patterns across a spectrum of binding affinities and enrichment of structural antigen features. These aspects underpinned the development of context-aware predictor of T cell antigens (CAPTAn), a deep learning model that predicts peptide antigens based on their affinity to HLA-II and full sequence of their source proteins. CAPTAn was instrumental in discovering prevalent T cell epitopes from bacteria in the human microbiome and a pan-variant epitope from SARS-CoV-2. Together CAPTAn and associated datasets present a resource for antigen discovery and the unraveling genetic associations of HLA alleles with immunopathologies.

Targeting hepatitis B vaccine escape using immunogenetics in Bangladeshi infants

Hepatitis B virus (HBV) vaccine escape mutants (VEM) are increasingly described, threatening progress in control of this virus worldwide. Here we studied the relationship between host genetic variation, vaccine immunogenicity and viral sequences implicating VEM emergence. In a cohort of 1,096 Bangladeshi children, we identified human leukocyte antigen (HLA) variants associated with response vaccine antigens. Using an HLA imputation panel with 9,448 south Asian individuals DPB1*04:01 was associated with higher HBV antibody responses (p=4.5×10-30). The underlying mechanism is a result of higher affinity binding of HBV surface antigen epitopes to DPB1*04:01 dimers. This is likely a result of evolutionary pressure at the HBV surface antigen 'a-determinant' segment incurring VEM specific to HBV. Prioritizing pre-S isoform HBV vaccines may tackle the rise of HBV vaccine evasion.

CD4+ T cell-mediated recognition of a conserved cholesterol-dependent cytolysin epitope generates broad antibacterial immunity

CD4⁺ T cell-mediated immunity against Streptococcus pneumoniae (pneumococcus) can protect against recurrent bacterial colonization and invasive pneumococcal diseases (IPDs). Although such immune responses are common, the pertinent antigens have remained elusive. We identified an immunodominant CD4⁺ T cell epitope derived from pneumolysin (Ply), a member of the bacterial cholesterol-dependent cytolysins (CDCs). This epitope was broadly immunogenic as a consequence of presentation by the pervasive human leukocyte antigen (HLA) allotypes DPB1^∗02 and DPB1^∗04 and recognition via architecturally diverse T cell receptors (TCRs). Moreover, the immunogenicity of Ply_427-444 was underpinned by core residues in the conserved undecapeptide region (ECTGLAWEWWR), enabling cross-recognition of heterologous bacterial pathogens expressing CDCs. Molecular studies further showed that HLA-DP4-Ply_427-441 was engaged similarly by private and public TCRs. Collectively, these findings reveal the mechanistic determinants of near-global immune focusing on a trans-phyla bacterial epitope, which could inform ancillary strategies to combat various life-threatening infectious diseases, including IPDs.

The dubious origin of beryllium toxicity

Four mechanisms have been proposed in the literature to explain beryllium toxicity; they can be divided in two groups of two mechanisms: (i) replacement type: models 1 and 2; (ii) addition type: models 3 and 4. At this moment is not possible to select the best model not even to establish if one of these models will be the ultimate mechanism of beryllium toxicity. However, it is important to know the still open discussion about something so important associated with one of the simplest elements of the periodic table.

A combination of HLA-DP α and β chain polymorphisms paired with a SNP in the DPB1 3' UTR region, denoting expression levels, are associated with atopic dermatitis

Introduction: Components of the immune response have previously been associated with the pathophysiology of atopic dermatitis (AD), specifically the Human Leukocyte Antigen (HLA) Class II region via genome-wide association studies, however the exact elements have not been identified. Methods: This study examines the genetic variation of HLA Class II genes using next generation sequencing (NGS) and evaluates the resultant amino acids, with particular attention on binding site residues, for associations with AD. The Genetics of AD cohort was used to evaluate HLA Class II allelic variation on 464 subjects with AD and 384 controls. Results: Statistically significant associations with HLA-DP α and β alleles and specific amino acids were found, some conferring susceptibility to AD and others with a protective effect. Evaluation of polymorphic residues in DP binding pockets revealed the critical role of P1 and P6 (P1: α31M + (β84G or β84V) [protection]; α31Q + β84D [susceptibility] and P6: α11A + β11G [protection]) and were replicated with a national cohort of children consisting of 424 AD subjects. Independently, AD susceptibility-associated residues were associated with the G polymorphism of SNP rs9277534 in the 3' UTR of the HLA-DPB1 gene, denoting higher expression of these HLA-DP alleles, while protection-associated residues were associated with the A polymorphism, denoting lower expression. Discussion: These findings lay the foundation for evaluating non-self-antigens suspected to be associated with AD as they potentially interact with particular HLA Class II subcomponents, forming a complex involved in the pathophysiology of AD. It is possible that a combination of structural HLA-DP components and levels of expression of these components contribute to AD pathophysiology.

Whole Exome Sequencing Identified Two Single Nucleotide Polymorphisms of Human Leukocyte Antigen-DRB5 in Familial Sarcoidosis in China

BACKGROUND

Sarcoidosis is a multisystem granulomatous disorder whose etiology is related to genetic and immunological factors. Familial aggregation and ethnic prevalence suggest a genetic predisposition and inherited susceptibility to sarcoidosis.

OBJECTIVE

This study aimed to identify suspected risk loci for familial sarcoidosis patients.

METHODS

We conducted whole exome sequencing on two sarcoidosis patients and five healthy family members in a Chinese family for a case-control study. The two sarcoidosis patients were siblings who showed chronic disease.

RESULTS

The Gene Ontology results showed single nucleotide polymorphisms in three genes, including human leukocyte antigen (HLA)-DRB1, HLA-DRB5, and KIR2DL4, associated with both 'antigen processing and presentation' and 'regulation of immune response.' Sanger sequencing verified two nonsynonymous mutations in HLA-DRB5 (rs696318 and rs115817940) located on 6p21.3 in the major histocompatibility complex (MHC) class II beta 1 region. The structural model simulated on Prot- Param protein analysis by the Expert Protein Analysis System predicted that the hydropathy index changed at two mutation sites (rs696318: p.F96L, -1.844 to -1.656 and rs115817940: p.T106N, -0.322 to -0.633), which indicated the probability of changes in peptide-binding selectivity.

CONCLUSION

Our results indicated that two nonsynonymous mutations of HLA-DRB5 have been identified in two sarcoidosis siblings, while their healthy family members do not have the mutations. The two HLA-DRB5 alleles may influence genetic susceptibility and chronic disease progression through peptide mutations on the MHC class II molecule among the two affected family members.

Human T cells recognize HLA-DP-bound peptides in two orientations

Human leukocyte antigen (HLA) molecules present small peptide antigens to T cells, thereby allowing them to recognize pathogen-infected and cancer cells. A central dogma over the last 50+ y is that peptide binding to HLA molecules is mediated by the docking of side chains of particular amino acids in the peptide into pockets in the HLA molecules in a conserved N- to C-terminal orientation. Whether peptides can be presented in a reversed C- to N-terminal orientation remains unclear. Here, we performed large-scale identification of peptides bound to HLA-DP molecules and observed that in addition to peptide binding in an N- to C-terminal orientation, in 9 out of 14 HLA-DP allotypes, reverse motifs are found, compatible with C- to N-terminal peptide binding. Moreover, we isolated high-avidity human cytomegalovirus (CMV)-specific HLA-DP-restricted CD4⁺ T cells from the memory repertoire of healthy donors and demonstrate that such T cells recognized CMV-derived peptides bound to HLA-DPB1*01:01 or *05:01 in a reverse C- to N-terminal manner. Finally, we obtained a high-resolution HLA-DPB1*01:01-CMVpp65_(142-158) peptide crystal structure, which is the molecular basis for C- to N-terminal peptide binding to HLA-DP. Our results point to unique features of HLA-DP molecules that substantially broaden the HLA class II bound peptide repertoire to combat pathogens and eliminate cancer cells.

Protective role of tissue-resident regulatory T cells in a murine model of beryllium-induced disease

CD4+ T cells drive the immunopathogenesis of chronic beryllium disease (CBD), and their recruitment to the lung heralds the onset of granulomatous inflammation. We have shown that regulatory CD4+ T cells (Tregs) control granuloma formation in an HLA-DP2 transgenic (Tg) model of CBD. In these mice, Be oxide (BeO) exposure resulted in the accumulation of three distinct CD4+ T cell subsets in the lung with the majority of tissue-resident memory cells expressing FoxP3. The amount of Be regulated the number of total and antigen-specific CD4+ T cells and Tregs in the lungs of HLA-DP2 Tg mice. Depletion of Tregs increased the number of IFN-γ-producing CD4+ T cells and enhanced lung injury while mice treated with IL2/αIL-2 complexes had increased Tregs and reduced inflammation and Be-responsive T cells in the lung. BeO-experienced resident Tregs suppressed anti-CD3-induced proliferation of CD4+ T cells in a contact-dependent manner. CLTLA-4 and ICOS blockade as well as addition of LPS to BeO-exposed mice increased the Teff/Treg ratio and enhanced lung injury. Collectively, these data show that the protective role of tissue-resident Tregs is dependent on quantity of Be exposure and is overcome by blocking immune regulatory molecules or additional environmental insults.

A new strategy for systematically classifying HLA alleles into serological specificities

HLA serological specificities were defined by the reactivity of HLA molecules with sets of sera and monoclonal antibodies. Many recently identified alleles defined by molecular typing lack their serotype assignment. We surveyed the literature describing the correlation of the reactivity of serologic reagents with AA residues. 20 - 25 AA residues determining epitopes (DEP) that correlated with 82 WHO serologic specificities were identified for HLA class I loci. Thirteen DEP each located in the beta-1 domains that correlated with 24 WHO serologic specificities were identified for HLA-DRB1 and -DQB1 loci. The designation of possible HLA-DPB1, -DQA1, -DPA1, and additional serological specificities that result from epitopes defined by residues located at both -DQA1 and -DQB1 subunits were also examined. HATS software was developed for automated serotype assignments to HLA alleles in one of the three hierarchical matching criteria: 1) all DEP (FULL); 2) selected DEP specific to each serological specificities (SEROTYPE); 3) one AA mismatch with one or more SEROTYPES (INCOMPLETE). Results were validated by evaluating the alleles whose serotypes do not correspond to the first field of the allele name listed in the HLA dictionary. Additional 85 and 21 DEP patterns that do not correspond to any WHO serologic specificities for common HLA class I and DRB1 alleles were identified, respectively. A comprehensive antibody identification panel would allow for accurate unacceptable antigen listing and compatibility predictions in solid organ transplantations. We propose that antibody-screening panels should include all serologic specificities identified in this study. This article is protected by copyright. All rights reserved.

Innate and Adaptive Immunity in Noninfectious Granulomatous Lung Disease

Sarcoidosis and chronic beryllium disease are noninfectious lung diseases that are characterized by the presence of noncaseating granulomatous inflammation. Chronic beryllium disease is caused by occupational exposure to beryllium containing particles, whereas the etiology of sarcoidosis is not known. Genetic susceptibility for both diseases is associated with particular MHC class II alleles, and CD4+ T cells are implicated in their pathogenesis. The innate immune system plays a critical role in the initiation of pathogenic CD4+ T cell responses as well as the transition to active lung disease and disease progression. In this review, we highlight recent insights into Ag recognition in chronic beryllium disease and sarcoidosis. In addition, we discuss the current understanding of the dynamic interactions between the innate and adaptive immune systems and their impact on disease pathogenesis.

Combinatorial in silico and in vivo evaluation of immune response elicitation by the affibody ZHER2

Due to the high affinity for binding to target molecules and also other unique attributes, affibodies have a great potential to be used in immunotherapeutic and diagnostic approaches. However, the possibility of undesirable immune response is still a great concern. In the current study, we investigated the possible antigenicity, allergenicity and cytotoxicity of the HER2-targeting affibody Z_HER2. The binding affinity of potential epitopes of the affibody to murine major histocompatibility complex (MHC) molecules was investigated by immunoinformatics tools and docking approaches. The possible interaction of Z_HER2 with human leukocyte antigens HLA-DP, HLA-DM, HLA-DQ and HLA-DR was also studied by protein-protein docking. Additionally, the synthesized affibody gene was expressed and the protein was purified for boosted immunization of Balb/c mice. Induced secretion of IFN-γ, IL-2, IL-4 and IL-10, and total serum IgG were assessed in the immunized mice. Furthermore, MTT cell viability test was performed to evaluate the cytotoxicity of Z_HER2 in splenocytes of the treated mice. In silico analyses showed the possible induction of the immune response by Z_HER2. While the affibody could elicit the secretion of cellular immune cytokines, it could not induce a significant humoral response in the treated mice and did not show any cytotoxic effects on the exposed splenocytes. These findings explain the practicability of Z_HER2 for therapeutic and in vivo diagnostic usages, though its ubiquitous application may need more studies.

CD4+ T cells in the lungs of acute sarcoidosis patients recognize an Aspergillus nidulans epitope

Löfgren’s syndrome (LS) is an acute form of sarcoidosis characterized by a genetic association with HLA-DRB1*03 (HLA-DR3) and an accumulation of CD4⁺ T cells of unknown specificity in the bronchoalveolar lavage (BAL). Here, we screened related LS-specific TCRs for antigen specificity and identified a peptide derived from NAD-dependent histone deacetylase hst4 (NDPD) of Aspergillus nidulans that stimulated these CD4⁺ T cells in an HLA-DR3–restricted manner. Using ELISPOT analysis, a greater number of IFN-γ– and IL-2–secreting T cells in the BAL of DR3⁺ LS subjects compared with DR3⁺ control subjects was observed in response to the NDPD peptide. Finally, increased IgG antibody responses to A. nidulans NDPD were detected in the serum of DR3⁺ LS subjects. Thus, our findings identify a ligand for CD4⁺ T cells derived from the lungs of LS patients and suggest a role of A. nidulans in the etiology of LS.

Detection of a novel allele, HLA-DPA1*01:58, originating from a recombination within exon 2 of the DPA1 gene

A crossover in exon 2 between DPA1*01:03:01:02 and DPA1*02:01:01:01 results in a novel hybrid allele, HLA-DPA1*01:58.

Prediction of beryllium clusters (Ben; n = 3-25) from first principles

Evolutionary searches using the USPEX method (Universal Structure Predictor: Evolutionary Xtallography) combined with density functional theory (DFT) calculations were performed to obtain the global minimum structures of beryllium (Be_n, n = 3-25) clusters. The thermodynamic stability, optoelectronic and photocatalytic properties as well as the nature of bonding are considered for the most stable clusters. It is found that the cluster with n = 15 is the transition point at which the configurations change from 3D hollow cages to filled cage structures (with an interior atom appearing in the structure). All the ground state structures are energetically favorable with negative binding energies, suggesting good synthetic feasibility for these structures. The calculated relative stabilities and electronic structure show that the Be₄, Be₁₀ and, Be₁₇ clusters are the most stable structures and can be considered as superatoms. The electron configurations of Be₄, Be₁₀ and Be₁₇ clusters with 8, 20 and 34 electrons are identified as 1S² 1P⁶, 1S² 1P⁶ 1D¹⁰ 2S², 1S² 1P⁶ 1D¹⁰ 2S² 1F¹⁴, respectively. Theoretical simulations determined that all the ground state structures exhibit excellent thermal stability, where the upper-limit temperature that the structures can tolerate is 900 K. During AIMD simulation of O₂ adsorption onto the Be₁₇ cluster an interesting phenomenon was happening in which the pristine Be₁₇ cluster becomes a new stable Be₁₇O₁₆ cluster. Based on ELF (electron localization function) analysis, it can be concluded that the Be-Be bonds in the small clusters are primarily of van der Waals type, while for the larger clusters, the bonds are of metallic nature. The Be_n clusters show very strong absorption in the UV and visible regions with absorption coefficients larger than 10⁵ cm^-1, which suggests a wide range of potential advanced optoelectronics applications. The Be₁₇ cluster has a suitable band alignment in the visible-light excitation region which will produce enhanced photocatalytic activities (making it a promising material for water splitting).

Major histocompatibility complex (MHC) class I and class II proteins: impact of polymorphism on antigen presentation

The major histocompatibility complex (MHC) loci are amongst the most polymorphic regions in the genomes of vertebrates. In the human population, thousands of MHC gene variants (alleles) exist that translate into distinct allotypes equipped with overlapping but unique peptide binding profiles. Understanding the differential structural and dynamic properties of MHC alleles and their interaction with critical regulators of peptide exchange bears the potential for more personalized strategies of immune modulation in the context of HLA-associated diseases.

Beryllium-specific CD4+ T cells induced by chemokine neoantigens perpetuate inflammation

Discovering dominant epitopes for T cells, particularly CD4+ T cells, in human immune-mediated diseases remains a significant challenge. Here, we used bronchoalveolar lavage (BAL) cells from HLA-DP2-expressing patients with chronic beryllium disease (CBD), a debilitating granulomatous lung disorder characterized by accumulations of beryllium-specific (Be-specific) CD4+ T cells in the lung. We discovered lung-resident CD4+ T cells that expressed a disease-specific public CDR3β T cell receptor motif and were specific to Be-modified self-peptides derived from C-C motif ligand 4 (CCL4) and CCL3. HLA-DP2-CCL/Be tetramer staining confirmed that these chemokine-derived peptides represented major antigenic targets in CBD. Furthermore, Be induced CCL3 and CCL4 secretion in the lungs of mice and humans. In a murine model of CBD, the addition of LPS to Be oxide exposure enhanced CCL4 and CCL3 secretion in the lung and significantly increased the number and percentage of CD4+ T cells specific for the HLA-DP2-CCL/Be epitope. Thus, we demonstrate a direct link between Be-induced innate production of chemokines and the development of a robust adaptive immune response to those same chemokines presented as Be-modified self-peptides, creating a cycle of innate and adaptive immune activation.

Distinct clinical features and prognosis between persistent and temporary thyroid dysfunctions by immune-checkpoint inhibitors

Immune-related adverse events in the thyroid glands (thyroid irAEs) during treatment with immune-checkpoint inhibitors (ICIs) are most frequent endocrine irAE. Thyroid irAE can be divided into that requiring continuous therapy for thyroid dysfunction (P-THY), and that requiring only temporal treatment (T-THY). However, predictive factors for those differential outcomes are unknown, and susceptibility of human leukocyte antigen (HLA) to thyroid irAE has never been investigated. This study aimed to elucidate clinical courses and prognosis of P-THY in comparison with T-THY in the aspect of thyroid immunity and HLA. Patients with P-THY (n = 15) that required L-T4 supplemental therapy for hypothyroidism for more than 3 months, and patients with T-THY who required no therapy or therapy within 1 month were enrolled in the study. Lower-value of TSH, higher-value of FT4, and lower value of TSH/FT4 were thought to be predictive markers to estimate P-THY. In addition, anti-thyroglobulin antibody (TgAb) levels were significantly higher in patients with P-THY than those in patients with T-THY. HLA-DPA1*01:03 and HLA-DPB1*02:01 allele, and their haplotype frequencies were significantly higher in patients with P-THY than those in controls. P-THY had better survival rate than T-THY. Pre-existing thyroid autoimmunity, the extent of thyroid dysfunction, and predisposing HLA were associated with the differential course of thyroid irAEs. It was suggested that thyroid function tests, TgAb, and HLA typing tests are useful for prediction of clinical course in thyroid irAEs.

[Management of occupational health for adverse health effects of beryllium and its compounds in workplaces - Recent trends and issues in Japan]

OBJECTIVES

Beryllium is primarily used in its metallic form, in alloys, or in beryllium oxide ceramics. Its physical and mechanical properties make it useful for many applications across a range of industries. Because beryllium is recognized as a sensitizing and carcinogenic agent, the management of occupational health for workers who may be occupationally exposed to beryllium has long been an important issue in the world. Under these circumstances, the U.S. Occupational Safety and Health Administration (OSHA) had published a rule in January 2017, to prevent the development of chronic beryllium disease and lung cancer. This rule strengthens the regulations governing the use of beryllium and its compounds. With the announcement of the OSHA rule in January 2017, the purpose of this study is to gain insight into the health problems and industrial hygiene associated with the use of beryllium and share the issues related to the management of occupational health for persons working with beryllium in Japan.

METHODS

We collected information regarding the beryllium industry, beryllium exposure, beryllium-induced health disorders, OSHA rule of January 2017, and regulations for beryllium use in Japan. After reviewing them, we discussed the issues concerning occupational health management of workers exposed to beryllium in Japan.

RESULTS

It has been reconfirmed that in recent years, the most serious health problem due to beryllium exposure is chronic beryllium disease caused by beryllium sensitization. Management of occupational health that emphasizes reduction of beryllium sensitization and early detection of beryllium-sensitized workers is important.

CONCLUSIONS

It was suggested that the following should be considered as the issues of management of occupational health of workers exposed to beryllium in Japan: (1) Collect epidemiologic data on health hazards from beryllium exposure in Japan. (2) Review the diagnostic items of special medical check-ups. (3) Review the definition of beryllium and its compounds in the Ordinance on Prevention of Hazards due to Specified Chemical Substances.

A consistent model for the key complex in chronic beryllium disease

A hypothesis on the structure of the key complex in chronic beryllium disease (CBD) is discussed with respect to the current knowledge on CBD, and with respect to the constraints implied by the coordination chemistry of beryllium and experimental data on the engaged protein complexes. The structure hypothesis is based on the [Be4O]6+ moiety as a coordination center, which is also found in the so called “basic beryllium carboxylates”. The structure of a small molecular model, optimized at the DFT level of theory, is used to compare the structural demands of this coordination center with a structure of the in vitro model of a beryllium immunoprotein complex determined previously by protein crystallography (Clayton & al., Cell 2014, 158, 132). 9Be NMR chemical shielding values, quadrupole coupling constants and asymmetry parameters (η) have been calculated.

Adaptive Immunity in Pulmonary Sarcoidosis and Chronic Beryllium Disease

Pulmonary sarcoidosis and chronic beryllium disease (CBD) are inflammatory granulomatous lung diseases defined by the presence of non-caseating granulomas in the lung. CBD results from beryllium exposure in the workplace, while the cause of sarcoidosis remains unknown. CBD and sarcoidosis are both immune-mediated diseases that involve Th1-polarized inflammation in the lung. Beryllium exposure induces trafficking of dendritic cells to the lung in a mechanism dependent on MyD88 and IL-1α. B cells are also recruited to the lung in a MyD88 dependent manner after beryllium exposure in order to protect the lung from beryllium-induced injury. Similar to most immune-mediated diseases, disease susceptibility in CBD and sarcoidosis is driven by the expression of certain MHCII molecules, primarily HLA-DPB1 in CBD and several HLA-DRB1 alleles in sarcoidosis. One of the defining features of both CBD and sarcoidosis is an infiltration of activated CD4+ T cells in the lung. CD4+ T cells in the bronchoalveolar lavage (BAL) of CBD and sarcoidosis patients are highly Th1 polarized, and there is a significant increase in inflammatory Th1 cytokines present in the BAL fluid. In sarcoidosis, there is also a significant population of Th17 cells in the lungs that is not present in CBD. Due to persistent antigen exposure and chronic inflammation in the lung, these activated CD4+ T cells often display either an exhausted or anergic phenotype. Evidence suggests that these T cells are responding to common antigens in the lung. In CBD there is an expansion of beryllium-responsive TRBV5.1+ TCRs expressed on pathogenic CD4+ T cells derived from the BAL of CBD patients that react with endogenous human peptides derived from the plexin A protein. In an acute form of sarcoidosis, there are expansions of specific TRAV12-1/TRBV2 T cell receptors expressed on BAL CD4+ T cells, indicating that these T cells are trafficking to and expanding in the lung in response to common antigens. The specificity of these pathogenic CD4+T cells in sarcoidosis are currently unknown.

Beryllium-associated diseases from a chemist’s point of view

Beryllium has long been considered the most toxic non-radioactive element to humans. However, it is shown that the acute toxicity of beryllium ions does not exceed that of other toxic cations like Cd2+, Ba2+, Hg2+ or As3+. The physiological mechanisms liable for the development of beryllium-associated diseases are discussed. Additionally an overview over proposed low-molecular model system for the beryllium species responsible for beryllioses is presented.

Molecular mechanism of Be2+-ion binding to HLA-DP2: tetrahedral coordination, conformational changes and multi-ion binding

Be small and positive: the smaller size and higher charge of the Be²⁺-ion results in strong binding between the M2 peptide and the β-chain of HLA-DP2, which induces conformational changes at the periphery suitable for TCR binding.

Immunologic Effects of Beryllium Exposure

Metal-induced hypersensitivity is driven by T-cell sensitization to metal ions. Although numerous metals are associated with the development of diffuse parenchymal lung disease, beryllium-induced hypersensitivity is the best-studied to date. This review focuses on the interaction between innate and adaptive immunity that leads to the development of chronic beryllium disease. After beryllium exposure, activation of the innate immune system occurs through the engagement of pattern-recognition receptors. This activation leads to cell death, release of alarmins, and activation and migration of dendritic cells to lung-draining lymph nodes. These events culminate in the development of an adaptive immune response that is characterized by beryllium-specific, T-helper type 1-polarized, CD4⁺ T-cells and granuloma formation in the lung. The unique ability of beryllium to bind to human leukocyte antigen-DP molecules that express a glutamic acid at position 69 of the β-chain alters the charge and conformation of the human leukocyte antigen-DP-peptide complex. These changes induce post-translational modifications that are recognized as non-self. In essence, the ability of beryllium to create neoantigens underlies the genesis of chronic beryllium disease, and demonstrates the similarity between beryllium-induced hypersensitivity and autoimmunity.

Response to hepatitis B vaccination is co-determined by HLA-DPA1 and -DPB1

BACKGROUND AND AIMS

No report explored the combined effects of HLA-DPA1 and -DPB1 with long-term response to hepatitis B (HB) vaccination (HBVac). The specific aims of the study were to assess the combined effects and relative contributions of DPA1 and DPB1 genes.

METHODS

The cases were 152 adolescents who had undetectable (<1.0 mIU/mL) post-booster anti-HBs titers and the controls were adolescents who had residual anti-HBs ≥ 10 mIU/mL at aged 16 years (n = 207) or had detectable (≥1.0 mIU/mL) anti-HBs titers after booster HBVac (n = 481). HLA-DPA1 and -DPB1 genotypes were determined by sequence-based typing.

RESULTS

HLA-DPA1*01:03:01 was correlated with lower ORs of undetectable anti-HBs titers, while -DPA1*02:02:02 and -DPB1*05:01:01 were correlated with higher ORs. The ORs for HLA-DPA1*01:03:01-DPB1*05:01:01 and DPA1*02:02:02-DPB1*protective combinatory types were significantly less than 1.0. As compared with subjects who had no protective allele, the adjusted ORs (95% CI) were 0.545 (0.328-0.906), 0.350 (0.174-0.702), and 0.122 (0.058-0.257), for subjects who had protective alleles on DPA1only, DPB1 only, and both genes, respectively. Analyses of amino acid polymorphisms showed that subjects who carried Arg81-Pro158-Val191-Pro259α + Met234β and Gln62-Arg82α + Met234β combinations had 4.3-to-4.6 folds of risks.

CONCLUSION

Both DPA1 and DPB1 genes contribute to the persistence of immunological response to primary infantile HBVac. The effects of HLA-DP risk alleles were dominated by the protective alleles and there were significant gene-gene interactions. Our findings provide evidences for the design of more potent HB vaccine.

A subset of HLA-DP molecules serve as ligands for the natural cytotoxicity receptor NKp44

Natural killer (NK) cells can recognize virus-infected and stressed cells1 using activating and inhibitory receptors, many of which interact with HLA class I. Although early studies also suggested a functional impact of HLA class II on NK cell activity2,3, the NK cell receptors that specifically recognize HLA class II molecules have never been identified. We investigated whether two major families of NK cell receptors, killer-cell immunoglobulin-like receptors (KIRs) and natural cytotoxicity receptors (NCRs), contained receptors that bound to HLA class II, and identified a direct interaction between the NK cell receptor NKp44 and a subset of HLA-DP molecules, including HLA-DP401, one of the most frequent class II allotypes in white populations4. Using NKp44ζ+ reporter cells and primary human NKp44+ NK cells, we demonstrated that interactions between NKp44 and HLA-DP401 trigger functional NK cell responses. This interaction between a subset of HLA-DP molecules and NKp44 implicates HLA class II as a component of the innate immune response, much like HLA class I. It also provides a potential mechanism for the described associations between HLA-DP subtypes and several disease outcomes, including hepatitis B virus infection5-7, graft-versus-host disease8 and inflammatory bowel disease9,10.

Proteomic studies of putative molecular signatures for biological effects by Korean Red Ginseng

Background

Korean Red Ginseng (KRG) has been widely used as an herbal medicine to normalize and strengthen body functions. Although many researchers have focused on the biological effects of KRG, more studies on the action mechanism of red ginseng are still needed. Previously, we investigated the proteomic changes of the rat spleen while searching for molecular signatures and the action mechanism of KRG. The proteomic analysis revealed that differentially expressed proteins (DEPs) were involved in the increased immune response and phagocytosis. The aim of this study was to evaluate the biological activities of KRG, especially the immune-enhancing response of KRG.

Methods

Rats were divided into 4 groups: 0 (control group), 500, 1000, and 2000 mg/kg administration of KRG powder for 6 weeks, respectively. Isobaric tags for relative and absolute quantitation was performed with Q-Exactive LC-MS/MS to compare associated proteins between the groups. The putative DEPs were identified by a current UniProt rat protein database search and by the Gene Ontology annotations.

Results

The DEPs appear to increase the innate and acquired immunity as well as immune cell movement. These results suggest that KRG can stimulate immune responses. This analysis refined our targets of interest to include the potential functions of KRG. Furthermore, we validated the potential molecular targets of the functions, representatively LCN2, CRAMP, and HLA-DQB1, by Western blotting.

Conclusion

These results may provide molecular signature candidates to elucidate the mechanisms of the immune response by KRG. Here, we demonstrate a strategy of tissue proteomics for the discovery of the molecular function of KRG.

Analysis of the genetic component of systemic sclerosis in Iranian and Turkish populations through a genome-wide association study

Objectives

SSc is an autoimmune disease characterized by alteration of the immune response, vasculopathy and fibrosis. Most genetic studies on SSc have been performed in European-ancestry populations. The aim of this study was to analyse the genetic component of SSc in Middle Eastern patients from Iran and Turkey through a genome-wide association study.

Methods

This study analysed data from a total of 834 patients diagnosed with SSc and 1455 healthy controls from Iran and Turkey. DNA was genotyped using high-throughput genotyping platforms. The data generated were imputed using the Michigan Imputation Server, and the Haplotype Reference Consortium as a reference panel. A meta-analysis combining both case-control sets was conducted by the inverse variance method.

Results

The highest peak of association belonged to the HLA region in both the Iranian and Turkish populations. Strong and independent associations between the classical alleles HLA-DRB1*11: 04 [P = 2.10 × 10-24, odds ratio (OR) = 3.14] and DPB1*13: 01 (P = 5.37 × 10-14, OR = 5.75) and SSc were observed in the Iranian population. HLA-DRB1*11: 04 (P = 4.90 × 10-11, OR = 2.93) was the only independent signal associated in the Turkish cohort. An omnibus test yielded HLA-DRB1 58 and HLA-DPB1 76 as relevant amino acid positions for this disease. Concerning the meta-analysis, we also identified two associations close to the genome-wide significance level outside the HLA region, corresponding to IRF5-TNPO3 rs17424921-C (P = 1.34 × 10-7, OR = 1.68) and NFKB1 rs4648133-C (P = 3.11 × 10-7, OR = 1.47).

Conclusion

We identified significant associations in the HLA region and suggestive associations in IRF5-TNPO3 and NFKB1 loci in Iranian and Turkish patients affected by SSc through a genome-wide association study and an extensive HLA analysis.

Bridging immunogenetics and immunoproteomics: Model positional scanning library analysis for Major Histocompatibility Complex class II DQ in Tursiops truncatus

The Major Histocompatibility Complex (MHC) is a critical element in mounting an effective immune response in vertebrates against invading pathogens. Studies of MHC in wildlife populations have typically focused on assessing diversity within the peptide binding regions (PBR) of the MHC class II (MHC II) family, especially the DQ receptor genes. Such metrics of diversity, however, are of limited use to health risk assessment since functional analyses (where changes in the PBR are correlated to recognition/pathologies of known pathogen proteins), are difficult to conduct in wildlife species. Here we describe a means to predict the binding preferences of MHC proteins: We have developed a model positional scanning library analysis (MPSLA) by harnessing the power of mixture based combinatorial libraries to probe the peptide landscapes of distinct MHC II DQ proteins. The algorithm provided by NNAlign was employed to predict the binding affinities of sets of peptides generated for DQ proteins. These binding affinities were then used to retroactively construct a model Positional Scanning Library screen. To test the utility of the approach, a model screen was compared to physical combinatorial screens for human MHC II DP. Model library screens were generated for DQ proteins derived from sequence data from bottlenose dolphins from the Indian River Lagoon (IRL) and the Atlantic coast of Florida, and compared to screens of DQ proteins from Genbank for dolphin and three other cetaceans. To explore the peptide binding landscape for DQ proteins from the IRL, combinations of the amino acids identified as active were compiled into peptide sequence lists that were used to mine databases for representation in known proteins. The frequency of which peptide sequences predicted to bind the MHC protein are found in proteins from pathogens associated with marine mammals was found to be significant (p values <0.0001). Through this analysis, genetic variation in MHC (classes I and II) can now be associated with the binding repertoires of the expressed MHC proteins and subsequently used to identify target pathogens. This approach may be eventually applied to evaluate individual population and species risk for outbreaks of emerging diseases.

Research to Practice Implications of High-Risk Genotypes for Beryllium Sensitization and Disease

OBJECTIVE

Beryllium workers may better understand their genetic susceptibility to chronic beryllium disease (CBD) expressed as population-based prevalence, rather than odds ratios from case-control studies.

METHODS

We calculated CBD prevalences from allele-specific DNA sequences of 853 workers for Human Leukocyte Antigen (HLA)-DPB1 genotypes and groups characterized by number of E69-containing alleles and by calculated surface electronegativity of HLA-DPB1.

RESULTS

Of 18 groups of at least 10 workers with specific genotypes, CBD prevalence was highest, 72.7%, for the HLA-DPB102:01:02/DPB117:01 genotype. Population-based grouped genotypes with two E69 alleles wherein one allele had -9 surface charge had a beryllium sensitization (BeS) of 52.6% and a CBD prevalence of 42.1%.

CONCLUSIONS

The high CBD and BeS prevalences associated with -9-charged E69 alleles and two E69s suggest that workers may benefit from knowing their genetic susceptibility in deciding whether to avoid future beryllium exposure.

Association of Japanese cedar pollinosis and sensitization with HLA-DPB1 in the Japanese adolescent

BACKGROUND

Allergic rhinitis (AR) is a heterogeneous disorder that significantly affects daily activity, work productivity, sleep, learning, and quality of life in all generations. Japanese cedar (JC) pollen is the most common allergen responsible for the development of AR in Japan. AR caused by JC pollen is considered to be a multifactorial inheritance disease that is caused by both environmental and genetic factors. The aim of this study was to investigate whether Human Leukocyte Antigen-DPB1 (HLA-DPB1) is associated with JC sensitization/pollinosis.

METHODS

Subjects in the present study were 544 students at the University of Tsukuba from 2013 to 2015. PCR-SSOP was performed to determine each individual's HLA-DPB1 alleles. Logistic regression analysis was performed to examine relationships between JC-related phenotypes and alleles/amino acid polymorphisms of HLA-DPB1.

RESULTS

HLA-DPB1*02 allele were significantly associated with both JC sensitization/pollinosis (q < 0.05). Furthermore, HLA-DPB1*02:01 and HLA-DPB1*02:02 had a protective tendency for JC sensitization/pollinosis, and HLA-DPB1*05:01 had a susceptible tendency for sensitization (P < 0.05). In amino acid polymorphism analyses, Glutamic acid in position 69, Glycine-Glycine-Proline-Methionine in positions 84-87, Threonine in position 170 and Methionine in position 205 were also observed to have a protective tendency for JC sensitization (P < 0.05). Amino acid positions 69 and 84-87 were located in binding pocket 5 and 1 of HLA-DPβ1, respectively.

CONCLUSIONS

Amino acid changes in the allergen-binding pocket of HLA-DPβ1 are likely to influence pollinosis/sensitization to the allergenic peptide of JC pollen and determine the pollinosis risk for each individual exposed to JC pollen.

Human leukocyte Antigen-DM polymorphisms in autoimmune diseases

Classical MHC class II (MHCII) proteins present peptides for CD4⁺ T-cell surveillance and are by far the most prominent risk factor for a number of autoimmune disorders. To date, many studies have shown that this link between particular MHCII alleles and disease depends on the MHCII's particular ability to bind and present certain peptides in specific physiological contexts. However, less attention has been paid to the non-classical MHCII molecule human leucocyte antigen-DM, which catalyses peptide exchange on classical MHCII proteins acting as a peptide editor. DM function impacts the presentation of both antigenic peptides in the periphery and key self-peptides during T-cell development in the thymus. In this way, DM activity directly influences the response to pathogens, as well as mechanisms of self-tolerance acquisition. While decreased DM editing of particular MHCII proteins has been proposed to be related to autoimmune disorders, no experimental evidence for different DM catalytic properties had been reported until recently. Biochemical and structural investigations, together with new animal models of loss of DM activity, have provided an attractive foundation for identifying different catalytic efficiencies for DM allotypes. Here, we revisit the current knowledge of DM function and discuss how DM function may impart autoimmunity at the organism level.

High-Affinity Interactions of Beryllium(2+) with Phosphatidylserine Result in a Cross-Linking Effect Reducing Surface Recognition of the Lipid

Beryllium has multiple industrial applications, but its manufacture is associated with a serious occupational risk of developing chronic inflammation in the lungs known as berylliosis, or chronic beryllium disease. Although the Be²⁺-induced abnormal immune responses have recently been linked to a specific MHC-II allele, the nature of long-lasting granulomas is not fully understood. Here we show that Be²⁺ binds with a micromolar affinity to phosphatidylserine (PS), the major surface marker of apoptotic cells. Isothermal titration calorimetry indicates that, like that of Ca²⁺, binding of Be²⁺ to PS liposomes is largely entropically driven, likely by massive desolvation. Be²⁺ exerts a compacting effect on PS monolayers, suggesting cross-linking through coordination by both phosphates and carboxyls in multiple configurations, which were visualized in molecular dynamics simulations. Electrostatic modification of PS membranes by Be²⁺ includes complete neutralization of surface charges at ∼30 μM, accompanied by an increase in the boundary dipole potential. The data suggest that Be²⁺ can displace Ca²⁺ from the surface of PS, and being coordinated in a tight shell of four oxygens, it can mask headgroups from Ca²⁺-mediated recognition by PS receptors. Indeed, 48 μM Be²⁺ added to IC-21 cultured macrophages specifically suppresses binding and engulfment of PS-coated silica beads or aged erythrocytes. We propose that Be²⁺ adsorption at the surface of apoptotic cells may potentially prevent normal phagocytosis, thus causing accumulation of secondary necrotic foci and the resulting chronic inflammation.

Proteochemometrics-Based Prediction of Peptide Binding to HLA-DP Proteins

Human leukocyte antigens (HLA) class II proteins are involved in the antigen processing in the antigen presenting cells. They form complexes with antigen peptide fragments. The peptide-HLA protein complexes are presented on the cell surface where they are recognized by helper T cells (Th cells). HLA-DP is one of the three HLA class II loci. The HLA-DP proteins are associated with a significant number of autoimmune diseases, as well as with a susceptibility or resistance to a number of infectious agents. In the present study, we apply proteochemometrics-a method for bioactivity modeling of multiple ligands binding to multiple target proteins-to derive and validate a robust model for peptide binding prediction to the 7 most frequent HLA-DP proteins. The model is able to identify 86% of the binders in the top 10% of the best predicted nonamers generated from one protein.

Using DR52c/Ni2+ mimotope tetramers to detect Ni2+ reactive CD4+ T cells in patients with joint replacement failure

T cell mediated hypersensitivity to nickel (Ni²⁺) is one of the most common causes of allergic contact dermatitis. Ni²⁺ sensitization may also contribute to the failure of Ni²⁺ containing joint implants, and revision to non-Ni²⁺ containing hardware can be costly and debilitating. Previously, we identified Ni²⁺ mimotope peptides, which are reactive to a CD4⁺ T cell clone, ANi2.3 (Vα1, Vβ17), isolated from a Ni²⁺ hypersensitive patient with contact dermatitis. This T cell is restricted to the major histocompatibility complex class II (MHCII) molecule, Human Leukocyte Antigen (HLA)-DR52c (DRA, DRB3*0301). However, it is not known if Ni²⁺ induced T cell responses in sensitized joint replacement failure patients are similar to subjects with Ni²⁺ induced contact dermatitis. Here, we generated DR52c/Ni²⁺ mimotope tetramers, and used them to test if the same Ni²⁺ T cell activation mechanism could be generalized to Ni²⁺ sensitized patients with associated joint implant failure. We confirmed the specificity of these tetramers by staining of ANi2.3T cell transfectomas. The DR52c/Ni²⁺ mimotope tetramer detected Ni²⁺ reactive CD4⁺ T cells in the peripheral blood mononuclear cells (PBMC) of patients identified as Ni²⁺ sensitized by patch testing and a positive Ni²⁺ LPT. When HLA-typed by a DR52 specific antibody, three out of four patients were DR52 positive. In one patient, Ni²⁺ stimulation induced the expansion of Vβ17 positive CD4⁺ T cells from 0.8% to 13.3%. We found that the percentage of DR52 positivity and Vβ17 usage in Ni²⁺ sensitized joint failure patients are similar to Ni sensitized skin allergy patients. Ni²⁺ independent mimotope tetramers may be a useful tool to identify the Ni²⁺ reactive CD4⁺ T cells.

HLA-DP84Gly constitutively presents endogenous peptides generated by the class I antigen processing pathway

Classical antigen processing leads to the presentation of antigenic peptides derived from endogenous and exogenous sources for MHC class I and class II molecules, respectively. Here we show that, unlike other class II molecules, prevalent HLA-DP molecules with β-chains encoding Gly84 (DP^84Gly) constitutively present endogenous peptides. DP^84Gly does not bind invariant chain (Ii) via the class II-associated invariant chain peptide (CLIP) region, nor does it present CLIP. However, Ii does facilitate the transport of DP^84Gly from the endoplasmic reticulum (ER) to the endosomal/lysosomal pathway by transiently binding DP^84Gly via a non-CLIP region(s) in a pH-sensitive manner. Accordingly, like class I, DP^84Gly constitutively presents endogenous peptides processed by the proteasome and transported to the ER by the transporter associated with antigen processing (TAP). Therefore, DP^84Gly, found only in common chimpanzees and humans, uniquely uses both class I and II antigen-processing pathways to present peptides derived from intracellular and extracellular sources.

The Presence, Persistence and Functional Properties of Plasmodium vivax Duffy Binding Protein II Antibodies Are Influenced by HLA Class II Allelic Variants

Background

The human malaria parasite Plasmodium vivax infects red blood cells through a key pathway that requires interaction between Duffy binding protein II (DBPII) and its receptor on reticulocytes, the Duffy antigen/receptor for chemokines (DARC). A high proportion of P. vivax-exposed individuals fail to develop antibodies that inhibit DBPII-DARC interaction, and genetic factors that modulate this humoral immune response are poorly characterized. Here, we investigate if DBPII responsiveness could be HLA class II-linked.

Methodology/Principal Findings

A community-based open cohort study was carried out in an agricultural settlement of the Brazilian Amazon, in which 336 unrelated volunteers were genotyped for HLA class II (DRB1, DQA1 and DQB1 loci), and their DBPII immune responses were monitored over time (baseline, 6 and 12 months) by conventional serology (DBPII IgG ELISA-detected) and functional assays (inhibition of DBPII–erythrocyte binding). The results demonstrated an increased susceptibility of the DRB1*13:01 carriers to develop and sustain an anti-DBPII IgG response, while individuals with the haplotype DRB1*14:02-DQA1*05:03-DQB1*03:01 were persistent non-responders. HLA class II gene polymorphisms also influenced the functional properties of DBPII antibodies (BIAbs, binding inhibitory antibodies), with three alleles (DRB1*07:01, DQA1*02:01 and DQB1*02:02) comprising a single haplotype linked with the presence and persistence of the BIAbs response. Modelling the structural effects of the HLA-DRB1 variants revealed a number of differences in the peptide-binding groove, which is likely to lead to altered antigen binding and presentation profiles, and hence may explain the differences in subject responses.

Conclusions/Significance

The current study confirms the heritability of the DBPII antibody response, with genetic variation in HLA class II genes influencing both the development and persistence of IgG antibody responses. Cellular studies to increase knowledge of the binding affinities of DBPII peptides for class II molecules linked with good or poor antibody responses might lead to the development of strategies for controlling the type of helper T cells activated in response to DBPII.

Vaccines are a crucial component of the current efforts to eliminate malaria, and much of the vaccine-related research on P. vivax has been focused on the Duffy binding protein II (DBPII), a ligand for human blood stage infection. A high proportion of individuals who are naturally exposed to P. vivax fail to develop neutralizing antibodies, but the host genetic factors modulating this immune response are poorly characterized. We investigated whether DBPII responsiveness was dependent on the variability of human leucocyte antigen (HLA) class II cell surface proteins involved in the regulation of immune responses. To obtain a reliable estimate of DBPII antibodies, we carried out a longitudinal study, collecting serum from the same individuals over a period of 12-months. The results confirmed the heritability of the DBPII immune response, with genetic variation in HLA class II genes influencing both the development and persistence of the antibody response. HLA class II genotype also influenced the ability of DBPII antibodies to block the ligand-receptor interaction in vitro. Computational approaches identified structural specificity between HLA variants, which we propose as an explanation for differences between a good or poor antibody responder. These results may have implications for vaccine development, and might lead to strategies for controlling the type of immune response activated in response to DBPII.

The orthologs of HLA-DQ and -DP genes display abundant levels of variability in macaque species

The human major histocompatibility complex (MHC) region encodes three types of class II molecules designated HLA-DR, -DQ, and -DP. Both the HLA-DQ and -DP gene region comprise a duplicated tandem of A and B genes, whereas in macaques, only one set of genes is present per region. A substantial sequencing project on the DQ and DP genes in various macaque populations resulted in the detection of previously 304 unreported full-length alleles. Phylogenetic studies showed that humans and macaques share trans-species lineages for the DQA1 and DQB1 genes, whereas the DPA1 and DPB1 lineages in macaques appear to be species-specific. Amino acid variability plot analyses revealed that each of the four genes displays more allelic variation in macaques than is encountered in humans. Moreover, the numbers of different amino acids at certain positions in the encoded proteins are higher than in humans. This phenomenon is remarkably prominent at the contact positions of the peptide-binding sites of the deduced macaque DPβ-chains. These differences in the MHC class II DP regions of macaques and humans suggest separate evolutionary mechanisms in the generation of diversity.

Antibodies against HLA-DP recognize broadly expressed epitopes

HLA matching and avoidance of pre-transplant donor-specific antibodies are important in selection of donors for solid organ transplant. Solid phase testing with single antigen beads allows resolution of antibody reactivity to the level of the allele. Single antigen bead testing results at a large transplant center were reviewed to identify selective reactivity patterns of anti-HLA antibodies. Many HLA-DP antibodies were identified in the context of other HLA antibodies, but some sera had antibodies against only HLA-DP. B cell flow crossmatch testing was positive for 2 out of 9 sera with HLA-DP antibodies. Many patterns of reactivity corresponded to epitopes in hypervariable regions C and F of DPB1, but some matched epitopes in other regions or DPA1. Through analysis of single antigen bead testing from a large number of patients, we report that anti-HLA-DP antibodies predominantly recognize broadly cross-reactive epitopes. The United Network for Organ Sharing has mandated HLA-DP typing on all deceased kidney donors, and HLA-DP epitopes should be considered as the major antigens for avoidance of pre-transplant donor-specific antibodies.

Association of variations in HLA class II and other loci with susceptibility to EGFR-mutated lung adenocarcinoma

Lung adenocarcinoma driven by somatic EGFR mutations is more prevalent in East Asians (30–50%) than in European/Americans (10–20%). Here we investigate genetic factors underlying the risk of this disease by conducting a genome-wide association study, followed by two validation studies, in 3,173 Japanese patients with EGFR mutation-positive lung adenocarcinoma and 15,158 controls. Four loci, 5p15.33 (TERT), 6p21.3 (BTNL2), 3q28 (TP63) and 17q24.2 (BPTF), previously shown to be strongly associated with overall lung adenocarcinoma risk in East Asians, were re-discovered as loci associated with a higher susceptibility to EGFR mutation-positive lung adenocarcinoma. In addition, two additional loci, HLA class II at 6p21.32 (rs2179920; P =5.1 × 10⁻¹⁷, per-allele OR=1.36) and 6p21.1 (FOXP4) (rs2495239; P=3.9 × 10⁻⁹, per-allele OR=1.19) were newly identified as loci associated with EGFR mutation-positive lung adenocarcinoma. This study indicates that multiple genetic factors underlie the risk of lung adenocarcinomas with EGFR mutations.

EGFR mutations in lung adenocarcinoma are more frequent in East Asians compared to other populations. Here, the authors carry out a genome-wide association study in EGFR mutant cancers and identify loci that are associated with risk of developing this molecular subtype of cancer.

Genetic risk of extranodal natural killer T-cell lymphoma: a genome-wide association study

BACKGROUND

Extranodal natural killer T-cell lymphoma (NKTCL), nasal type, is a rare and aggressive malignancy that occurs predominantly in Asian and Latin American populations. Although Epstein-Barr virus infection is a known risk factor, other risk factors and the pathogenesis of NKTCL are not well understood. We aimed to identify common genetic variants affecting individual risk of NKTCL.

METHODS

We did a genome-wide association study of 189 patients with extranodal NKTCL, nasal type (WHO classification criteria; cases) and 957 controls from Guangdong province, southern China. We validated our findings in four independent case-control series, including 75 cases from Guangdong province and 296 controls from Hong Kong, 65 cases and 983 controls from Guangdong province, 125 cases and 1110 controls from Beijing (northern China), and 60 cases and 2476 controls from Singapore. We used imputation and conditional logistic regression analyses to fine-map the associations. We also did a meta-analysis of the replication series and of the entire dataset.

FINDINGS

Associations exceeding the genome-wide significance threshold (p<5 × 10(-8)) were seen at 51 single-nucleotide polymorphisms (SNPs) mapping to the class II MHC region on chromosome 6, with rs9277378 (located in HLA-DPB1) having the strongest association with NKTCL susceptibility (p=4·21 × 10(-19), odds ratio [OR] 1·84 [95% CI 1·61-2·11] in meta-analysis of entire dataset). Imputation-based fine-mapping across the class II MHC region suggests that four aminoacid residues (Gly84-Gly85-Pro86-Met87) in near-complete linkage disequilibrium at the edge of the peptide-binding groove of HLA-DPB1 could account for most of the association between the rs9277378*A risk allele and NKTCL susceptibility (OR 2·38, p value for haplotype 2·32 × 10(-14)). This association is distinct from MHC associations with Epstein-Barr virus infection.

INTERPRETATION

To our knowledge, this is the first time that a genetic variant conferring an NKTCL risk is noted at genome-wide significance. This finding underlines the importance of HLA-DP antigen presentation in the pathogenesis of NKTCL.

FUNDING

Top-Notch Young Talents Program of China, Special Support Program of Guangdong, Specialized Research Fund for the Doctoral Program of Higher Education (20110171120099), Program for New Century Excellent Talents in University (NCET-11-0529), National Medical Research Council of Singapore (TCR12DEC005), Tanoto Foundation Professorship in Medical Oncology, New Century Foundation Limited, Ling Foundation, Singapore National Cancer Centre Research Fund, and the US National Institutes of Health (1R01AR062886, 5U01GM092691-04, and 1R01AR063759-01A1).

Beryllium-Induced Hypersensitivity: Genetic Susceptibility and Neoantigen Generation

Chronic beryllium (Be) disease is a granulomatous lung disorder that results from Be exposure in a genetically susceptible host. The disease is characterized by the accumulation of Be-responsive CD4(+) T cells in the lung, and genetic susceptibility is primarily linked to HLA-DPB1 alleles possessing a glutamic acid at position 69 of the β-chain. Recent structural analysis of a Be-specific TCR interacting with a Be-loaded HLA-DP2-peptide complex revealed that Be is coordinated by amino acid residues derived from the HLA-DP2 β-chain and peptide and showed that the TCR does not directly interact with the Be(2+) cation. Rather, the TCR recognizes a modified HLA-DP2-peptide complex with charge and conformational changes. Collectively, these findings provide a structural basis for the development of this occupational lung disease through the ability of Be to induce posttranslational modifications in preexisting HLA-DP2-peptide complexes, resulting in the creation of neoantigens.

Negatively-charged amino acids at the peptide-binding pocket of HLA-DPB1 alleles are associated with susceptibility to anti-topoisomerase I-positive systemic sclerosis

We investigated shared characteristics of amino acid sequences in the at risk HLA-DPB1 alleles in systemic sclerosis (SSc). Amino acid sequences and their structural features of HLA-DP molecules in 127 Korean SSc patients and 548 healthy Korean controls were analyzed with a focus on known HLA-DP binding motifs. The binding grooves containing more negatively-charged triplets (NCT) had higher odds ratios of anti-topoisomerase I antibody (ATA)-positive SSc. In particular, the co-existence of a NCT at position 82-85 and more than one additional NCT were critical for increased risk of ATA-positive SSc. Molecular dynamic simulations showed that the model peptide with positive charge from topoisomerase I fits more closely into HLA-DP alleles possessing more NCTs. ATA-positive SSc patients share NCTs at the peptide-binding groove of HLA-DPB1 molecules.