Glycoproteomic Analysis of Seven Major Allergenic Proteins Reveals Novel Post-translational Modifications

Allergenic proteins such as grass pollen and house dust mite (HDM) proteins are known to trigger hypersensitivity reactions of the immune system, leading to what is commonly known as allergy. Key allergenic proteins including sequence variants have been identified but characterization of their post-translational modifications (PTMs) is still limited.Here, we present a detailed PTM¹ characterization of a series of the main and clinically relevant allergens used in allergy tests and vaccines. We employ Orbitrap-based mass spectrometry with complementary fragmentation techniques (HCD/ETD) for site-specific PTM characterization by bottom-up analysis. In addition, top-down mass spectrometry is utilized for targeted analysis of individual proteins, revealing hitherto unknown PTMs of HDM allergens. We demonstrate the presence of lysine-linked polyhexose glycans and asparagine-linked N-acetylhexosamine glycans on HDM allergens. Moreover, we identified more complex glycan structures than previously reported on the major grass pollen group 1 and 5 allergens, implicating important roles for carbohydrates in allergen recognition and response by the immune system. The new findings are important for understanding basic disease-causing mechanisms at the cellular level, which ultimately may pave the way for instigating novel approaches for targeted desensitization strategies and improved allergy vaccines.Allergic respiratory disease is a global health problem and current clinical guidelines recommend a combination of allergen avoidance, pharmacotherapy, and allergen specific immunotherapy for treatment (1–4). At present allergy testing and vaccines are based on isolated crude antigen preparations from natural sources (i.e. HDM, pollens, etc.), but a move toward recombinant allergen design is ongoing (5, 6). This could have important functional implications because the production host will determine the repertoire of post-translational modifications (PTMs) and in particular glycan modifications presented on allergens.The carbohydrate structures found on allergens are in most cases not found in mammals and therefore frequently lead to the induction IgE antibodies named Cross-reactive Carbohydrate Determinants (CCD) (7–11). Moreover, glycans may directly be involved in and promote uptake and target allergens to carbohydrate lectin receptors on antigen presenting cells (APC) (12–14). Therefore, a full structural characterization of the glycans on the natural allergens is a prerequisite for understanding both antibody reactivity and lectin receptor mediated allergen recognition and modulation of the immune response (15, 16). Furthermore, a detailed characterization of PTMs of allergens is important for standardization of allergen products for diagnostic purposes as well as for vaccine use (17, 18). Although many major allergens and their etiology have been characterized in some detail, structural information on for example their immunological important PTM status is still incomplete (19–21).Mass spectrometry-based technologies offer sensitive and accurate analyses for identification and characterization of proteins. The common proteomics workflow typically adopts the bottom-up approach, i.e. in vitro proteolytic digestion of proteins followed by nanoflow-liquid chromatography-tandem mass spectrometry (nLC-MS/MS) for protein identification and PTM characterization. Electron- or collision-driven fragmentation techniques, e.g. electron transfer dissociation (ETD) (22) or higher energy collisional dissociation (HCD) (23) have enabled accurate identification of peptides of purified proteins, e.g. allergens (21, 24), or complex biological samples (25–27) with concurrent characterization of their PTMs. One advantage of bottom-up mass spectrometry is the ability to resolve modified peptides within a narrow chromatographic time frame thereby enabling in-depth characterization of site-specific features, e.g. glycoforms, on peptides. This peptide-level information is subsequently used to generate a protein-level view on the PTM status for a given protein. Importantly, the PTM connectivity of the protein (28) is lost upon proteolytic digestion, and alternative approaches are often required for comprehensive characterization of all proteoforms (29). Top-down mass spectrometry has emerged as an alternative approach to bottom-up proteomics, offering complementary MS and MS/MS information that may be used for protein identification and characterization (30, 31). With top-down MS, intact proteins are typically analyzed by high-resolution FTMS and characterized at the MS/MS level by CID, HCD, ECD, or ETD. This technique provides instant protein-level information on analytes, e.g. sequence variants, amino acid substitutions, PTMs, etc., which can be verified at the MS/MS level by different fragmentation modes. The combination of bottom-up and top-down mass spectrometry is therefore a powerful tool for the identification and characterization of proteins. Here, we combine top-down and bottom-up mass spectrometry for comprehensive characterization of seven major allergens as a first step toward unraveling the molecular mode of action of allergens with complex PTMs. By these methods, we demonstrate hitherto unknown PTMs of HDM allergens and identify more complex glycan structures than previously reported on the major grass pollen group 1 and 5 allergens. The new findings implicate important roles for carbohydrates in allergen recognition and response by the immune system.     

Expression of renal distal tubule transporters TRPM6 and NCC in a rat model of cyclosporine nephrotoxicity and effect of EGF treatment

Renal magnesium (Mg(2+)) and sodium (Na(+)) loss are well-known side effects of cyclosporine (CsA) treatment in humans, but the underlying mechanisms still remain unclear. Recently, it was shown that epidermal growth factor (EGF) stimulates Mg(2+) reabsorption in the distal convoluted tubule (DCT) via TRPM6 (Thébault S, Alexander RT, Tiel Groenestege WM, Hoenderop JG, Bindels RJ. J Am Soc Nephrol 20: 78-85, 2009). In the DCT, the final adjustment of renal sodium excretion is regulated by the thiazide-sensitive Na(+)-Cl(-) cotransporter (NCC), which is activated by the renin-angiotensin-aldosterone system (RAAS). The aim of this study was to gain more insight into the molecular mechanisms of CsA-induced hypomagnesemia and hyponatremia. Therefore, the renal expression of TRPM6, TRPM7, EGF, EGF receptor, claudin-16, claudin-19, and the NCC, and the effect of the RAAS on NCC expression, were analyzed in vivo in a rat model of CsA nephrotoxicity. Also, the effect of EGF administration on these parameters was studied. CsA significantly decreased the renal expression of TRPM6, TRPM7, NCC, and EGF, but not that of claudin-16 and claudin-19. Serum aldosterone was significantly lower in CsA-treated rats. In control rats treated with EGF, an increased renal expression of TRPM6 together with a decreased fractional excretion of Mg(2+) (FE Mg(2+)) was demonstrated. EGF did not show this beneficial effect on TRPM6 and FE Mg(2+) in CsA-treated rats. These data suggest that CsA treatment affects Mg(2+) homeostasis via the downregulation of TRPM6 in the DCT. Furthermore, CsA downregulates the NCC in the DCT, associated with an inactivation of the RAAS, resulting in renal sodium loss.     

Weight loss and improved gross motor coordination in children as a result of multidisciplinary residential obesity treatment

This study evaluated the short‐term effectiveness of a multidisciplinary residential obesity treatment program by describing changes in body weight, related measures, and gross motor co‐ordination. Secondarily, it was examined to what extent the amount of relative weight loss achieved by overweight and obese (OW/OB) participants explained the projected improvement in gross motor co‐ordination. Thirty‐six OW/OB children (aged 10.5 ± 1.4 years, 12 girls and 24 boys) were recruited at the Zeepreventorium VZW (De Haan, Belgium), where they followed a specific program consisting of moderate dietary restriction, psychological support, and physical activity. For reference purposes, an additional group of 36 age‐ and gender‐matched healthy‐weight (HW) children was included in the study. Anthropometric measures were recorded and gross motor co‐ordination was assessed using the Körperkoordinationstest für Kinder (KTK) on two occasions with an interval of 4 months. Regardless of the test moment, OW/OB participants displayed significantly poorer KTK performances (P < 0.001). However, treatment was found to be efficacious in decreasing body weight (Δ 17.9 ± 3.1%, P < 0.001) and generating a significant progress in gross motor co‐ordination performance, with a greater increase in KTK score(s) from baseline to re‐test as compared to HW peers (P < 0.01). Within the OW/OB group, the amount of relative weight loss explained 26.9% of the variance in improvement in overall KTK performance. Therefore, multidisciplinary residential treatment and concomitant weight loss can be considered an important means to upgrade OW/OB children's level of gross motor co‐ordination, which in turn may promote physical activity participation.     

X-linked neonatal-onset epileptic encephalopathy associated with a gain-of-function variant p.R660T in GRIA3

The X-linked GRIA3 gene encodes the GLUA3 subunit of AMPA-type glutamate receptors. Pathogenic variants in this gene were previously reported in neurodevelopmental diseases, mostly in male patients but rarely in females. Here we report a de novo pathogenic missense variant in GRIA3 (c.1979G>C; p. R660T) identified in a 1-year-old female patient with severe epilepsy and global developmental delay. When exogenously expressed in human embryonic kidney (HEK) cells, GLUA3_R660T showed slower desensitization and deactivation kinetics compared to wildtype (wt) GLUA3 receptors. Substantial non-desensitized currents were observed with the mutant but not for wt GLUA3 with prolonged exposure to glutamate. When co-expressed with GLUA2, the decay kinetics were similarly slowed in GLUA2/A3_R660T with non-desensitized steady state currents. In cultured cerebellar granule neurons, miniature excitatory postsynaptic currents (mEPSCs) were significantly slower in R660T transfected cells than those expressing wt GLUA3. When overexpressed in hippocampal CA1 neurons by in utero electroporation, the evoked EPSCs and mEPSCs were slower in neurons expressing R660T mutant compared to those expressing wt GLUA3. Therefore our study provides functional evidence that a gain of function (GoF) variant in GRIA3 may cause epileptic encephalopathy and global developmental delay in a female subject by enhancing synaptic transmission.     

Genetic variation in functional traits influences arthropod community composition in aspen (Populus tremula L.)

We conducted a study of natural variation in functional leaf traits and herbivory in 116 clones of European aspen, Populus tremula L., the Swedish Aspen (SwAsp) collection, originating from ten degrees of latitude across Sweden and grown in a common garden. In surveys of phytophagous arthropods over two years, we found the aspen canopy supports nearly 100 morphospecies. We identified significant broad-sense heritability of plant functional traits, basic plant defence chemistry, and arthropod community traits. The majority of arthropods were specialists, those coevolved with P. tremula to tolerate and even utilize leaf defence compounds. Arthropod abundance and richness were more closely related to plant growth rates than general chemical defences and relationships were identified between the arthropod community and stem growth, leaf and petiole morphology, anthocyanins, and condensed tannins. Heritable genetic variation in plant traits in young aspen was found to structure arthropod community; however no single trait drives the preferences of arthropod folivores among young aspen genotypes. The influence of natural variation in plant traits on the arthropod community indicates the importance of maintaining genetic variation in wild trees as keystone species for biodiversity. It further suggests that aspen can be a resource for the study of mechanisms of natural resistance to herbivores.     

AICA-ribosiduria: a novel, neurologically devastating inborn error of purine biosynthesis caused by mutation of ATIC

In a female infant with dysmorphic features, severe neurological defects, and congenital blindness, a positive urinary Bratton-Marshall test led to identification of a massive excretion of 5-amino-4-imidazolecarboxamide (AICA)-riboside, the dephosphorylated counterpart of AICAR (also termed "ZMP"), an intermediate of de novo purine biosynthesis. ZMP and its di- and triphosphate accumulated in the patient's erythrocytes. Incubation of her fibroblasts with AICA-riboside led to accumulation of AICAR, not observed in control cells, suggesting impairment of the final steps of purine biosynthesis, catalyzed by the bifunctional enzyme AICAR transformylase/IMP cyclohydrolase (ATIC). AICAR transformylase was profoundly deficient, whereas the IMP cyclohydrolase level was 40% of normal. Sequencing of ATIC showed a K426R change in the transformylase region in one allele and a frameshift in the other. Recombinant protein carrying mutation K426R completely lacks AICAR transformylase activity.     

The Contribution of Caseins to the Amino Acid Supply for Lactococcus lactis Depends on the Type of Cell Envelope Proteinase

The ability of caseins to fulfill the amino acid requirements of Lactococcus lactis for growth was studied as a function of the type of cell envelope proteinase (P_I versus P_III type). Two genetically engineered strains of L. lactis that differed only in the type of proteinase were grown in chemically defined media containing α_s1-, β-, and κ-caseins (alone or in combination) as the sources of amino acids. Casein utilization resulted in limitation of the growth rate, and the extent of this limitation depended on the type of casein and proteinase. Adding different mixtures of essential amino acids to the growth medium made it possible to identify the nature of the limitation. This procedure also made it possible to identify the amino acid deficiency which was growth rate limiting for L. lactis in milk (S. Helinck, J. Richard, and V. Juillard, Appl. Environ. Microbiol. 63:2124–2130, 1997) as a function of the type of proteinase. Our results were compared with results from previous in vitro experiments in which casein degradation by purified proteinases was examined. The results were in agreement only in the case of the P_I-type proteinase. Therefore, our results bring into question the validity of the in vitro approach to identification of casein-derived peptides released by a P_III-type proteinase.     

The Association between Belgian Older Adults’ Physical Functioning and Physical Activity: What Is the Moderating Role of the Physical Environment?

Background

Better physical functioning in the elderly may be associated with higher physical activity levels. Since older adults spend a substantial part of the day in their residential neighborhood, the neighborhood physical environment may moderate associations between functioning and older adults’ physical activity. The present study investigated the moderating role of the objective and perceived physical environment on associations between Belgian older adults’ physical functioning and transport walking, recreational walking, and moderate-to-vigorous physical activity.

Methods

Data from 438 older adults were included. Objective physical functioning was assessed using the Short Physical Performance Battery. Potential moderators included objective neighborhood walkability and perceptions of land use mix diversity, access to recreational facilities, access to services, street connectivity, physical barriers for walking, aesthetics, crime-related safety, traffic speeding-related safety, and walking infrastructure. Transport and recreational walking were self-reported, moderate-to-vigorous physical activity was assessed through accelerometers. Multi-level regression analyses were conducted using MLwiN to examine two-way interactions between functioning and the environment on both walking outcomes. Based on a previous study where environment x neighborhood income associations were found for Belgian older adults’ moderate-to-vigorous physical activity, three-way functioning x environment x income interactions were examined for moderate-to-vigorous physical activity.

Results

Objectively-measured walkability moderated the association between functioning and transport walking; this positive association was only present in high-walkable neighborhoods. Moreover, a three-way interaction was observed for moderate-to-vigorous physical activity. Only in high-income, high-walkable neighborhoods, there was a positive association between functioning and moderate-to-vigorous physical activity. No functioning x walkability interactions were observed for recreational walking, and none of the perceived environmental variables moderated the positive association between physical functioning and the physical activity outcomes.

Conclusions

For older adults with better physical functioning, living in a high-walkable neighborhood could be beneficial to engage in more transport walking. Living in high-income, high-walkable neighborhoods and having better functioning might also be beneficial for more engagement in moderate-to-vigorous physical activity. This might suggest a protective role of neighborhood walkability for preventing declining physical functioning and consequently decreasing physical activity levels in older adults. However, given the cross-sectional design of the present study, this suggestion needs to be confirmed through longitudinal assessment investigating over-time changes in the observed associations.     

Allele imputation for the killer cell immunoglobulin-like receptor KIR3DL1/S1

Highly polymorphic interaction of KIR3DL1 and KIR3DS1 with HLA class I ligands modulates the effector functions of natural killer (NK) cells and some T cells. This genetically determined diversity affects severity of infections, immune-mediated diseases, and some cancers, and impacts the course of immunotherapies, including transplantation. KIR3DL1 is an inhibitory receptor, and KIR3DS1 is an activating receptor encoded by the KIR3DL1/S1 gene that has more than 200 diverse and divergent alleles. Determination of KIR3DL1/S1 genotypes for medical application is hampered by complex sequence and structural variation, requiring targeted approaches to generate and analyze high-resolution allele data. To overcome these obstacles, we developed and optimized a model for imputing KIR3DL1/S1 alleles at high-resolution from whole-genome SNP data. We designed the model to represent a substantial component of human genetic diversity. Our Global imputation model is effective at genotyping KIR3DL1/S1 alleles with an accuracy ranging from 88% in Africans to 97% in East Asians, with mean specificity of 99% and sensitivity of 95% for alleles >1% frequency. We used the established algorithm of the HIBAG program, in a modification named Pulling Out Natural killer cell Genomics (PONG). Because HIBAG was designed to impute HLA alleles also from whole-genome SNP data, PONG allows combinatorial diversity of KIR3DL1/S1 with HLA-A and -B to be analyzed using complementary techniques on a single data source. The use of PONG thus negates the need for targeted sequencing data in very large-scale association studies where such methods might not be tractable.