Utjecaj genskih i okolišnih čimbenika na N-glikozilaciju imunoglobulina G i ukupnih plazmatskih proteina određen studijom na blizancima

Glycans constitute the most abundant and diverse form of the post-translational modifications. While genes unequivocally determine the structure of each polypeptide, there is no genetic template for the glycan part. Instead, hundreds of genes and their products interact in the very complex pathway of glycan biosynthesis which is further complicated by environmental influences. Therefore, the aim of this thesis was to determine the extent to which individual differences in immunoglobulin G and total plasma proteins glycosylation patterns reflect genetic versus environmental influences. A twin study design was used and study subjects were twins enrolled in the TwinsUK registry, a national register of adult twins. More than 4500 samples were analyzed by HILIC-UPLC (Hydrophilic Interaction Ultra Performance Liquid Chromatography). A high contribution of the genetic component to N-glycome composition was found. Variation in levels of 51 of the 76 IgG glycan traits studied was at least 50% heritable and only a small proportion of N-glycan traits had a low genetic contribution. Heritability of plasma N-glycome was also high, with half of the plasma glycan traits being at least 50% heritable. Further, epigenome-wide association (EWA) analysis showed that methylation levels at some genes are also implicated in glycome composition, both in those with high heritability and those with a lower genetic contribution. The study to investigate the potential role of glycosylation in kidney function was also conducted. Fourteen IgG glycan traits were associated with renal function in discovery population and remained significant after validation in an independent subset of monozygotic twins discordant for renal disease, reflecting difference in galactosylation, sialylation, and level of bisecting N-acetylglucosamine. Using the weighted correlation network analysis (WGCNA) for IgG glycan traits, a correlation between low back pain (LBP) and glycan modules was established. There was a weak positive correlation between pain phenotypes and "proantibody- dependent cell-mediated cytotoxicity (ADCC)" WGCNA glycan modules (high bisecting Nacetylglucosamine and low core fucose) and a weak negative correlation between pain phenotypes and "anti-ADCC" module (high core fucose, no bisecting N-acetylglucosamine). This suggests that glycans are promising candidates for biomarkers in many different diseases.Glikani predstavljaju najzastupljeniji i najraznolikiji oblik posttranslacijske modifikacije. Dok geni nedvosmisleno određuju strukturu svakog polipeptida, za sintezu glikana ne postoji genski predložak. Umjesto toga, stotine gena i njihovih produkata sudjeluju u vrlo kompleksnoj biosintezi glikana koju okolišni utjecaji čine još složenijom. Stoga je cilj ovog doktorskog rada odrediti razmjer kojim genski i okolišni čimbenici utječu na N-glikane imunoglobulina G (IgG) i ukupnih glikoproteina plazme. Da bi se postigao navedeni cilj, upotrijebljena je studija na blizancima. Ispitanici su regrutirani TwinsUK registrom, najvećim registrom blizanaca u Velikoj Britaniji. Više od 4500 uzoraka analizirano je HILIC-UPLC metodom (kromatografijom vrlo visoke djelotvornosti temeljenoj na hidrofilnim interakcijama, eng. Hydrophilic Interaction Ultra Performance Liquid Chromatography). Velika genska komponenta (heritabilnost ≥ 50%) pokazana je za 51 od 76 glikanskih svojstava IgG-a. Nasuprot tome, samo je 12 glikanskih svojstava IgG-a pokazalo malu gensku komponentu. Heritabilnost plazmatskog N-glikoma također se pokazala velikom. Polovica plazmatskih glikanskih svojstava bila je barem 50% heritabilna. Epigenomska asocijacijska analiza pokazala je da razina metilacije na nekim genima također utječe na sastav glikoma, i to na visokoheritabilne i niskoheritabilne glikane. Također je provedeno prvo istraživanje potencijalne uloge IgG glikozilacije u funkciji bubrega. U prvoj je analizi pronađena značajna povezanost s bubrežnom funkcijom za 14 glikanskih svojstava, a ostala je značajna i nakon validacije na neovisnoj podskupini monozigotnih blizanaca diskordantnih za bubrežnu funkciju. Ta glikanska svojstva pripadaju trima glavnim glikozilacijskim karakteristikama IgG-a: galaktozilaciji, sijalinizaciji i razini račvajućeg Nacetilglukozamina. Koristeći se WGCNA (eng. weighted correlation network analysis) metodologijom, provedena je mrežna analiza razina IgG glikana kod blizanaca, da bi se uspostavili klasteri koreliranih glikana. Pronađene su povezanosti između tih klastera i fenotipova boli kod blizanaca s LBP-om. Opažena je pozitivna korelacija između fenotipova boli i „pro-stanična citotoksičnost ovisna o protutijelima (eng. antibody-dependent cell-mediated cytotoxicity, ADCC)“ WGCNA glikanskog modula (visoka razina račvajućeg N-acetilglukozamina i niska razina sržne fukoze) te negativna korelacija između fenotipova boli i „anti-ADCC“ modula (visoka razina sržne fukoze, bez račvajućeg N-acetilglukozamina). Rezultati pokazuju da su glikani obećavajući biomarkeri za mnoge bolesti

Fucosylated AGP glycopeptides as biomarkers of HNF1A-Maturity onset diabetes of the young

Aims: We previously demonstrated that antennary fucosylated N-glycans on plasma proteins are regulated by HNF1A and can identify cases of Maturity-Onset Diabetes of the Young caused by HNF1A variants (HNF1A-MODY). Based on literature data, we further postulated that N-glycans with best diagnostic value mostly originate from alpha-1-acid glycoprotein (AGP). In this study we analyzed fucosylation of AGP in subjects with HNF1A-MODY and other types of diabetes aiming to evaluate its diagnostic potential. Methods: A recently developed LC-MS method for AGP N-glycopeptide analysis was utilized in two independent cohorts: a) 466 subjects with different diabetes subtypes to test the fucosylation differences, b) 98 selected individuals to test the discriminative potential for pathogenic HNF1A variants. Results: Our results showed significant reduction in AGP fucosylation associated to HNF1A-MODY when compared to other diabetes subtypes. Additionally, ROC curve analysis confirmed significant discriminatory potential of individual fucosylated AGP glycopeptides, where the best performing glycopeptide had an AUC of 0.94 (95% CI 0.90–0.99). Conclusions: A glycopeptide based diagnostic tool would be beneficial for patient stratification by providing information about the functionality of HNF1A. It could assist the interpretation of DNA sequencing results and be a useful addition to the differential diagnostic process.publishedVersio

Asymmetric Primaquine and Halogenaniline Fumardiamides as Novel Biologically Active Michael Acceptors

Novel primaquine (PQ) and halogenaniline asymmetric fumardiamides 4a–f, potential Michael acceptors, and their reduced analogues succindiamides 5a–f were prepared by simple three-step reactions: coupling reaction between PQ and mono-ethyl fumarate (1a) or mono-methyl succinate (1b), hydrolysis of PQ-dicarboxylic acid mono-ester conjugates 2a, b to corresponding acids 3a, b, and a coupling reaction with halogenanilines. 1- [bis(Dimethylamino)methylene]-1H-1, 2, 3- triazolo[4, 5-b]pyridinium 3-oxide hexafluorophosphate (HATU) was used as a coupling reagent along with Hünig′s base. Compounds 4 and 5 were evaluated against a panel of bacteria, several Mycobacterium strains, fungi, a set of viruses, and nine different human tumor cell lines. p-Chlorofumardiamide 4d showed significant activity against Staphylococcus aureus, Streptococcus pneumoniae and Acinetobacter baumannii, but also against Candida albicans (minimum inhibitory concentration (MIC) 6.1–12.5 µg/mL). Together with p-fluoro and p-CF3 fumardiamides 4b, f, compound 4d showed activity against Mycobacterium marinum and 4b, f against M. tuberculosis. In biofilm eradication assay, most of the bacteria, particularly S. aureus, showed susceptibility to fumardiamides. m-CF3 and m- chloroaniline fumardiamides 4e and 4c showed significant antiviral activity against reovirus- 1, sindbis virus and Punta Toro virus (EC50 = 3.1–5.5 µM), while 4e was active against coxsackie virus B4 (EC50 = 3.1 µM). m-Fluoro derivative 4a exerted significant cytostatic activity (IC50 = 5.7–31.2 μM). Acute lymphoblastic leukemia cells were highly susceptible towards m-substituted derivatives 4a, c, e (IC50 = 6.7–8.9 μM). Biological evaluations revealed that fumardiamides 4 were more active than succindiamides 5 indicating importance of Michael conjugated system

Systematic Evaluation of Normalization Methods for Glycomics Data Based on Performance of Network Inference

Glycomics measurements, like all other high-throughput technologies, are subject to technical variation due to fluctuations in the experimental conditions. The removal of this non-biological signal from the data is referred to as normalization. Contrary to other omics data types, a systematic evaluation of normalization options for glycomics data has not been published so far. In this paper, we assess the quality of different normalization strategies for glycomics data with an innovative approach. It has been shown previously that Gaussian Graphical Models (GGMs) inferred from glycomics data are able to identify enzymatic steps in the glycan synthesis pathways in a data-driven fashion. Based on this finding, here, we quantify the quality of a given normalization method according to how well a GGM inferred from the respective normalized data reconstructs known synthesis reactions in the glycosylation pathway. The method therefore exploits a biological measure of goodness. We analyzed 23 different normalization combinations applied to six large-scale glycomics cohorts across three experimental platforms: Liquid Chromatography – ElectroSpray Ionization-Mass Spectrometry (LC-ESI-MS), Ultra High Performance Liquid Chromatography with Fluorescence Detection (UHPLC-FLD), and Matrix Assisted Laser Desorption Ionization – Furier Transform Ion Cyclotron Resonance – Mass Spectrometry (MALDI-FTICR-MS). Based on our results, we recommend normalizing glycan data using the ‘Probabilistic Quotient’ method followed by log-transformation, irrespective of the measurement platform. This recommendation is further supported by an additional analysis, where we ranked normalization methods based on their statistical associations with age, a factor known to associate with glycomics measurements

Association of systemic lupus erythematosus associates with decreased immunosuppressive potential of the IgG glycome

Objective: Glycans attached to the Fc portion of IgG are important modulators of IgG effector functions. Interindividual differences in IgG glycome composition are large and they associate strongly with different inflammatory and autoimmune diseases. IKZF1, HLA–DQ2A/B, and BACH2 genetic loci that affect IgG glycome composition show pleiotropy with systemic lupus erythematosus (SLE), indicating a potentially causative role of aberrant IgG glycosylation in SLE. We undertook this large multicenter case–control study to determine whether SLE is associated with altered IgG glycosylation. Methods: Using ultra-performance liquid chromatography analysis of released glycans, we analyzed the composition of the IgG glycome in 261 SLE patients and 247 matched controls of Latin American Mestizo origin (the discovery cohort) and in 2 independent replication cohorts of different ethnicity (108 SLE patients and 193 controls from Trinidad, and 106 SLE patients and 105 controls from China). Results: Multiple statistically significant differences in IgG glycome composition were observed between patients and controls. The most significant changes included decreased galactosylation and sialylation of IgG (which regulate proinflammatory and antiinflammatory actions of IgG) as well as decreased core fucose and increased bisecting N-acetylglucosamine (which affect antibody-dependent cell-mediated cytotoxicity). Conclusion: The IgG glycome in SLE patients is significantly altered in a way that decreases immunosuppressive action of circulating immunoglobulins. The magnitude of observed changes is associated with the intensity of the disease, indicating that aberrant IgG glycome composition or changes in IgG glycosylation may be an important molecular mechanism in SLE

IgG glycosylation and DNA methylation are interconnected with smoking

Background: Glycosylation is one of the most common post-translation modifications with large influences on protein structure and function. The effector function of immunoglobulin G (IgG) alters between pro- and anti-inflammatory, based on its glycosylation. IgG glycan synthesis is highly complex and dynamic. Methods: With the use of two different analytical methods for assessing IgG glycosylation, we aim to elucidate the link between DNA methylation and glycosylation of IgG by means of epigenome-wide association studies. In total, 3000 individuals from 4 cohorts were analyzed. Results: The overlap of the results from the two glycan measurement panels yielded DNA methylation of 7 CpG-sites on 5 genomic locations to be associated with IgG glycosylation: cg25189904 (chr.1, GNG12); cg05951221, cg21566642 and cg01940273 (chr.2, ALPPL2); cg05575921 (chr.5, AHRR); cg06126421 (6p21.33); and cg03636183 (chr.19, F2RL3). Mediation analyses with respect to smoking revealed that the effect of smoking on IgG glycosylation may be at least partially mediated via DNA methylation levels at these 7 CpG-sites. Conclusion: Our results suggest the presence of an indirect link between DNA methylation and IgG glycosylation that may in part capture environmental exposures. General significance: An epigenome-wide analysis conducted in four population-based cohorts revealed an association between DNA methylation and IgG glycosylation patterns. Presumably, DNA methylation mediates the effect of smoking on IgG glycosylation

Glycosylation of immunoglobulin G is regulated by a large network of genes pleiotropic with inflammatory diseases

Effector functions of immunoglobulin G (IgG) are regulated by the composition of a glycan moiety, thus affecting activity of the immune system. Aberrant glycosylation of IgG has been observed in many diseases, but little is understood about the underlying mechanisms. We performed a genome-wide association study of IgG N-glycosylation (N = 8090) and, using a data-driven network approach, suggested how associated loci form a functional network. We confirmed in vitro that knockdown of IKZF1 decreases the expression of fucosyltransferase FUT8, resulting in increased levels of fucosylated glycans, and suggest that RUNX1 and RUNX3, together with SMARCB1, regulate expression of glycosyltransferase MGAT3. We also show that variants affecting the expression of genes involved in the regulation of glycoenzymes colocalize with variants affecting risk for inflammatory diseases. This study provides new evidence that variation in key transcription factors coupled with regulatory variation in glycogenes modifies IgG glycosylation and has influence on inflammatory diseases

Association of Systemic Lupus Erythematosus With Decreased Immunosuppressive Potential of the IgG Glycome

OBJECTIVE: Glycans attached to the Fc portion of IgG are important modulators of IgG effector functions. Interindividual differences in IgG glycome composition are large and they associate strongly with different inflammatory and autoimmune diseases. IKZF1, HLA–DQ2A/B, and BACH2 genetic loci that affect IgG glycome composition show pleiotropy with systemic lupus erythematosus (SLE), indicating a potentially causative role of aberrant IgG glycosylation in SLE. We undertook this large multicenter case–control study to determine whether SLE is associated with altered IgG glycosylation. METHODS: Using ultra‐performance liquid chromatography analysis of released glycans, we analyzed the composition of the IgG glycome in 261 SLE patients and 247 matched controls of Latin American Mestizo origin (the discovery cohort) and in 2 independent replication cohorts of different ethnicity (108 SLE patients and 193 controls from Trinidad, and 106 SLE patients and 105 controls from China). RESULTS: Multiple statistically significant differences in IgG glycome composition were observed between patients and controls. The most significant changes included decreased galactosylation and sialylation of IgG (which regulate proinflammatory and antiinflammatory actions of IgG) as well as decreased core fucose and increased bisecting N‐acetylglucosamine (which affect antibody‐dependent cell‐mediated cytotoxicity). CONCLUSION: The IgG glycome in SLE patients is significantly altered in a way that decreases immunosuppressive action of circulating immunoglobulins. The magnitude of observed changes is associated with the intensity of the disease, indicating that aberrant IgG glycome composition or changes in IgG glycosylation may be an important molecular mechanism in SLE

Comparison of 2-Aminobenzamide, Procainamide and RapiFluor-MS as Derivatizing Agents for High-Throughput HILIC-UPLC-FLR-MS N-glycan Analysis

Rising awareness of the universal importance of protein N-glycosylation governs the development of further advances in N-glycan analysis. Nowadays it is well known that correct glycosylation is essential for proper protein function, which emanates from its important role in many physiological processes. Furthermore, glycosylation is involved in pathophysiology of multiple common complex diseases. In the vast majority of cases, N-glycosylation profiles are analyzed from enzymatically released glycans, which can be further derivatized in order to enhance the sensitivity of the analysis. Techniques wherein derivatized N-glycans are profiled using hydrophilic interaction chromatography (HILIC) with fluorescence (FLR) and mass spectrometry (MS) detection are now routinely performed in a high-throughput manner. Therefore, we aimed to examine the performance of frequently used labeling compounds −2-aminiobenzamide (2-AB) and procainamide (ProA), and the recently introduced RapiFluor-MS (RF-MS) fluorescent tag. In all experiments N-glycans were released by PNGase F, fluorescently derivatized, purified by HILIC solid phase extraction and profiled using HILIC-UPLC-FLR-MS. We assessed sensitivity, linear range, limit of quantification (LOQ), repeatability and labeling efficiency for all three labels. For this purpose, we employed in-house prepared IgG and a commercially available IgG as a model glycoprotein. All samples were analyzed in triplicates using different amounts of starting material. We also tested the performance of all three labels in a high-throughput setting on 68 different IgG samples, all in duplicates and 22 identical IgG standards. In general, ProA labeled glycans had the highest FLR sensitivity (15-fold and 4-fold higher signal intensities compared to 2-AB and RF-MS respectively) and RF-MS had the highest MS sensitivity (68-fold and 2-fold higher signal intensities compared to 2-AB and ProA, respectively). ProA and RF-MS showed comparable limits of quantification with both FLR and MS detection, whilst 2-AB exhibited the lowest sensitivity. All labeling procedures showed good and comparable repeatability. Furthermore, the results indicated that labeling efficiency was very similar for all three labels. In conclusion, all three labels are a good choice for N-glycan derivatization in high-throughput HILIC-UPLC-FLR-MS N-glycan analysis, although ProA and RF-MS are a better option when higher sensitivity is needed

The Association between Low Back Pain and Composition of IgG Glycome

Low back pain (LBP) is a common debilitating condition which aetiology and pathogenesis are poorly understood. We carried out a first so far analysis of associations between LBP and plasma IgG N-glycome in a sample of 4511 twins from TwinsUK database assessed for LBP, lumbar disc degeneration (LDD) as its possible cause, and IgG-glycan levels. Using weighted correlation network analysis, we established a correlation between LBP and glycan modules featured by glycans that either promote or block antibody-dependent cell-mediated cytotoxicity (ADCC). The levels of four glycan traits representing two of those modules were statistically significantly different in monozygotic twins discordant for LBP. Also, the trend to higher prevalence of systemic inflammatory disorders was shown for twins with low level of fucosylated glycans and high level of non-fucosylated glycans. Core fucosylation of IgG is a "safety switch" reducing ADCC, thus our results suggest the involvement of ADCC and associated inflammation in pathogenesis of LBP. No correlation between LDD scores and glycans was found assuming that the inflammation may not be a part of LDD. These data provide a new insight into understanding the complex pathophysiology of LBP and suggest glycan levels as a possible biomarker for inflammation-related subtypes of LBP