Computational classification of core and outer fucosylation of N-glycoproteins in human plasma using collision-induced dissociation in mass spectrometry

RATIONALE

Glycoprotein fucosylation, one of the major posttranslational modifications, is known to be highly involved in proteins related to various cancers. Fucosylation occurs in the core and/or outer sites of N-glycopeptides. Elucidation of the fucosylation type of N-glycoproteins is therefore important. However, it has remained a challenge to classify the fucosylation types of N-glycopeptides using collision-induced dissociation (CID) tandem mass (MS/MS) spectra.

METHODS

The relative intensities of the Y₁ F, Y₂ F, Y₃ F, and Y₄ F product ions in the CID-MS/MS spectra of the IgG N-glycopeptides were measured for core fucosylation. The Core Fucose Index (CFI) was then calculated by multiplication of the relative intensities with a weight factor from logistic regression to differentiate between the core and none fucosylation. From the relative intensities of the B₂ F and B₃ SF ions of the MS/MS spectra of the AGP N-glycopeptides for outer fucosylation, the Outer Fucose Index (OFI) was calculated to differentiate between the outer and none fucosylation.

RESULTS

In order to classify core and/or outer fucosylation of N-glycoproteins, we defined the fucosylation score (F-score) by a sigmoidal equation using a combination of the CFI and the OFI. For application, we classified the fucosylation types of N-glycoproteins in human plasma with 99.7% accuracy from the F-score. Human plasma samples showed 54.4%, 33.3%, 10.3%, and 1.6% for none, core, outer, and dual fucosylated N-glycopeptides, respectively. Core fucosylation was abundant at mono- and bi-antennary N-glycopeptides. Outer fucosylation was abundant at tri- and tetra-antennary N-glycopeptides. In total, 113 N-glycopeptides of 29 glycoproteins from 3365 glycopeptide spectral matches (GPSMs) were classified for different types of fucosylation.

CONCLUSIONS

We established an F-score to classify three different fucosylation types: core, outer, and dual types of N-glycopeptides. The fucosylation types of 20 new N-glycopeptides from 11 glycoproteins in human plasma were classified using the F-score. Therefore, the F-score can be useful for the automatic classification of different types of fucosylation in N-glycoproteins of biological fluids including plasma, serum, and urine.

Machine Learning Classifies Core and Outer Fucosylation of N-Glycoproteins Using Mass Spectrometry

Protein glycosylation is known to be involved in biological progresses such as cell recognition, growth, differentiation, and apoptosis. Fucosylation of glycoproteins plays an important role for structural stability and function of N-linked glycoproteins. Although many of biological and clinical studies of protein fucosylation by fucosyltransferases has been reported, structural classification of fucosylated N-glycoproteins such as core or outer isoforms remains a challenge. Here, we report for the first time the classification of N-glycopeptides as core- and outer-fucosylated types using tandem mass spectrometry (MS/MS) and machine learning algorithms such as the deep neural network (DNN) and support vector machine (SVM). Training and test sets of more than 800 MS/MS spectra of N-glycopeptides from the immunoglobulin gamma and alpha 1-acid-glycoprotein standards were selected for classification of the fucosylation types using supervised learning models. The best-performing model had an accuracy of more than 99% against manual characterization and area under the curve values greater than 0.99, which were calculated by probability scores from target and decoy datasets. Finally, this model was applied to classify fucosylated N-glycoproteins from human plasma. A total of 82N-glycopeptides, with 54 core-, 24 outer-, and 4 dual-fucosylation types derived from 54 glycoproteins, were commonly classified as the same type in both the DNN and SVM. Specifically, outer fucosylation was dominant in tri- and tetra-antennary N-glycopeptides, while core fucosylation was dominant in the mono-, bi-antennary and hybrid types of N-glycoproteins in human plasma. Thus, the machine learning methods can be combined with MS/MS to distinguish between different isoforms of fucosylated N-glycopeptides.

P279 Standard dose of rivaroxaban in Asian patients with atrial fibrillation: 20ms vs.15mg? Off label dose reduction of rivaroxaban should be avoided

Background

Rivaroxaban emerged as potential alternatives to warfarin for the prevention of thromboembolisim in patients with atrial fibrillation (AF). Because of the concern for the risk of major bleeding with rivaroxaban in Asian patients, off label rivaroxaban dose reduction to15mg is common in Asian real-world practice. We aimed to set standard rivaroxaban dose in Asian patients with AF by comparison between on-label rivaroxaban 20mg and off-label reduced rivaroxaban dose 15mg.

Methods

A total of 2,208 consecutive non-valvular AF patients were enrolled between 2011 and 2017. After propensity score matching, both warfarin (n = 804) and rivaroxaban group (n = 804) had comparable baseline characteristics. Rivaroxaban group was further divided into on-label rivaroxaban 20mg group (n = 390) and off-label reduced rivaroxaban 15mg group (n = 333). Efficacy outcome was stroke/systemic embolism. Safety outcome was major bleeding. Primary net clinical benefit (NCB) was defined as the composite of stroke, systemic embolism, major bleeding and all-cause mortality. Secondary NCB was defined as the composite of stroke, systemic embolism and major bleeding. Patients were followed upto one-year or until the first occurrence of any study outcomes.

Results

Both Rivaroxaban groups had comparable efficacy compared to warfarin. However, both on-label rivaroxaban 20mg (hazard ratio [HR] 0.40, 95% confidence interval [CI] 0.18-0.90, p = 0.026) and off-label reduced rivaroxaban 15mg (HR 0.37, 95% CI 0.16-0.88, p = 0.025) significantly reduced major bleeding. There were no differences in efficacy and safety outcomes between on-label rivaroxaban 20mg and off-label reduced rivaroxaban 15mg group. On-label rivaroxaban 20mg significantly reduced primary (HR 0.44, 95% CI 0.25-0.79, p = 0.006) and secondary (HR 0.51, 95% CI 0.27-0.96, p = 0.038) NCBs compared to warfarin. However, off-label reduced rivaroxaban 15mg did not reduce both primary and secondary NCBs.

Conclusion

Off-label rivaroxaban dose reduction to 15mg had no benefit compared to on-label rivaroxaban 20mg. Compared to warfarin, on-label rivaroxaban 20mg significantly improved primary and secondary NCBs, whereas off-label reduced rivaroxaban 15mg did not. Therefore, rivaroxaban 20mg is favorable as standard dose in Asian patients.

P99 Rapid ventricular stimulation induces augmented conduction delay in Brugada syndrome patients

Background

The exact mechanism for Brugada Syndrome (BrS) is still not clear. There are two main physiologic hypotheses that have been suggested: the repolarization and the depolarization disorder models. Right ventricular (RV) activation delay was verified by echocardiography, conduction time in an explanted heart or in computer simulation. Verification of prolonged longitudinal activation time in human RV of only 5 patients of type-1 BrS and 5 controls was reported in 2008.

Methods

Bidirectional longitudinal activation times were assessed between RV outflow tract (RVot) and RV-apex (RVa) by stimulating and mapping RV endocardium in BrS patients. Conduction velocity was calculated considering ventricle size and distance between catheters.

Results

The studies were performed in controls (n = 18) and BrS patients (n = 6). There was no statistical difference in RP interval and QRS duration (PR 146 ± 21.7 vs 167 ± 45.2 ms, p = 0.325; QRS 102 ± 28.2 vs 122 ± 32.2 ms, p = 0.163). There was no difference of longitudinal activation time on stimulation at 500 ms (RVa to RVot: 63 ± 14.3 versus 80 ± 34.2 ms, p = 0.290; RVot to RVa: 50 ± 12.2 versus 76 ± 35.1 ms, p = 0.122). The BrS patients had longer longitudinal activation time on stimulation at 400 ms (RVa to RVot: 61 ± 15.2 versus 87 ± 28.7 ms, p = 0.009; RVot to RVa: 52 ± 11.1 versus 76 ± 35.3 ms, p = 0.029). The difference was not significant when isoproterenol was infused.

Conclusions

BrS patients display bidirectional longitudinal conduction delay when rapid stimulation. These findings support that BrS might be partly attributable to depolarization abnormality.

P1526Pre-dialysis left atrial function assessed by two-dimensional speckle tracking echocardiography as a predictor of upcoming heart failure in hemodialysis patients

Background

Left atrial global longitudinal strain (LA GLS) by 2-dimensional speckle tracking echocardiography is a useful tool to assess LA function and left ventricular (LV) diastolic function. The authors assessed prognostic value of LA GLS, and other diastolic functional parameters in patients undergoing hemodialysis.

Methods

A total of 78 (49 male) patients undergoing hemodialysis who checked echocardiography due to heart failure (HF) symptoms were included for this analysis. Echocardiography wasperformed at the same day of, and before hemodialysis session. Besides conventional echocardiographic measurements, GLS of the LA and the LV were checked and compared. Incidence of rehospitalization due to HF symptoms during mean follow up duration of 381.4±197.5 days was investigated and echocardiographic parameters were compared between patients who experienced rehospitalization and who did not.

Results

16 (20.1%) patients experienced rehospitalization due to HF. HF rehospitalization group had significantly low baseline LV ejection fraction (55.7±7.2 vs. 61.3±7.1%, p=0.006) and LV GLS (14.7±3.4 vs. 18.2±3.9%, p=0.002), while LV geometry (LV end-diastolic volume index and LV wall thickness) did not show significant differences. In HF rehospitalization group, baseline LA function and diastolic function were significantly impaired as reflected by LA GLS (18.8±2.6 vs. 23.8±3.6%, p<0.001), E/E' ratio (20.8±3.3 vs. 15.8±4.6%, p<0.001), and right ventricular systolic pressure (61.4±9.6 vs. 53.4±12.8%, p=0.022). LA end-systolic volume index was not significantly different between the 2 groups. Among various echocardiographic parameters, receiver operation characteristic curve analysis revealed that LA GLS had the strongest power (cutoff value 20.6%, sensitivity 0.813 and specificity 0.790, area under curve 0.849) in prediction of future rehospitalization due to HF.

Predictor of future HF: ROC analysis

Conclusions

The present study demonstrated that functional changes of the LA as measured by LA GLS before hemodialysis session can be used as an echocardiographic parameter to predict future rehospitalization due to HF. Further studies are required to evaluate prognostic value of LA function in predicting other cardiovascular events in hemodialysis patients.

P688Cardiac dysfunction as a predictor of hepatic sinusoidal obstruction syndrome after hematopoietic cell transplantation

Background

Hepatic sinusoidal obstruction syndrome (HSOS) is a well-known fatal complication of hematopoietic cell transplantation (HCT), but the impact of cardiac abnormalities on the occurrence of HSOS has been poorly evaluated. Therefore, the authors investigated whether the structural changes or dysfunction of the heart before HCT is associated with the future occurrence of HSOS.

Methods

A total of 92 patients who underwent HCT were divided into 2 groups; HSOS group (n=11, 6 males, 53.8±15.9 years) vs no HSOS group (n=81, 51 males, 48.6±14.7 years). According to the modified Seattle criteria, HSOS was defined as otherwise unexplained occurrence of 2 or more of the following events within 20 days of HCT; serum total bilirubin >2 mg/dL, hepatomegaly or right upper quadrant pain, sudden weight gain due to fluid accumulation (>2% of baseline body weight). Echocardiography examinations were performed 1 month before HCT, and echocardiographic findings were compared between the groups.

Results

HSOS was developed in 11 patients (12.0%). HSOS group had significantly larger left ventricular end-diastolic volume index (LVEDVI) (65.2±4.9 vs 53.2±6.9 ml/m2, p<0.001) and relatively worse systolic function than no HSOS group (LV ejection fraction: 56.4±3.4 vs 65.1±5.9%, p<0.001, LV global longitudinal strain: −17.9±1.4 vs −20.1±2.0%, p=0.001). LV diastolic functional parameters were also significantly worse in HSOS group than in no HSOS group (E/E' ratio: 11.3±1.8 vs 9.1±2.0, p=0.002, left atrial global longitudinal strain: 27.7±3.3 vs 34.9±5.9%, p<0.001). However, left atrial volume index was not different between the groups (30.8±2.8 vs 29.0±3.3 ml/m2, p=0.078). By receiver operation characteristic curve analysis, among significantly different variables, LVEDVI was the most powerful predictor for HSOS, and the optimal cutoff value was 59.25 mL/m2. (81.8% sensitivity and 77.8% specificity, AUC 0.909).

Predictor of HSOS: ROC analysis

Conclusions

The present study demonstrated that structural changes or dysfunction of the heart are more prevalent in patients with HSOS after HCT and larger LVEDVI, among them, can be a useful predictor of upcoming HSOS. Routine echocardiographic study before HCT would be useful to identify high risk group for HSOS, and the development of HSOS should be carefully monitored in HCT patients with cardiac structural changes or dysfunction on echocardiography.

Characterization of Site-Specific N-Glycopeptide Isoforms of α-1-Acid Glycoprotein from an Interlaboratory Study Using LC-MS/MS

Glycoprotein conformations are complex and heterogeneous. Currently, site-specific characterization of glycopeptides is a challenge. We sought to establish an efficient method of N-glycoprotein characterization using mass spectrometry (MS). Using alpha-1-acid glycoprotein (AGP) as a model N-glycoprotein, we identified its tryptic N-glycopeptides and examined the data reproducibility in seven laboratories running different LC-MS/MS platforms. We used three test samples and one blind sample to evaluate instrument performance with entire sample preparation workflow. 165 site-specific N-glycopeptides representative of all N-glycosylation sites were identified from AGP 1 and AGP 2 isoforms. The glycopeptide fragmentations by collision-induced dissociation or higher-energy collisional dissociation (HCD) varied based on the MS analyzer. Orbitrap Elite identified the greatest number of AGP N-glycopeptides, followed by Triple TOF and Q-Exactive Plus. Reproducible generation of oxonium ions, glycan-cleaved glycopeptide fragment ions, and peptide backbone fragment ions was essential for successful identification. Laboratory proficiency affected the number of identified N-glycopeptides. The relative quantities of the 10 major N-glycopeptide isoforms of AGP detected in four laboratories were compared to assess reproducibility. Quantitative analysis showed that the coefficient of variation was <25% for all test samples. Our analytical protocol yielded identification and quantification of site-specific N-glycopeptide isoforms of AGP from control and disease plasma sample.

Analysis of fucosylation in liver-secreted N-glycoproteins from human hepatocellular carcinoma plasma using liquid chromatography with tandem mass spectrometry

Fucosylation of N-glycoproteins has been implicated in various diseases, such as hepatocellular carcinoma (HCC). However, few studies have performed site-specific analysis of fucosylation in liver-secreted proteins. In this study, we characterized the fucosylation patterns of liver-secreted proteins in HCC plasma using a workflow to identify site-specific N-glycoproteins, where characteristic B- and/or Y-ion series with and without fucose in collision-induced dissociation were used in tandem mass spectrometry. In total, 71 fucosylated N-glycopeptides from 13 major liver-secreted proteins in human plasma were globally identified by LC-MS/MS. Additionally, 37 fucosylated N-glycopeptides were newly identified from nine liver-secreted proteins, including alpha-1-antichymotrypsin, alpha-1-antitrypsin, alpha-2-HS-glycoprotein, ceruloplasmin, alpha-1-acid glycoprotein 1/2, alpha-2-macroglobulin, serotransferrin, and beta-2-glycoprotein 1. Of the fucosylated N-glycopeptides, bi- and tri-antennary glycoforms were the most common ones identified in liver-secreted proteins from HCC plasma. Therefore, we suggest that this analytical method is effective for characterizing fucosylation in liver-secreted proteins. Graphical abstract A global map of fucosylated and non-fucosylated glycopeptides from 13 liver-secreted glycoproteins in hepatocellular carcinoma plasma.

Structure determination of new analogues of vardenafil and sildenafil in dietary supplements

New analogues of vardenafil and sildenafil illegally added to dietary supplements were detected by high-performance liquid chromatography (HPLC) analysis with a photodiode array detector (PDA). These compounds were isolated and their structures elucidated by mass spectrometry (MS), infrared (IR) spectroscopy, one- and two-dimensional nuclear magnetic resonance (NMR). One of the new analogues given the trivial name pseudovardenafil (compound 1) was structurally elucidated and shown to be 1-[[3-(1,4-dihydro-5-methyl-4-oxo-7-propylimidazo[5,1-f][1,2,4]triazin-2-yl)-4-ethoxyphenyl]sulfonyl]-piperidine. It was a vardenafil analogue isolated from a dietary supplement capsule. Compared with vardenafil, the piperidine ring was substituted for the ethylpiperazine group. The second new analogue, trivially named hydroxyhongdenafil (compound 2), was separated from bulk powder used as a raw material for a dietary supplement. The piperazine and phenyl groups were connected through an acetyl group instead of a sulfonyl group, and hydroxyethylpiperazine was substituted for the methylpiperazine of sildenafil. It was structurally elucidated as 5-[2-ethoxy-5-[[4-(2-hydroxyethyl)-1-piperazinyl]acetyl]phenyl]-1,4-dihydro-1-methyl-3-propyl-7H-pyrazolo[4,3-d]pyrimidin-7-one.

Comparison of radioactivity measurements with radionuclide calibrators in the Republic of Korea

Recognizing the importance of comparisons of radionuclide calibrators in nuclear medicine and the need to provide access to activity standards that are traceable to the international measurement system, the Korea Food & Drug Administration (KFDA) as a national secondary standard dosimetry laboratory (SSDL), started a comparison program in 2002. The first two comparisons were conducted with (131)I (71 participants) and (99m)Tc (72 participants). The results indicated that only 61% of reported activities for (131)I and 65% for (99m)Tc were within +/-5% of the correct value. These numbers increased to 84% for (131)I and 83% for (99m)Tc when a +/-10% limit was applied. Follow-up action on those calibrators with results outside the +/-10% limits only produced a small improvement. There was also a marked difference in performance between the various calibrator types used. The results have shown that such comparisons are necessary to improve the quality of the measurements and to identify those radionuclide calibrators that are not functioning correctly.

The cerebrovascular response to traditional acupuncture after stroke

Acupuncture is useful in treating the nausea and vomiting related to chemotherapy, adult postoperative surgery pain and postoperative dental pain. We obtained single-photon emission computed tomography (SPECT) brain perfusion images of six patients with middle cerebral artery occlusion obtained before and after acupuncture and compared the changes in regional cerebral blood flow (rCBF) to those in normal control. Images were obtained before and after acupuncture at six traditional acupoints (LI 4, 10, 11, 15 and 16 and TE5) in the affected arm. The baseline image was subtracted from the postacupuncture image, to produce a subtraction image displaying only voxels with values >2 SD from the mean and those voxels were coregistered to the baseline SPECT or T2-weighted MRI. Similar images were obtained before and after acupuncture of eight normal volunteers. Statistical parametric mapping with a threshold of P =0.001 and a corrected P of 0.05 was performed for group comparison between postacupuncture and baseline SPECT. Focally increased CBF was seen in all patients especially in the hypoperfused zone surrounding the ischaemic lesion, the ipsilateral or contralateral sensorimotor area, or both. Normal subjects showed increased rCBF mainly in the parahippocampal gyrus, premotor area, frontal and temporal areas bilaterally and ipsilateral globus pallidus. Acupuncture stimulation after stroke patients appears to activate perilesional or use-dependent reorganised sites and might be a way of looking at brain reorganisation.

Immunological characterization of 130 kDa phospholipase C-beta 4 isozyme in rat cerebellar Purkinje cells

We have developed a monoclonal antibody, beta4-22-9 that recognizes an epitope on pleckstrin homology (PH) domain (1-136 amino acids) located at the amino terminus of rat 130 kDa phospholipase C-beta4 (PLC-beta4). Tissue distribution of 130 kDa PLC-beta4 was determined with this monoclonal antibody. One hundred and thirty kiloDalton PLC-beta4 was exclusively expressed in the nervous tissues including cerebellum and cerebrum, especially at very high levels in cerebellum. The expression of 130 kDa PLC-beta4 in cerebellum was gradually increased from 5 days after birth to adulthood. In the adult cerebellum, especially high level of 130 kDa PLC-beta4 was localized on the periphery of Purkinje cells in the patch-like pattern. These data implies that 130 kDa PLC-beta4 may a role in cerebellar Purkinje cells.

Intrinsic mutagenicity and electrophilicity of 1-sulfooxy-3-methylcholanthrene: implications for metabolic activation of the carcinogen 3-methylcholanthrene

Hydroxylation of a meso-anthracenic carbon atom with subsequent formation of a reactive ester bearing a good leaving group (e.g., sulfate) has been proposed as a possible biochemical mechanism responsible for DNA binding, mutagenicity and tumorigenicity of 3-methylcholanthrene, one of the most potent carcinogenic polycyclic aromatic hydrocarbons in experimental animals. In support of this supposition, the chemically synthesized sulfuric acid ester, 1-sulfooxy-3-methylcholanthrene (1-SMC) was directly mutagenic in bacteria and covalently bound to DNA without metabolic activation. The intrinsic mutagenicity of this reactive ester was significantly potentiated by addition of extra acetate or chloride anions to the media. Reduced glutathione and ascorbic acid protected against 1-SMC-induced mutagenesis. These findings suggest 1-SMC as a potential ultimate electrophilic and tumorigenic metabolite of 3-methylcholanthrene.

Bioactivation of 5-hydroxymethyl-2-furaldehyde to an electrophilic and mutagenic allylic sulfuric acid ester

5-Hydroxymethyl-2-furaldehyde (HMF), a ubiquitous food contaminant, has been proposed to be metabolically activated through sulfonation of its allylic hydroxyl functional group. In support of this idea, we have found the strong direct mutagenicity of chemically synthesized sulfuric acid ester, 5-sulfooxymethylfurfural (SMF), in Salmonella typhimurium TA104. The intrinsic mutagenicity of this reactive ester was significantly inhibited by glutathione and glutathione S-transferase activity in dialyzed rat liver cytosol. The metabolic formation of SMF was elucidated by enhanced mutagenicity of HMF in the presence of rat hepatic cytosol enriched with the sulfo-group donor, 3'-phosphoadenosine-5'-phosphosulfate (PAPS). The PAPS- and cytosol-dependent mutagenicity of HMF was markedly lessened by sulfotransferase inhibitors such as 2,6-dichloro-4-nitrophenol and dehydroepiandrosterone. These results suggest that HMF can be metabolically activated to an allylic sulfuric acid ester which may play a role as an ultimate electrophilic metabolite in toxification of the parent compound in vivo.