Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis

Glycoproteomics is a powerful yet analytically challenging research tool. Software packages aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but their relative performance remains untested. Conducted through the HUPO Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates solutions for system-wide glycopeptide analysis. The same mass spectrometrybased glycoproteomics datasets from human serum were shared with participants and the relative team performance for N- and O-glycopeptide data analysis was comprehensively established by orthogonal performance tests. Although the results were variable, several high-performance glycoproteomics informatics strategies were identified. Deep analysis of the data revealed key performance-associated search parameters and led to recommendations for improved 'high-coverage' and 'high-accuracy' glycoproteomics search solutions. This study concludes that diverse software packages for comprehensive glycopeptide data analysis exist, points to several high-performance search strategies and specifies key variables that will guide future software developments and assist informatics decision-making in glycoproteomics.

GlycopeptideGraphMS: Improved Glycopeptide Detection and Identification by Exploiting Graph Theoretical Patterns in Mass and Retention Time

The leading proteomic method for identifying N-glycosylated peptides is liquid chromatography coupled with tandem fragmentation mass spectrometry (LCMS/MS) followed by spectral matching of MS/MS fragment masses to a database of possible glycan and peptide combinations. Such database-dependent approaches come with challenges such as needing high-quality informative MS/MS spectra, ignoring unexpected glycan or peptide sequences, and making incorrect assignments because some glycan combinations are equivalent in mass to amino acids. To address these challenges, we present GlycopeptideGraphMS, a graph theoretical bioinformatic approach complementary to the database-dependent method. Using the AXL receptor tyrosine kinase (AXL) as a model glycoprotein with multiple N-glycosylation sites, we show that those LCMS features that could be grouped into graph networks on the basis of glycan mass and retention time differences were actually N-glycopeptides with the same peptide backbone but different N-glycan compositions. Conversely, unglycosylated peptides did not exhibit this grouping behavior. Furthermore, MS/MS sequencing of the glycan and peptide composition of just one N-glycopeptide in the graph was sufficient to identify the rest of the N-glycopeptides in the graph. By validating the identifications with exoglycosidase cocktails and MS/MS fragmentation, we determined the experimental false discovery rate of identifications to be 2.21%. GlycopeptideGraphMS detected more than 500 unique N-glycopeptides from AXL, triple the number found by a database search with Byonic software, and detected incorrect assignments due to a nonspecific protease cleavage. This method overcomes some limitations of the database approach and is a step closer to comprehensive automated glycoproteomics.

Effects of flexible-dose fesoterodine on overactive bladder symptoms and treatment satisfaction: an open-label study

AIMS

To evaluate the efficacy and tolerability of flexible-dose fesoterodine in subjects with overactive bladder (OAB) who were dissatisfied with previous tolterodine treatment.

METHODS

This was a 12-week, open-label, flexible-dose study of adults with OAB (> or = 8 micturitions and > or = 3 urgency episodes per 24 h) who had been treated with tolterodine (immediate- or extended-release) for OAB within 2 years of screening and reported dissatisfaction with tolterodine treatment. Subjects received fesoterodine 4 mg once daily for 4 weeks; thereafter, daily dosage was maintained at 4 mg or increased to 8 mg based on the subject's and physician's subjective assessment of efficacy and tolerability. Subjects completed 5-day diaries, the Patient Perception of Bladder Condition (PPBC) and the Overactive Bladder Questionnaire (OAB-q) at baseline and week 12 and rated treatment satisfaction at week 12 using the Treatment Satisfaction Question (TSQ). Safety and tolerability were assessed.

RESULTS

Among 516 subjects treated, approximately 50% opted for dose escalation to 8 mg at week 4. Significant improvements from baseline to week 12 were observed in micturitions, urgency urinary incontinence episodes, micturition-related urgency episodes and severe micturition-related urgency episodes per 24 h (all p < 0.0001). Approximately 80% of subjects who responded to the TSQ at week 12 reported satisfaction with treatment; 38% reported being very satisfied. Using the PPBC, 83% of subjects reported improvement at week 12 with 59% reporting improvement > or = 2 points. Significant improvements from baseline (p < 0.0001) exceeding the minimally important difference (10 points) were observed in OAB-q Symptom Bother and Health-Related Quality of Life (HRQL) scales and all four HRQL domains. Dry mouth (23%) and constipation (5%) were the most common adverse events; no safety issues were identified.

CONCLUSION

Flexible-dose fesoterodine significantly improved OAB symptoms, HRQL, and rates of treatment satisfaction and was well tolerated in subjects with OAB who were dissatisfied with prior tolterodine therapy.

Effects of nitric oxide synthases on detrusor overactivity after removal of bladder outlet obstruction in rats

OBJECTIVES

Nitric oxide is a neurotransmitter that is related to overactive bladder. This study was undertaken to evaluate the expression of nitric oxide synthases (NOS) in relation to bladder function after the removal of the bladder outlet obstruction in rats.

MATERIALS AND METHODS

50 rats were divided into a control group (n = 10) and an experimental group (n = 40). The bladders in the experimental group were partially obstructed for 3 weeks. 3 weeks after removal, cystometrograms (CMG) were performed. On the basis of CMG results, the experimental group was subdivided into 'normalized' and 'overactive' groups. Expression of neuronal, inducible, and endothelial NOS mRNA in bladders of each group was analyzed by reverse transcriptase polymerase chain reaction (RT-PCR).

RESULTS

On the CMG, the contraction interval of the overactive group was markedly decreased. RT-PCR results showed significantly decreased expression of nNOS and iNOS mRNA in the normalized group compared to the control group, and increased nNOS levels in the overactive group, compared to the normalized group (p < 0.05). A marked increase in eNOS mRNA expression was evident in the normalized and overactive groups compared to the control group (p < 0.05).

CONCLUSIONS

Our results clearly show increases in nNOS and eNOS expression according to bladder function, which may be related to a persistently overactive bladder or irritative symptoms, following the removal of a bladder outlet obstruction.

Functional evaluation of Tadenan on micturition and experimental prostate growth induced with exogenous dihydrotestosterone

OBJECTIVES

To evaluate the effect of Tadenan (TAD; Pygeum africanum extract) pretreatment on the micturition characteristics of conscious and anesthetized rats consequent to dihydrotestosterone (DHT) administration and to examine the influence of such treatment on the growth of the prostate.

METHODS

Studies using 40 adult Sprague-Dawley male rats were performed during a 7-week period. These animals were treated with DHT 1.25 mg/kg subcutaneously dissolved in peanut oil and/or TAD 100 mg/kg orally dissolved in sesame oil, except for the controls, which received vehicle only. Rats were divided into four groups: group 1 (control), vehicle only; group 2, DHT administered during weeks 3 and 4; group 3, TAD pretreatment, administered during weeks 1 and 2, followed by the combined administration of DHT and TAD during weeks 3 and 4 and TAD only during weeks 5 to 7; and group 4, continuous TAD treatment for 7 weeks. Micturition of conscious rats was evaluated in metabolic chambers, and in anesthetized rats, cystometrograms were done at the end of 7 weeks.

RESULTS

DHT or DHT plus TAD did not produce significant changes in the volume but did reduce the frequency of micturition. TAD given alone significantly increased the volume of micturition and the rate of urine production. Cystometrographic studies in anesthetized rats revealed that DHT produced micturition characteristics similar to obstruction. The DHT plus TAD and TAD pretreatment data showed no significant difference from controls, suggesting that in the presence of TAD, the effects of DHT were negated. The total prostate weight of DHT and DHT plus TAD pretreated rats increased, and in the TAD group, these values decreased to lower than controls; growth of the ventral lobes was suppressed in the presence of TAD.

CONCLUSIONS

These results demonstrate that TAD pretreatment significantly reduces the "obstructive" effects of DHT on micturition, counteracts the hormone-induced enlargement of the prostate, and reduces prostate weight in the ventral but not the dorsal lobe.

The alterations of cellular metabolism in the contralateral testis following spermatic cord torsion in rats

Cellular metabolic study was performed on the contralateral testis after torsion to delineate early testicular changes. In 9-week-old Sprague-Dawley rats the left testicle was rotated and fixed to the scrotum for 3, 8 and 24 hours in 3 groups (I, II and III). Each group was divided into 3 subgroups (a, b and c) by the length of detorsion of 0, 4 hours and 14 days. We measured adenosine triphosphate, total adenosine nucleotides and adenylate energy charge of the contralateral testis by high performance liquid chromatography. Compared to controls, no subgroups showed differences in the histological parameters. Also in subgroups Ia, Ib, Ic and IIa none of the metabolic parameters were significantly altered. However, subgroups IIb and IIc, and group III and its subgroups showed significantly decreased levels of all metabolic parameters. Therefore, it appears that unilateral testicular torsion (greater than 8 hours) and detorsion affect the contralateral testicular metabolism without gross histological changes in rats, and these changes seem to be reversible in terms of cellular recoverability because the maximally decreased level of adenylate energy charge among all subgroups is only 13% compared to controls. These findings suggest that some systemic mechanisms rather than an immunological or local inflammatory process is involved in this early period after torsion.

Flow-cytometric analysis of testes in infertile men: a comparison of the ploidy to routine histopathologic study

DNA flow-cytometric analysis was performed on the testicular needle biopsies of 25 infertile men with azoospermia or oligozoospermia to evaluate the ability of DNA histograms in order to detect and quantify alterations in spermatogenesis. Concomitant histopathologic study was performed on the tissues from needle biopsy. In contrast to difficulty in quantifying spermatogenesis in histopathologic examination, flow-cytometric analysis revealed characteristic ploidy patterns in the relative proportions of haploid (1 n), diploid (2 n) and tetraploid (4 n) cells corresponding to the histopathologic appearances of normal spermatogenesis, hypospermatogenesis, maturation arrest and aspermatogenesis. Findings evaluated with flow cytometry were well correlated with those from routine histopathologic study. In 21 of these patients (84%) there was concordance between histopathologic and flow-cytometric diagnoses. However, in 4 patients (16%) there was discordance between two diagnostic modalities. In conclusion, DNA flow cytometry of testicular biopsies was a reproducible, objective and quantitative approach in evaluating infertile men, and it is a promising method to investigate spermatogenesis in an outpatient clinic in lieu of formal testicular histopathologic study.