Glyco(proteo)mic workflows for cancer biomarker discovery

In prostate (PCa) and colorectal (CRC) cancer, there is a need to improve patient stratification techniques that aid diagnostic and prognostic decision-making. To fulfill this unmet clinical need, the measurement of disease-related biological parameters known as “biomarkers” from biofluids is an approach with the potential to develop noninvasive tests as well as achieve greater clinical accuracy and personalized medicine. Thus, this thesis focused on developing a better understanding of biomarkers relevant to PCa and CRC as well as advancing analytical methodology and achieving methodological advancements for the purpose of biomarker discovery. In chapters two and three, a large diversity of prostate-specific antigen (PSA) cleaved and non-cleaved proteoforms (PCa) with different N-glycosylation patterns were determined in urine and seminal fluid using capillary electrophoresis-electrospray ionization-mass spectrometry (CE-ESI-MS), some of which are relevant for PCa patient stratification. In addition, the data processing workflow was improved in chapter three in order to enable larger studies of intact proteoforms to be performed. Furthermore, chapter four developed a reversed phase-liquid chromatography (RPLC)-MS method whereby it was possible to determine sialic acid linkages and positional isomers in released N-glycans following fluorescent labeling and sialic acid derivatization. This method was applied in chapter five to study serum N-glycosylation profiles in CRC and it was demonstrated that specific N-glycan isomers are implicated in the disease and differences between histological types were eradicated following surgery.This work was supported by the European Union’s Horizon 2020 Research and Innovation Program GlySign, grant number 722095.LUMC / Geneeskund

The role of the Flb protein family in the life cycle of Aspergillus niger

Genes flbA-E are involved in sporulation and vegetative growth in Aspergillus nidulans. Inactivation of either of these genes results in a fluffy phenotype with delayed or even abolished sporulation. Previously, a non-sporulating phenotype was obtained by inactivating flbA in Aspergillus niger, which was accompanied by lysis, thinner cell walls, and an increased secretome complexity. Here, we further studied the role of the flb genes of A. niger. Strains ΔflbA, ΔflbB and ΔflbE showed increased biomass formation, while inactivation of flbA-D reduced, or even abolished, formation of conidia. Strain ΔflbA was more sensitive to H2O2, DTT, and the cell wall integrity stress compounds SDS and Congo Red (CR). Also, ΔflbC was more sensitive to SDS, while ΔflbB, ΔflbD, and ΔflbE were more sensitive to CR. On the other hand, inactivation of flbE increased resistance to H2O2. Enzyme secretion was impacted when the Δflb strains were grown on xylose. Strain ΔflbE showed reduced xylanase, cellulase and amylase secretion. On the other hand, amylase secretion at the periphery of the ΔflbA colony was reduced but not in its center, while secretion of this enzyme was increased in the center of the ΔflbB colony but not at its periphery. Inactivation of flbC and flbD also impacted zonal cellulase and amylase activity. Together, the Flb protein family of A. niger function in biomass formation, sporulation, stress response, and protein secretion

Software-assisted data processing workflow for intact glycoprotein mass spectrometry

Intact protein analysis by mass spectrometry is important for several applications such as assessing post-translational modifications and biotransformation. In particular, intact protein analysis allows the detection of proteoforms that are commonly missed by other approaches such as proteolytic digestion followed by bottom-up analysis. Two quantification methods are mainly used for intact protein data quantification, namely the extracted ion and deconvolution approaches. However, a consensus with regard to a single best practice for intact protein data processing is lacking. Furthermore, many data processing tools are not fit-for-purpose and, as a result, the analysis of intact proteins is laborious and lacks the throughput required to be implemented for the analysis of clinical cohorts. Therefore, in this study, we investigated the application of a software-assisted data analysis and processing workflow in order to streamline intact protein integration, annotation, and quantification via deconvolution. In addition, the assessment of orthogonal data sets generated via middle-up and bottom-up analysis enabled the cross-validation of cleavage proteoform assignments present in seminal prostate-specific antigen (PSA). Furthermore, deconvolution quantification of PSA from patients’ urine revealed results that were comparable with manually performed quantification based on extracted ion electropherograms. Overall, the presented workflow allows fast and efficient processing of intact protein data. The raw data is available on MassIVE using the identifier MSV000086699. Proteomic

Disks, Tori, and Cocoons: Emission and Absorption Diagnostics of AGN Environments

One of the most important problems in the study of active galaxies is understanding the detailed geometry, physics, and evolution of the central engines and their environments. The leading models involve an accretion disk and torus structure around a central dense object, thought to be a supermassive black hole. Gas found in the environment of AGN is associated with different structures: molecular accretion disks, larger scale atomic tori, ionized and neutral "cocoons" in which the nuclear regions can be embedded. All of them can be studied at radio wavelengths by various means. Here, we summarize the work that has been done to date in the radio band to characterize these structures. Much has been learned about the central few parsecs of AGN in the last few decades with contemporary instruments but the picture remains incomplete. In order to be able to define a more accurate model of this region, significant advances in sensitivity, spectral and angular resolution, and bandpass stability are required. The necessary advances will only be provided by the Square Kilometer Array and we discuss the possibilities that these dramatic improvements will open for the study of the gas in the central region of AGN.Comment: To appear in "Science with the Square Kilometer Array," eds. C. Carilli and S. Rawlings, New Astronomy Reviews (Elsevier: Amsterdam); 17 pages, 7 figures (four of them in separate gif/tif files) The full paper with high resolution images can be downloaded from http://www.astron.nl/~morganti/Papers/AGNenvironment.ps.g

Profiling the proteoforms of urinary prostate-specific antigen by capillary electrophoresis-mass spectrometry

Early detection of prostate cancer may lead to the overdiagnosis and overtreatment of patients as well as missing significant cancers. The current diagnostic approach uses elevated serum concentrations of prostate-specific antigen (PSA) as an indicator of risk. However, this test has been widely criticized as it shows poor specificity and sensitivity. In order to improve early detection and diagnosis, several studies have investigated whether different PSA proteoforms are correlated to prostate cancer. Until now, studies and methodologies for the comprehensive characterization of PSA proteoforms from biofluids are scarce. For this purpose, we developed an intact protein assay to analyze PSA by capillary electrophoresis-electrospray ionization-mass spectrometry after affinity purification from patients? urine. Here, we determined six proteolytic cleavage variants. In regard to glycosylation, tri-, di-, mono- and non-sialylated complex-type N-glycans were found on non-cleaved PSA, as well as the non-glycosylated variant. The performance of the intact protein assay was assessed using a pooled sample, obtaining an inter-day variability of 15%. Furthermore, urinary patient samples were analyzed by intact protein analysis and a bottom-up approach (glycopeptide analysis). This combined approach revealed complimentary information on both levels, demonstrating the benefit of using two orthogonal techniques to provide a thorough profile of urinary PSA.Significance: The detection of clinically relevant prostate cancer requires a more specific and sensitive biomarker and, in this case, several PSA proteoforms may be able to aid or improve the current PSA test. However, a comprehensive analysis of the intact PSA proteoform profile is still lacking. This study investigated the PSA proteoforms present in urine and, in particular, determined the relative contribution of cleaved PSA and noncleaved PSA forms to the total glycosylation profile. Importantly, intact protein analysis did not require further sample treatment before being measured by CE-ESI-MS. Furthermore, its glycosylation was also assessed in a bottom-up approach to provide complementary information. Overall, these results represent an important basis for future characterization and biomarker studies.Proteomic

The pleiotropic phenotype of FlbA of Aspergillus niger is explained in part by the activity of seven of its downstream-regulated transcription factors

Inactivation of flbA in Aspergillus niger results in thinner cell walls, increased cell lysis, abolished sporulation, and an increased secretome complexity. A total of 36 transcription factor (TF) genes are differentially expressed in ΔflbA. Here, seven of these genes (abaA, aslA, aslB, azf1, htfA, nosA, and srbA) were inactivated. Inactivation of each of these genes affected sporulation and, with the exception of abaA, cell wall integrity and protein secretion. The impact on secretion was strongest in the case of ΔaslA and ΔaslB that showed increased pepsin, cellulase, and amylase activity. Biomass was reduced of agar cultures of ΔabaA, ΔaslA, ΔnosA, and ΔsrbA, while biomass was higher in liquid shaken cultures of ΔaslA and ΔaslB. The ΔaslA and ΔhtfA strains showed increased resistance to H2O2, while ΔaslB was more sensitive to this reactive oxygen species. Together, inactivation of the seven TF genes impacted biomass formation, sporulation, protein secretion, and stress resistance, and thereby these genes explain at least part of the pleiotropic phenotype of ΔflbA of A. niger

Evaluating the capability of regional-scale air quality models to cature the vertical distribution of pollutants

This study is conducted in the framework of the Air Quality Modelling Evaluation International Initiative (AQMEII) and aims at the operational evaluation of an ensemble of 12 regional-scale chemical transport models used to predict air quality over the North American (NA) and European (EU) continents for 2006. The modelled concentrations of ozone and CO, along with the meteorological fields of wind speed (WS) and direction (WD), temperature (T), and relative humidity (RH), are compared against high-quality in-flight measurements collected by instrumented commercial aircraft as part of the Measurements of OZone, water vapour, carbon monoxide and nitrogen oxides by Airbus In-service airCraft (MOZAIC) programme. The evaluation is carried out for five model domains positioned around four major airports in NA (Portland, Philadelphia, Atlanta, and Dallas) and one in Europe (Frankfurt), from the surface to 8.5 km. We compare mean vertical profiles of modelled and measured variables for all airports to compute error and variability statistics, perform analysis of altitudinal error correlation, and examine the seasonal error distribution for ozone, including an estimation of the bias introduced by the lateral boundary conditions (BCs). The results indicate that model performance is highly dependent on the variable, location, season, and height (e.g. surface, planetary boundary layer (PBL) or free troposphere) being analysed. While model performance for T is satisfactory at all sites (correlation coefficient in excess of 0.90 and fractional bias ≤ 0.01 K), WS is not replicated as well within the PBL (exhibiting a positive bias in the first 100 m and also underestimating observed variability), while above 1000 m, the model performance improves (correlation coefficient often above 0.9). The WD at NA airports is found to be biased in the PBL, primarily due to an overestimation of westerly winds. RH is modelled well within the PBL, but in the free troposphere large discrepancies among models are observed, especially in EU. CO mixing ratios show the largest range of modelled-to-observed standard deviations of all the examined species at all heights and for all airports. Correlation coefficients for CO are typically below 0.6 for all sites and heights, and large errors are present at all heights, particularly in the first 250 m. Model performance for ozone in the PBL is generally good, with both bias and error within 20%. Profiles of ozone mixing ratios depend strongly on surface processes, revealed by the sharp gradient in the first 2 km (10 to 20 ppb km−1). Modelled ozone in winter is biased low at all locations in the NA, primarily due to an underestimation of ozone from the BCs. Most of the model error in the PBL is due to surface processes (emissions, transport, photochemistry), while errors originating aloft appear to have relatively limited impact on model performance at the surface. Suggestions for future work include interpretation of the model-to-model variability and common sources of model bias, and linking CO and ozone bias to the bias in the meteorological fields. Based on the results from this study, we suggest possible in-depth, process-oriented and diagnostic investigations to be carried out next

Uterotonics for prevention of postpartum haemorrhage: EN-BIRTH multi-country validation study

Background Postpartum haemorrhage (PPH) is a leading cause of preventable maternal mortality worldwide. The World Health Organization (WHO) recommends uterotonic administration for every woman after birth to prevent PPH. There are no standardised data collected in large-scale measurement platforms. The Every Newborn Birth Indicators Research Tracking in Hospitals (EN-BIRTH) is an observational study to assess the validity of measurement of maternal and newborn indicators, and this paper reports findings regarding measurement of coverage and quality for uterotonics. Methods The EN-BIRTH study took place in five hospitals in Bangladesh, Nepal and Tanzania, from July 2017 to July 2018. Clinical observers collected tablet-based, time-stamped data. We compared observation data for uterotonics to routine hospital register-records and women’s report at exit-interview survey. We analysed the coverage and quality gap for timing and dose of administration. The register design was evaluated against gap analyses and qualitative interview data assessing the barriers and enablers to data recording and use. Results Observed uterotonic coverage was high in all five hospitals (> 99%, 95% CI 98.7–99.8%). Survey-report underestimated coverage (79.5 to 91.7%). “Don’t know” replies varied (2.1 to 14.4%) and were higher after caesarean (3.7 to 59.3%). Overall, there was low accuracy in survey data for details of uterotonic administration (type and timing). Register-recorded coverage varied in four hospitals capturing uterotonics in a specific column (21.6, 64.5, 97.6, 99.4%). The average coverage measurement gap was 18.1% for register-recorded and 6.0% for survey-reported coverage. Uterotonics were given to 15.9% of women within the “right time” (1 min) and 69.8% within 3 min. Women’s report of knowing the purpose of uterotonics after birth ranged from 0.4 to 64.9% between hospitals. Enabling register design and adequate staffing were reported to improve routine recording. Conclusions Routine registers have potential to track uterotonic coverage – register data were highly accurate in two EN-BIRTH hospitals, compared to consistently underestimated coverage by survey-report. Although uterotonic coverage was high, there were gaps in observed quality for timing and dose. Standardisation of register design and implementation could improve data quality and data flow from registers into health management information reporting systems, and requires further assessment

Search for the lepton-flavor-violating decays Bs0→e±μ∓ and B0→e±μ∓

A search for the lepton-flavor-violating decays Bs0→e±μ∓ and B0→e±μ∓ is performed with a data sample, corresponding to an integrated luminosity of 1.0  fb-1 of pp collisions at √s=7  TeV, collected by the LHCb experiment. The observed number of Bs0→e±μ∓ and B0→e±μ∓ candidates is consistent with background expectations. Upper limits on the branching fractions of both decays are determined to be B(Bs0→e±μ∓)101  TeV/c2 and MLQ(B0→e±μ∓)>126  TeV/c2 at 95% C.L., and are a factor of 2 higher than the previous bounds