Probing the O-glycoproteome of gastric cancer cell lines for biomarker discovery

Circulating O-glycoproteins shed from cancer cells represent important serum biomarkers for diagnostic and prognostic purposes. We have recently shown that selective detection of cancer-associated aberrant glycoforms of circulating O-glycoprotein biomarkers can increase specificity of cancer biomarker assays. However, the current knowledge of secreted and circulating O-glycoproteins is limited. Here, we used the COSMC KO "Simple- Cell" (SC) strategy to characterize the O-glycoproteome of two gastric cancer SimpleCell lines (AGS, MKN45) as well as a gastric cell line (KATO III) which naturally expresses at least partially truncated O-glycans. Overall, we identified 499 O-glycoproteins and 1236 O-glycosites in gastric cancer SimpleCells, and a total 47 O-glycoproteins and 73 O-glycosites in the KATO III cell line. We next modified the glycoproteomic strategy to apply it to pools of sera from gastric cancer and healthy individuals to identify circulating O-glycoproteins with the STn glycoform. We identified 37 O-glycoproteins in the pool of cancer sera, and only nine of these were also found in sera from healthy individuals. Two identified candidate O-glycoprotein biomarkers (CD44 and GalNAc-T5) circulating with the STn glycoform were further validated as being expressed in gastric cancer tissue. A proximity ligation assay was used to show that CD44 was expressed with the STn glycoform in gastric cancer tissues. The study provides a discovery strategy for aberrantly glycosylated O-glycoproteins and a set of O-glycoprotein candidates with biomarker potential in gastric cancer.This work was supported by The Danish Research Councils, The Mizutani Foundation, The Danish National Research Foundation (DNRF107) and Fundacão para a Ciência e a Tecnologia (FCT) and COMPETE (Programa Operacional Temático Factores de Competitividade, comparticipado pelo fundo comunitário europeu FEDER) in the framework of the projects: PTDC/BBB-EBI/0786/2012; EXPL/CTM-BIO/0762/2013. Grants were received from FCT (SFRH/BD/73717/2010 to DC), (SFRH/BPD/75871/2011 to AM), (SFRH/BPD/96510/2013 to CG) and (SFRH/BPD/66288/2009 to JAF). IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology and Higher Education, and is partially supported by FCT

Structural and biochemical characterization of the exopolysaccharide deacetylase Agd3 required for Aspergillus fumigatus biofilm formation

The exopolysaccharide galactosaminogalactan (GAG) is an important virulence factor of the fungal pathogen Aspergillus fumigatus. Deletion of a gene encoding a putative deacetylase, Agd3, leads to defects in GAG deacetylation, biofilm formation, and virulence. Here, we show that Agd3 deacetylates GAG in a metal-dependent manner, and is the founding member of carbohydrate esterase family CE18. The active site is formed by four catalytic motifs that are essential for activity. The structure of Agd3 includes an elongated substrate-binding cleft formed by a carbohydrate binding module (CBM) that is the founding member of CBM family 87. Agd3 homologues are encoded in previously unidentified putative bacterial exopolysaccharide biosynthetic operons and in other fungal genomes. The exopolysaccharide galactosaminogalactan (GAG) is an important virulence factor of the fungal pathogen Aspergillus fumigatus. Here, the authors study an A. fumigatus enzyme that deacetylates GAG in a metal-dependent manner and constitutes a founding member of a new carbohydrate esterase family.Bio-organic Synthesi

Number of addictive substances used related to increased risk of unnatural death: A combined medico-legal and case-record study

<p>Abstract</p> <p>Background</p> <p>Substance use disorders have repeatedly been found to lead to premature death, i.e. drug-related death by disease, fatal intoxications, or trauma (accidents, suicide, undetermined suicide, and homicide). The present study examined the relationship between multi-drug substance use and natural and unnatural death.</p> <p>Methods</p> <p>All consecutive, autopsied patients who had been in contact with the Addiction Centre in Malmö University Hospital from 1993 to 1997 inclusive were investigated. Drug abuse was investigated blindly in the case records and related to the cause of death in 387 subjects.</p> <p>Results</p> <p>Every substance apart from alcohol used previously in life added to the risk of unnatural death in a linear way. There were independent increased risks of fatal heroin overdoses or undetermined suicide. Death by suicide and violent death were unrelated to additional abuse.</p> <p>Conclusion</p> <p>The number of drugs used was related to an increased risk of unnatural death by undetermined suicide (mainly fatal intoxications) and heroin overdose.</p

Somatic health among heroin addicts before and during opioid maintenance treatment: a retrospective cohort study

<p>Abstract</p> <p>Background</p> <p>The long-term impact of opioid maintenance treatment (OMT) on morbidity and health care utilization among heroin addicts has been insufficiently studied. The objective of this study was to investigate whether health care utilization due to somatic disease decreased during OMT, and if so, whether the reduction included all kinds of diseases and whether a reduction was related to abstinence from drug use.</p> <p>Methods</p> <p>Cohort study with retrospective registration of somatic disease incidents (health problems, acute or sub-acute, or acute problems related to chronic disease, resulting in a health care contact). Medical record data were collected from hospitals, Outpatients' Departments, emergency wards and from general practitioners (GPs) and prospective data on substance use during OMT were available from 2001 onwards. The observation period was five years before and up to five years during OMT. The cohort consisted of 35 out of 40 patients who received OMT between April 1999 and January 2005 in a Norwegian district town. Statistical significance concerning changes in number of incidents and inpatient and outpatient days during OMT compared with the pre OMT period was calculated according to Wilcoxon signed rank test. Significance concerning pre/during OMT changes in disease incidents by relation to the type of health service contacts, as well as the impact of ongoing substance use during OMT on the volume of contacts, was calculated according to Pearson chi-square and Fisher's exact tests.</p> <p>Results</p> <p>278 disease incidents were registered. There was a reduction in all incidents by 35% (p = 0.004), in substance-related incidents by 62% (p < 0.001) and in injection-related incidents by 70% (p < 0.001). There was an insignificant reduction in non-fatal overdose incidents by 44% (p = 0.127) and an insignificant increase in non-substance-related incidents by 13% (p = 0.741). Inpatient and outpatient days were reduced by 76% (p = 0.003) and 46% (p = 0.060), respectively. The disease incidents were less often drug-related during OMT (p < 0.001). Patients experienced a reduction in substance-related disease incidents regardless of ongoing substance use, however there was a trend towards greater reductions in those without ongoing abuse.</p> <p>Conclusion</p> <p>Although as few as 35 patients were included, this study demonstrates a significant reduction in health care utilization due to somatic disease incidents during OMT. The reduction was most pronounced for incidents related to substance use and injection. Inpatient and outpatient days were reduced. Most probably these findings reflect somatic health improvement among heroin addicts during OMT.</p

Fatal poisonings in Oslo: a one-year observational study

<p>Abstract</p> <p>Background</p> <p>Acute poisonings are common and are treated at different levels of the health care system. Since most fatal poisonings occur outside hospital, these must be included when studying characteristics of such deaths. The pattern of toxic agents differs between fatal and non-fatal poisonings. By including all poisoning episodes, cause-fatality rates can be calculated.</p> <p>Methods</p> <p>Fatal and non-fatal acute poisonings in subjects aged ≥16 years in Oslo (428 198 inhabitants) were included consecutively in an observational multi-centre study including the ambulance services, the Oslo Emergency Ward (outpatient clinic), and hospitals, as well as medico-legal autopsies from 1st April 2003 to 31st March 2004. Characteristics of fatal poisonings were examined, and a comparison of toxic agents was made between fatal and non-fatal acute poisoning.</p> <p>Results</p> <p>In Oslo, during the one-year period studied, 103 subjects aged ≥16 years died of acute poisoning. The annual mortality rate was 24 per 100 000. The male-female ratio was 2:1, and the mean age was 44 years (range 19-86 years). In 92 cases (89%), death occurred outside hospital. The main toxic agents were opiates or opioids (65% of cases), followed by ethanol (9%), tricyclic anti-depressants (TCAs) (4%), benzodiazepines (4%), and zopiclone (4%). Seventy-one (69%) were evaluated as accidental deaths and 32 (31%) as suicides. In 70% of all cases, and in 34% of suicides, the deceased was classified as drug or alcohol dependent. When compared with the 2981 non-fatal acute poisonings registered during the study period, the case fatality rate was 3% (95% C.I., 0.03-0.04). Methanol, TCAs, and antihistamines had the highest case fatality rates; 33% (95% C.I., 0.008-0.91), 14% (95% C.I., 0.04-0.33), and 10% (95% C.I., 0.02-0.27), respectively.</p> <p>Conclusions</p> <p>Three per cent of all acute poisonings were fatal, and nine out of ten deaths by acute poisonings occurred outside hospital. Two-thirds were evaluated as accidental deaths. Although case fatality rates were highest for methanol, TCAs, and antihistamines, most deaths were caused by opiates or opioids.</p

Burden of waterpipe smoking and chewing tobacco use among women of reproductive age group using data from the 2012-13 Pakistan Demographic and Health Survey

Background: Despite the general decline in cigarette smoking, use of alternative forms of tobacco has increased particularly in developing countries. Waterpipe (WP) and Chewing Tobacco (CT) are two such alternative forms, finding their way into many populations. However, the burden of these alternative forms of tobacco and their socio demographic determinants are still unclear. We assessed the prevalence of WP and CT use among women of reproductive age group in Pakistan. Methods: Data from the most recent Pakistan Demographic and Health Survey 2012–13 (n = 13,558) was used for this analysis. Information obtained from ever married women, aged between 15 and 49 years were analyzed using two separate data subgroups; exclusive WP smokers (total n = 12,995) and exclusive CT users (total n = 12,771). Univariate and Multivariate logistic regression analyses were conducted and results were reported as crude and adjusted Odds Ratio with 95 % confidence intervals. Results: Prevalence of WP smoking and CT were 4 % and 2 %, respectively. After multivariate adjustments, ever married women who were: older than 35 years (OR; 4.68 95 % CI, 2.62–8.37), were poorest (OR = 4.03, 95 % CI 2.08–7.81), and had no education (OR = 9.19, 95 % CI 5.10–16.54), were more likely to be WP smokers. Similarly, ever married women who were: older than 35 years (OR = 3.19, 95 % CI 1.69–6.00), had no education (OR = 4.94, 95 % CI 2.62–9.33), were poor (OR = 1.64, 95 % CI 1.07–2.48) and had visited health facility in last 12 months (OR = 1.81, 95 % CI 1.22–2.70) were more likely to be CT users as well. Conclusion: Older women with lower socio-economic profile were more likely to use WP and CT. Focused policies aiming towards reducing the burden of alternate forms of tobacco use among women is urgently needed to control the tobacco epidemic in the country

Identification of Extracellular Segments by Mass Spectrometry Improves Topology Prediction of Transmembrane Proteins

Transmembrane proteins play crucial role in signaling, ion transport, nutrient uptake, as well as in maintaining the dynamic equilibrium between the internal and external environment of cells. Despite their important biological functions and abundance, less than 2% of all determined structures are transmembrane proteins. Given the persisting technical difficulties associated with high resolution structure determination of transmembrane proteins, additional methods, including computational and experimental techniques remain vital in promoting our understanding of their topologies, 3D structures, functions and interactions. Here we report a method for the high-throughput determination of extracellular segments of transmembrane proteins based on the identification of surface labeled and biotin captured peptide fragments by LC/MS/MS. We show that reliable identification of extracellular protein segments increases the accuracy and reliability of existing topology prediction algorithms. Using the experimental topology data as constraints, our improved prediction tool provides accurate and reliable topology models for hundreds of human transmembrane proteins

Search for resonant WZ production in the fully leptonic final state in proton–proton collisions at √s=13 TeV with the ATLAS detector

A search for a WZ resonance, in the fully leptonic final state (electrons or muons), is performed using 139&nbsp;fb - 1 of data collected at a centre-of-mass energy of 13&nbsp;TeV by the ATLAS detector at the Large Hadron Collider. The results are interpreted in terms of a singly charged Higgs boson of the Georgi–Machacek model, produced by WZ fusion, and of a Heavy Vector Triplet, with the resonance produced by WZ fusion or the Drell–Yan process. No significant excess over the Standard Model prediction is observed and limits are set on the production cross-section times branching ratio as a function of the resonance mass for these processes

Measurement of the nuclear modification factor of b-jets in 5.02 TeV Pb+Pb collisions with the ATLAS detector

This paper presents a measurement of b-jet production in Pb+Pb and pp collisions at √sNN = 5.02 TeV with the ATLAS detector at the LHC. The measurement uses 260 pb−1 of pp collisions collected in 2017 and 1.4 nb−1 of Pb+Pb collisions collected in 2018. In both collision systems, jets are reconstructed via the anti-kt algorithm. The b-jets are identified from a sample of jets containing muons from the semileptonic decay of b-quarks using template fits of the muon momentum relative to the jet axis. In pp collisions, b-jets are reconstructed for radius parameters R = 0.2 and R = 0.4, and only R = 0.2 jets are used in Pb+Pb collisions. For comparison, inclusive R = 0.2 jets are also measured using 1.7 nb−1 of Pb+Pb collisions collected in 2018 and the same pp collision data as the b-jet measurement. The nuclear modification factor, RAA, is calculated for both b-jets and inclusive jets with R = 0.2 over the transverse momentum range of 80–290 GeV. The nuclear modification factor for b-jets decreases from peripheral to central collisions. The ratio of the b-jet RAA to inclusive jet RAA is also presented and suggests that the RAA for b-jets is larger than that for inclusive jets in central Pb+Pb collisions. The measurements are compared with theoretical calculations and suggest a role for mass and colour-charge effects in partonic energy loss in heavy-ion collisions