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Supplementary Tables 1-2 from Gene Expression Profiles Associated with Treatment Response in Oligodendrogliomas

Supplementary Table 3 from Gene Expression Profiles Associated with Treatment Response in Oligodendrogliomas

Oligodendrogliomas are a specific subtype of brain tumor of which the majority responds favorably to chemotherapy. In this study, we made use of expression profiling to identify chemosensitive oligodendroglial tumors. Correlation of expression profiles to loss of heterozygosity on 1p and 19q, common chromosomal aberrations associated with response to treatment, identified 376, 64, and 60 differentially expressed probe sets associated with loss of 1p, 19q or 1p, and 19q, respectively. Correlation of expression profiles to the tumors' response to treatment identified 16 differentially expressed probe sets. Because transcripts associated with chemotherapeutic response were identified independent of common chromosomal aberrations, expression profiling may be used as an alternative approach to the tumors' 1p status to identify chemosensitive oligodendroglial tumors. Finally, we correlated expression profiles to survival of the patient after diagnosis and identified 103 differentially expressed probe sets. The observation that many genes are differentially expressed between long and short survivors indicates that the genetic background of the tumor is an important factor in determining the prognosis of the patient. Furthermore, these transcripts can help identify patient subgroups that are associated with favorable prognosis. Our study is the first to correlate gene expression with chromosomal aberrations and clinical performance (response to treatment and survival) in oligodendrogliomas. The differentially expressed transcripts can help identify patient subgroups with good prognosis and those that will benefit from chemotherapeutic treatments. (Cancer Res 2005; 65(24): 11335-44)

Alcohol-free beers have gained popularity in the last few decades because they provide a healthier alternative to alcoholic beers and can be more widely consumed. Consumers are becoming more aware of the benefits of reducing their alcohol consumption, and this has increased the sales of nonalcoholic alternatives. However, there are still many challenges for the brewing industry to produce an alcohol-free beer that resembles the pleasant fruity flavor and overall sensory experience of regular beers. The aim of this review is to give a comprehensive overview of alcohol-free beer focusing on aroma chemistry. The formation of the most important aroma compounds, such as Strecker aldehydes, higher alcohols, and esters, is reviewed, aiming to outline the gaps in current knowledge. The role of ethanol as a direct and indirect flavor-active compound is examined separately. In parallel, the influence of the most common methods to reduce alcohol content, such as physical (dealcoholization) or biological, on the organoleptic characteristics and consumer perception of the final product, is discussed.

The increasing popularity of alcohol-free beers (AFBs) fosters the industry interest in delivering the best possible product. Yet, a remaining sensory defect of AFBs is the over-perception of wort flavour, caused by elevated concentrations of small volatile flavour compounds (i.e. aldehydes). Previously, molecular sieves (hydrophobic ZSM-5 type zeolites) were found most suitable to remove these flavours by adsorption with high selectivity from the AFBs. In this work, a flavour-improved beer is produced at pilot-scale using this novel technology, and its chemical composition, sensory profile and stability are evaluated against a reference. Aldehyde concentrations in the flavour-improved product were found 79–93% lower than in the reference. The distinct difference was confirmed with a trained sensory panel and could be conserved even after three months ageing at 30 °C. Future work will focus on the process design to scale up this technology.

Alcohol-free beers (AFBs) brewed by cold-contact fermentation exhibit a flavor reminiscent of wort which affects consumer acceptability. The aims of this study were to identify the odor-active compounds in AFB and elucidate the contribution of these to the overall aroma and worty character of the beer. Using a sensomics approach, 27 odor-active aroma compounds were identified and quantitated using gas chromatography–mass spectrometry. The most odor-active compound was methional (boiled potato-like aroma), followed by 3-methylbutanal (cocoa-like), (E)-β-damascenone (apple, jam-like), 5-ethyl-3-hydroxy-4-methyl-2(5H)-furanone (curry, spicy-like), and phenylacetaldehyde (floral, honey-like). The important contribution of these flavor compounds to the worty and honey aroma of AFB was determined by sensory assessment of the recombinate in a beer-like matrix with omission tests. The role of 5-ethyl-3-hydroxy-4-methyl-2(5H)-furanone in AFB aroma was reported for the first time. The outcomes from this study are of relevance for the brewing industry to design strategies for the reduction of the wortiness of AFB.

Although present in concentrations in microgrammes per litre level, aldehydes, in particular those derived from Strecker degradation, are known to majorly contribute to the undesired wort flavour of alcohol-free beers. In order to improve currently available products, one needs to understand the underlying cause for the over-prevalence and identify leverage points and methods to selectively reduce the aldehydes in alcohol-free beers. This work gives a short overview on relevant flavour-active wort flavours identified in alcohol-free beer and on their involved chemical formation pathways. Consequently, aldehyde removal technologies in general and in brewing industry are presented. Adsorptive removal of off-flavours by aldehyde-scavenging groups is already widely exploited in the packaging industry and may achieve reduction of these components to near depletion, depending on the process conditions. Its principles are adaptable to recovering off-flavours before filling. Also, supercritical CO2extraction has been successfully applied to separate flavours from food matrices. In brewing, the focus has been set to biologic conversion by restricted fermentation steps, but the reduction of key components of more than 70% is not achieved. Newer developments focus on thermal separation techniques that not only include non-specific physical dealcoholisation but also more selective technologies such as pervaporation, where aldehydes are reduced to near depletion. However, for most unit operations, selectivity and capacity are not yet investigated. Future research should explore the shortcomings of current techniques and overcome bottlenecks either by developing more specific methods for aldehyde removal and/or a clever combination of unit operations to optimise the separation and process integration.

Detection thresholds are used routinely to determine the odour-active compounds in foods. The composition of a food matrix, such as hydrophobicity or solids content, has an impact on the release of flavour compounds, and thus on thresholds. In the case of beer, thresholds determined in alcoholic beer may not be the same for alcohol-free beer (AFB). Therefore, the aim of this study was to determine detection thresholds for aroma compounds typically found in beer, within a model AFB. The model was designed to match the sugar concentration and pH of an AFB brewed by a cold contact process. Thresholds were measured using a 3-AFC procedure and calculated using either Best Estimate Threshold (BET) method or by logistic regression. Moreover, an algorithm for the removal of false positives was applied to adjust the assessors' raw responses. Retronasal thresholds were generally lower than orthonasal. Those calculated by BET were significantly higher (p

peer-reviewed The full text of this article will not be available in ULIR until the embargo expires on the 20/05/2021 BACKGROUND: Recently, a new process concept has been proposed to selectively adsorb wort offflavours, i.e. aldehydes, from alcohol-free beers with hydrophobic zeolites. RESULTS: In this work, we investigated the uptake of a mixture of wort flavour compounds (2-methylpropanal, 2-methylbutanal, 3methylbutanal, furfural and methional), from a model solution onto binderless, hydrophobic ZSM-5 zeolite granules in order to quantify mass transfer parameters and identify bottlenecks. Subsequently, the homogenous solid diffusion model was employed to regress the effective diffusion coefficients for each molecule and experimental condition, which ranged between 10-15 and 10-13 m2/s, indicating strong intraparticle mass transfer limitation. Furthermore, it was found that the effective diffusion coefficient is inversely correlated to the molecules’ hydrophobicity, expressed as the logD value and its isotherm affinity constant. CONCLUSION: These results give valuable insight to design and improved adsorbent material and an off-flavour removal unit for industrial scale.

Background An automated multiplex platform using capillary blood can promote greater throughput and more comprehensive studies in celiac disease (CD). Diagnostic accuracy should be improved using likelihood ratios for the post-test probability of ruling-in disease. Methods The Ig_plex™ Celiac Disease Panel on the sqidlite™ automated platform measured IgA and IgG antibodies to tTG and DGP in n = 224 CD serum or plasma samples. Diagnostic accuracy metrics were applied to the combined multiplex test results for several CD populations and compared to conventional single antibody ELISA tests. Results With multiple positive antibody results, the post-test probability for ruling-in untreated and treated CD increased to over 90%. The number of samples positive for more than one antibody also increased in untreated CD to ≥90%. Measurement of all four CD antibodies generate cut-off dependent accuracy profiles that can monitor response to treatment with the gluten-free diet (GFD). Higher positive tTG and DGP antibodies are seen more frequently in confirmed CD without (81%–94%) than with GFD treatment (44%–64%). In CD lacking biopsy confirmation, overall agreement of plasma to serum was ≥98% for all antibodies, and 100% for venous to capillary plasma. Conclusions The Ig_plex Celiac Disease Panel increases the likelihood of confirming CD based on the post-test probability of disease results for multi-reactive markers. Specific positivity profiles and cut-off intervals can be used to monitor GFD treatment and likely disease progression. Using serum, venous and capillary plasma yield comparable and accurate results.

peer-reviewed Flavor-active esters, produced during fermentation, are vital components and important contributors to the aroma of beer. In order to separate trace amounts of esters, their adsorption behavior in the presence of high concentrations of ethanol and their thermodynamic behavior under the influence of temperature needs to be understood. This study reports the influence of temperature on single component adsorption isotherms of four esters (i.e. ethyl acetate, isopentyl acetate, ethyl 4-methylpentanoate, and ethyl hexanoate) on two hydrophobic resins (i.e. Amberlite XAD16N, and Sepabeads SP20SS) and the estimation of heat, entropy, and Gibbs energy of adsorption. Higher heat and entropy of adsorption are obtained for ethyl hexanoate and ethyl 4-methylpentanoate in comparison, due to their higher hydrophobicity, stronger binding, and the exothermic nature of their adsorption. A higher concentration of ethanol (tested from 1 to 30% (v/v)), lowers the activity coefficient of esters in the aqueous phase, and subsequently lowers adsorption and Langmuir affinity parameters. Increase of temperature from 284.15 to 325.15 K shows a reverse influence on maximum adsorption capacity and Langmuir affinity parameters. Langmuir affinity parameters are obtained at various ethanol concentrations and temperatures. The reported parameters and thermodynamic properties in this paper, are essential for designing an industrial scale adsorption step for separation of flavor-active esters under non-isothermal conditions.

GC-MS/O (gas chromatography-mass spectrometry/olfactometry) is an indispensable technique to associate individual volatile odorants to odors perceived by human assessors. Interpretation of GC-MS/O data is, however, hampered in practice by different factors related to the instrumental set-up and by heterogeneity among odor descriptions given by the assessors (olfactometer). In this paper, a novel automated approach is presented, which deals with these GC-MS/O challenges and enables visualization and interpretation of GC-MS/O data. It includes signal warping via COW (correlation optimized warping), synchronizing MS and O data via detection of odor areas and construction of a TOC (total odor count) to visualize odor heterogeneity, respectively. Our approach is implemented in practice, and we successfully associated odors to compounds in data sets of two alcoholic beverages with different flavor compositions. It leads to a faster and less biased association of odors to compounds compared to current practice, reducing the time and effort needed for interpreting GC-MS/O data.

Autoantibodies are increasingly used as biomarkers in the detection of autoimmune disorders and cancer. Disease specific antibodies are generally detected by their binding to specific antigens. As an alternative approach, we propose to identify specific complementarity determining regions (CDR) of IgG that relate to an autoimmune disorder or cancer instead of the specific antigen(s). In this manuscript, we tested the technical feasibility to detect and identify CDRs of specific antibodies by mass spectrometry. We used a commercial pooled IgG preparation as well as purified serum IgG fractions that were spiked with different amounts of a fully human monoclonal antibody (adalimumab). These samples were enzymatically digested and analyzed by nanoLC Orbitrap mass spectrometry. In these samples, we were able to identify peptides derived from the CDRs of adalimumab. These peptides could be detected at an amount of 110 attomole, 5 orders of magnitude lower than the total IgG concentration in these samples. Using higher energy collision induced dissociation (HCD) fragmentation and subsequent de novo sequencing, we could successfully identify 50% of the detectable CDR peptides of adalimumab. In addition, we demonstrated that an affinity purification with anti-dinitrophenol (DNP) monoclonal antibody enhanced anti-DNP derived CDR detection in a serum IgG background. In conclusion, specific CDR peptides could be detected and sequenced at relatively low levels (attomole-femtomole range) which should allow the detection of clinically relevant CDR peptides in patient samples. Electronic supplementary material The online version of this article (doi:10.1007/s00216-010-4361-9) contains supplementary material, which is available to authorized users.

Clinical trials in malignant glioma have demonstrated excellent safety of recombinant adenovirus type 5 (Ad5) but lack of convincing efficacy. The overall low expression levels of the Coxsackie and Adenovirus receptor and the presence of high anti-Ad5-neutralizing antibody (NAb) titers in the human population are considered detrimental for consistency of clinical results. To identify an adenoviral vector better suited to infect primary glioma cells, we tested a library of fiber-chimeric Ad5-based adenoviral vectors on 12 fresh human glioma cell suspensions. Significantly improved marker gene expression was obtained with several Ad5-chimeric vectors, predominantly vectors carrying fiber molecules derived from B-group viruses (Ad11, Ad16, Ad35 and Ad50). We next tested Ad35 sero prevalence in sera derived from 90 Dutch cancer patients including 30 glioma patients and investigated the transduction efficiency of this vector in glioma cell suspensions. Our results demonstrate that the sero prevalence and the titers of NAb against Ad35 are significantly lower than against Ad5. Also, recombinant Ad35 has significantly increased ability to transfer a gene to primary glioma cells compared to Ad5. We thus conclude that Ad35 represents an interesting candidate vector for gene therapy of malignant glioma.

The overall median survival of patients with a malignant glioma is1 y. Because malignant gliomas rarely metastasize outside the skull, locoregional treatment strategies, such as gene therapy, are under investigation. Recently, convection-enhanced delivery (CED) has been presented as a method to improve delivery of large molecules. The goal of this study was to evaluate whether CED improves intratumoral delivery of adenoviral vectors and compare it with single injection (SI) and multiple injection (4x, MI).A replication-deficient adenoviral vector encoding the herpes simplex virus thymidine kinase (HSV-tk) and the human somatostatin receptor subtype 2 (sst(2)) was administered into nude mice bearing subcutaneous U87 xenografts. Tumors were injected with 1.5 x 10(9) plaque-forming units of Ad5.tk.sstr by CED, SI, or MI. Three days later, [(99m)Tc-N(4)(0-1),Asp(0),Tyr(3)]octreotate ((99m)Tc-Demotate 2) was injected intravenously to monitor the virus-induced sst(2) expression. gamma-Camera imaging was performed for in vivo imaging, and the tumor uptake of (99m)Tc-Demotate 2 was determined by gamma-counter. Furthermore, the tumor was sectioned and ex vivo autoradiography was performed. After decay of radioactivity, adjacent sections were submitted to in vitro autoradiography with (125)I-DOTA-Tyr(3)-octreotate, which was used to calculate the transduced areas.Transfected xenograft tissues showed high sst(2) expression and were clearly visualized with a gamma-camera. Accumulation of radioactivity was 2-fold higher in the tumors that were injected with MI compared with CED and SI (P = 0.01). CED and SI resulted in equal uptake of radioactivity in the tumors. The measured areas of transduction in ex vivo and in vitro autoradiographs showed a high concordance (r(2) = 0.89, P0.0001). The maximum area of transfection was significantly larger after MI than after CED (P0.05) or SI (P = 0.05). Also, the measured volume of distribution was twice as high after administration of Ad5.tk.sstr by MI (56.6 mm(3)) compared with SI (25.3 mm(3)) or CED (26.4 mm(3)).CED does not increase adenoviral vector distribution in a glioma xenograft model compared with SI. Therefore, in the clinic MI is probably the most effective delivery method for the large adenoviral particle (70 nm) in malignant gliomas.

Oligodendrogliomas are a specific subtype of brain tumor of which the majority responds favorably to chemotherapy. In this study, we made use of expression profiling to identify chemosensitive oligodendroglial tumors. Correlation of expression profiles to loss of heterozygosity on 1p and 19q, common chromosomal aberrations associated with response to treatment, identified 376, 64, and 60 differentially expressed probe sets associated with loss of 1p, 19q or 1p, and 19q, respectively. Correlation of expression profiles to the tumors' response to treatment identified 16 differentially expressed probe sets. Because transcripts associated with chemotherapeutic response were identified independent of common chromosomal aberrations, expression profiling may be used as an alternative approach to the tumors' 1p status to identify chemosensitive oligodendroglial tumors. Finally, we correlated expression profiles to survival of the patient after diagnosis and identified 103 differentially expressed probe sets. The observation that many genes are differentially expressed between long and short survivors indicates that the genetic background of the tumor is an important factor in determining the prognosis of the patient. Furthermore, these transcripts can help identify patient subgroups that are associated with favorable prognosis. Our study is the first to correlate gene expression with chromosomal aberrations and clinical performance (response to treatment and survival) in oligodendrogliomas. The differentially expressed transcripts can help identify patient subgroups with good prognosis and those that will benefit from chemotherapeutic treatments. (Cancer Res 2005; 65(24): 11335-44)

Although successful in many rodent models of malignant gliomas, results of clinical adenoviral gene therapy trials using replication deficient vectors have been disappointing. One of the explanations of the discrepancy between results in animal models and clinical trials is the low expression of the Coxsackie Adenovirus receptor (CAR), the main high affinity receptor for binding of adenovirus serotype 5, on primary glioma cells as opposed to established glioma cell lines. To obtain improved adenoviral vectors, we made use of the differential tropism of the naturally occurring 51 human adenoviral serotypes to test the hypothesis that adenoviral vectors, binding to other receptors than CAR, would result in improved infection of primary glioma cells.