Presentation of arthritogenic peptide to antigen-specific T cells by fibroblast-like synoviocytes

Objective To assess the ability of rheumatoid arthritis (RA) fibroblast-like synoviocytes (FLS) to function as antigen-presenting cells (APCs) for arthritogenic autoantigens found within inflamed joint tissues. Methods Human class II major histocompatibility complex (MHC)–typed FLS were used as APCs for murine class II MHC–restricted CD4 T cell hybridomas. Interferon-Γ (IFNΓ)–treated, antigen-loaded FLS were cocultured with T cell hybridomas specific for immunodominant portions of human cartilage gp-39 (HC gp-39) or human type II collagen (CII). T cell hybridoma activation was measured by enzyme-linked immunosorbent assay of culture supernatants for interleukin-2. Both synthetic peptide and synovial fluid (SF) were used as sources of antigen. APC function in cocultures was inhibited by using blocking antibodies to human class II MHC, CD54, or CD58, or to murine CD4, CD11a, or CD2. Results Human FLS could present peptides from the autoantigens HC gp-39 and human CII to antigen-specific MHC-restricted T cell hybridomas. This response required pretreatment of FLS with IFNΓ, showed MHC restriction, and was dependent on human class II MHC and murine CD4 for effective antigen presentation. Furthermore, FLS were able to extract and present antigens found within human SF to both the HC gp-39 and human CII T cell hybridomas in an IFNΓ-dependent and MHC-restricted manner. Conclusion RA FLS can function as APCs and are able to present peptides derived from autoantigens found within joint tissues to activated T cells in vitro. In the context of inflamed synovial tissues, FLS may be an important and hitherto overlooked subset of APCs that could contribute to autoreactive immune responses.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/56038/1/22573_ftp.pd

Acute symptoms during the course of head and neck radiotherapy or chemoradiation are strong predictors of late dysphagia

AbstractPurposeTo determine if acute symptoms during definitive radiotherapy (RT) or chemoradiation (CHRT) are prognostic factors for late dysphagia in head and neck cancer (HNC).Material and methodsThis prospective cohort study consisted of 260 HNC patients who received definitive RT or CHRT. The primary endpoint was grade 2–4 swallowing dysfunction at 6months after completing RT (SWALM6). During treatment, acute symptoms, including oral mucositis, xerostomia and dysphagia, were scored, and the scores were accumulated weekly and entered into an existing reference model for SWALM6 that consisted of dose–volume variables only.ResultsBoth acute xerostomia and dysphagia were strong prognostic factors for SWALM6. When acute scores were added as variables to the reference model, model performance increased as the course of treatment progressed: the AUC rose from 0.78 at the baseline to 0.85 in week 6. New models built for weeks 3–6 were significantly better able to identify patients with and without late dysphagia.ConclusionAcute xerostomia and dysphagia during the course of RT are strong prognostic factors for late dysphagia. Including accumulated acute symptom scores on a weekly basis in prediction models for late dysphagia significantly improves the identification of high-risk and low-risk patients at an early stage during treatment and might facilitate individualized treatment adaptation

Genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader

Anaerobic gut fungi represent a distinct early-branching fungal phylum (Neocallimastigomycota) and reside in the rumen, hindgut, and feces of ruminant and nonruminant herbivores. The genome of an anaerobic fungal isolate, Orpinomyces sp. strain C1A, was sequenced using a combination of Illumina and PacBio single-molecule real-time (SMRT) technologies. The large genome (100.95 Mb, 16,347 genes) displayed extremely low G+C content (17.0%), large noncoding intergenic regions (73.1%), proliferation of microsatellite repeats (4.9%), and multiple gene duplications. Comparative genomic analysis identified multiple genes and pathways that are absent in Dikarya genomes but present in early-branching fungal lineages and/or nonfungal Opisthokonta. These included genes for posttranslational fucosylation, the production of specific intramembrane proteases and extracellular protease inhibitors, the formation of a complete axoneme and intraflagellar trafficking machinery, and a near-complete focal adhesion machinery. Analysis of the lignocellulolytic machinery in the C1A genome revealed an extremely rich repertoire, with evidence of horizontal gene acquisition from multiple bacterial lineages. Experimental analysis indicated that strain C1A is a remarkable biomass degrader, capable of simultaneous saccharification and fermentation of the cellulosic and hemicellulosic fractions in multiple untreated grasses and crop residues examined, with the process significantly enhanced by mild pretreatments. This capability, acquired during its separate evolutionary trajectory in the rumen, along with its resilience and invasiveness compared to prokaryotic anaerobes, renders anaerobic fungi promising agents for consolidated bioprocessing schemes in biofuels production.Peer reviewedMicrobiology and Molecular GeneticsBiosystems and Agricultural Engineerin

Development and validation of a prediction model for tube feeding dependence after curative (chemo-) radiation in head and neck cancer

BACKGROUND: Curative radiotherapy or chemoradiation for head and neck cancer (HNC) may result in severe acute and late side effects, including tube feeding dependence. The purpose of this prospective cohort study was to develop a prediction model for tube feeding dependence 6 months (TUBEM6) after curative (chemo-) radiotherapy in HNC patients. PATIENTS AND METHODS: Tube feeding dependence was scored prospectively. To develop the multivariable model, a group LASSO analysis was carried out, with TUBEM6 as the primary endpoint (n = 427). The model was then validated in a test cohort (n = 183). The training cohort was divided into three groups based on the risk of TUBEM6 to test whether the model could be extrapolated to later time points (12, 18 and 24 months). RESULTS: Most important predictors for TUBEM6 were weight loss prior to treatment, advanced T-stage, positive N-stage, bilateral neck irradiation, accelerated radiotherapy and chemoradiation. Model performance was good, with an Area under the Curve of 0.86 in the training cohort and 0.82 in the test cohort. The TUBEM6-based risk groups were significantly associated with tube feeding dependence at later time points (p<0.001). CONCLUSION: We established an externally validated predictive model for tube feeding dependence after curative radiotherapy or chemoradiation, which can be used to predict TUBEM6

Large-Scale Meta-GWAS Reveals Common Genetic Factors Linked to Radiation-Induced Acute Toxicities across Cancers

BACKGROUND: This study was designed to identify common genetic susceptibility and shared genetic variants associated with acute radiation-induced toxicity (RIT) across four cancer types (prostate, head and neck, breast, and lung).METHODS: A GWAS meta-analysis was performed using 19 cohorts including 12,042 patients. Acute standardized total average toxicity (rSTATacute) was modelled using a generalized linear regression model for additive effect of genetic variants adjusted for demographic and clinical covariates. LD score regression estimated shared SNP-based heritability of rSTATacute in all patients and for each cancer type.RESULTS: Shared SNP-based heritability of STATacute among all cancer types was estimated at 10% (se = 0.02), and was higher for prostate (17%, se = 0.07), head and neck (27%, se = 0.09), and breast (16%, se = 0.09) cancers. We identified 130 suggestive associated SNPs with rSTATacute (5.0x10-8&lt;P-value&lt;1.0x10-5) across 25 genomic regions. rs142667902 showed the strongest association (effect allele A; effect size -0.17; P-value=1.7x10-7), which is located near DPPA4, encoding a protein involved in pluripotency in stem cells, which are essential for repair of radiation-induced tissue injury. Gene-set enrichment analysis identified 'RNA splicing via endonucleolytic cleavage and ligation' (P = 5.1 x10-6, Pcorrected =0.079) as the top gene set associated with rSTATacute among all patients. In-silico gene expression analysis showed the genes associated with rSTATacute were statistically significantly up-regulated in skin (not sun exposed Pcorrected=0.004; sun exposed Pcorrected=0.026).CONCLUSIONS: There is shared SNP-based heritability for acute RIT across and within individual cancer sites. Future meta-GWAS among large radiotherapy patient cohorts are worthwhile to identify the common causal variants for acute radiotoxicity across cancer types.</p

Mechanistyczne badania reakcji CO-PROX prowadzonej na nanosześcianach spinelu kobaltowego

Usuwanie śladowych ilości CO w strumieniu wodoru, zapobiegające zatruwaniu katalizatora, można prowadzić poprzez reakcję preferencyjnego utleniania tlenku węgla (CO-PROX) do niereaktywnego CO2. Jednoczesne utlenianie H2 jako reakcja uboczna jest niepożądane, ponieważ z jednej strony zmniejsza stężenie H2 w strumieniu a z drugiej prowadzi do dezaktywacji katalizatora poprzez wiązanie H2O do miejsc aktywnych. Dlatego zapotrzebowanie na stabilny, specyficzny i aktywny katalizator dla omawianej reakcji jest duże. Metale szlachetne, chociaż wykazują wysoką aktywność katalityczną, mają nieodłączne wady do których zaliczamy przede wszystkim ich wysoki koszt wynikający z ograniczonej dostępności. Dlatego uwagę w tym kontekście zyskują tlenki metali przejściowych, na przykład na bazie tlenku miedzi i kobaltu, jako alternatywa dla metali nieszlachetnych. Szczególnie nanokryształy spinelu kobaltu, charakteryzujące się łatwą kontrolą składu (domieszkowanie) i morfologii, oraz wykazujące dostrajalne właściwości redoks i wysoką aktywność w kierunku utleniania CO w niskiej temperaturze, są doskonałymi kandydatami dla katalizowania reakcji CO-PROX. Większość dotychczasowych badań koncentrowała się na prowadzeniu reakcji na wysoce niestabilnej powierzchni (110) spinelu kobaltowego, zaś mniej uwagi poświęcono najbardziej stabilnej płaszczyźnie (100) eksponowanej przez łatwo syntetyzowalne nanosześciany Co3O4, mimo że te ostatnie wykazały wysoką aktywność w utlenianiu CO. W związku z tym nadal brakuje dogłębnego opisu zachowania spinelu kobaltu na poziomie molekularnym w mieszaninie wieloskładnikowej CO / O2 / H2 typowej dla warunków reakcji CO-PROX. Wychodząc naprzeciw tej sytuacji, w ramach niniejszej pracy przeprowadzono kompleksowe badania metodami termodynamiki atomistycznej (w oparciu o teorię DFT+U) dotyczące interakcji CO / CO2, H2 / H2O i O2 / O z powierzchnią (100) eksponowaną przez nanosześciany spinelu kobaltowego. Najpierw zidentyfikowano i opisano na poziomie molekularnym dużą liczbą adduktów CO, w tym jednowiązalnych (η1), dwuwiązalnych (μ-η2) i mostkowych (μ-η1: η1), i zaprezentowano szczegółowy opis ich struktury elektronowej i magnetycznej. Wykazano, że adsorpcja CO jest ograniczona do centrów kationowych i zachodzi bezaktywacyjnie głównie poprzez atom węgla. W przeciwieństwie do tego adsorpcja H2 jest procesem aktywowanym i prowadzi do dysocjacji cząsteczki a atomy wodoru (w postaci jonów H+) są stabilizowane wyłącznie na centrach tlenkowych. Skonstruowano diagramy termodynamiczne ΘCO/O2 = f (pCO, pO2, T) i ΘH2/O2 = f (pH2, pO2, T) i wykorzystano je do interpretacji adsorpcji CO i H2 oraz termodynamiki utleniania. Wyniki badań wykazały że cząsteczka CO może być utleniana już w niskich temperaturach (około 100 °C) poprzez mechanizm Eley-Rideala zachodzący na mono- i diatomowych reaktywnych formach tlenu, ze spontaniczną desorpcją powstałej cząsteczki CO2. Utlenianie cząsteczki H2 zachodzi najprawdopodobniej poprzez aktywację wodoru na reaktywnych formach tlenu, po czym wytworzony H2O zatruwa aktywne centra katalizatora aż do wysokich temperatur (~300 °C).The removal of trace amounts of CO in a hydrogen-rich gas stream to prevent catalyst poisoning may be performed by the preferential oxidation of carbon monoxide (CO-PROX), where CO is oxidized to non-reactive CO2. Oxidation of H2 as a side reaction is undesirable as it decreases the H2 concentration in the stream and because its product, H2O, blocks the catalyst’s active sites for CO oxidation. Therefore, the need for a stable, specific, and active catalyst is high. Noble metals, although showing high catalytic activity, have the intrinsic drawbacks of high costs and limited availability. Therefore, the attention has shifted toward transition metal oxides, such as copper and cobalt oxide based catalysts as non-noble-metal alternatives. In this framework, cobalt spinel nanocrystals, showing easily controlled morphology, composition, tunable redox properties and high activity towards low temperature CO oxidation, are excellent candidates for the CO-PROX reaction. Most studies have focused on CO oxidation over the highly instable (110) surface, but the most abundant and easily synthesised cobalt spinel nanocubes, presenting a (100) termination have been neglected even though they have shown great potential for CO oxidation. In that regard an in-depth molecular-level description of the cobalt spinel behavior in the multicomponent CO/O2/H2 mixture is still lacking. We performed a comprehensive DFT + U, atomistic thermodynamic investigation into the CO/CO2, H2/H2O and O2/O interactions with the (100) surface exposed by cobalt spinel nanocubes. A large variety of monodentate (η1), bridging bidentate (µ-η2) and bridging monodentate (µ-η1:η1) CO adducts were identified, and described at molecular level, including a detailed description of their electronic and magnetic structure. It was shown that the CO adsorption is limited to cationic sites and occurs mainly through the carbon moiety. In contrast H2 adsorption is a dissociative process and H adspecies are stabilized on the anionic O2- sites exclusively. Thermodynamic ΘCO/O2 = f(pCO,pO2,T) and ΘH2/O2 = f(pH2,pO2,T) diagrams were constructed and used for interpretation of CO and H2 adsorption and oxidation thermodynamics, revealing that CO may be oxidized at low temperatures (at about 100 °C) via the Eley-Rideal mechanism either on reactive oxygen species or dioxygen, with spontaneous desorption of resulting CO2 molecule. Oxidation of H2 most likely occurs through hydrogen activation on a reactive oxygen species after which the produced H2O poisons the active centers of catalyst even at elevated temperatures (~300 °C)

Fingerprinting fragments of fragile interstellar molecules: dissociation chemistry of pyridine and benzonitrile revealed by infrared spectroscopy and theory

Fragmentation pathways of benzonitrile and pyridine are elucidated using cryogenic infrared ion spectroscopy, quantum-chemical calculations and molecular dynamics simulations