Association of biomarkers for human papillomavirus with survival among adults with Barrett high-grade dysplasia and esophageal adenocarcinoma

Importance: The presence of high-risk human papillomavirus (HPV) has been associated with a favorable outcome in Barrett high-grade dysplasia (HGD) and esophageal adenocarcinoma (EAC). Nevertheless, the prognostic significance of other HPV-related biomarkers (ie, retinoblastoma protein [pRb], cyclin D1 [CD1], minichromosome maintenance protein [MCM2] and Ki-67) is unknown. Objective: To examine the association between HPV-related biomarkers and survival in adult patients with Barrett HGD and EAC. Design, Setting, and Participants: This retrospective case-control study examined the hypothesis that the HPV-related cell cycle markers (pRb, CD1, and Ki-67) and the viral surrogate marker (MCM2) may be associated with a favorable prognosis in Barrett HGD and EAC. Pretreatment biopsies were used for HPV DNA determination via polymerase chain reaction and immunohistochemistry for the HPV-related biomarkers. Recruitment of patients occurred in secondary and tertiary referral centers, with 151 patients assessed for eligibility. The study period was from December 1, 2002, to November 28, 2017, and the dates of analysis were from September 9, 2011, to November 28, 2017. Main Outcomes and Measures: Disease-free survival and overall survival. Results: Of 151 patients assessed for eligibility, 9 were excluded. Among the 142 patients with Barrett HGD or EAC (126 [88.7%] men; mean [SD] age, 66.0 [12.1] years; 142 [100%] white), 37 were HPV positive and 105 were HPV negative. No association with disease-free survival was noted for pRb, CD1, Ki-67, and MCM2. In regard to overall survival, only low expression of CD1 had a favorable prognosis (hazard ratio [HR], 0.53; 95% CI, 0.30-0.95; adjusted P = .03). All the biomarkers stratified by HPV status showed significant associations with survival. Patients with HPV-positive, low-expression pRb esophageal tumors were associated with a significantly improved disease-free survival compared with the HPV-negative, high-expression Rb tumors (HR, 0.33; 95% CI, 0.12-0.93; adjusted P = .04). Similarly, HPV-positive, low-expression CD1 was associated with a significantly favorable disease-free survival (HR, 0.26; 95% CI, 0.09-0.76; adjusted P = .01), as was HPV-positive, high-expression MCM2 (HR, 0.27; 95% CI, 0.09-0.78; adjusted P = .02). In regard to overall survival, HPV was significantly associated only with low CD1 (HR, 0.38; 95% CI, 0.15-0.94; adjusted P = .04). Conclusions and Relevance: This study's findings suggest that low expression of CD1 appears to be an independent prognostic marker in Barrett HGD and EAC. Human papillomavirus positivity in combination with pRb, CD1, MCM2, and Ki-67 was associated with a survival benefit in esophageal tumors. These findings suggest the possibility of personalization of therapy for Barrett HGD and EAC based on viral status

Efficacy and safety of subcutaneous tocilizumab in rheumatoid arthritis over 1 year: a UK real-world, open-label study

Objective. The ACT-MOVE study assessed the real-world efficacy and safety of s.c. tocilizumab (TCZSC), provided as monotherapy or in combination with conventional synthetic DMARDs (csDMARDs) over 1 year, in patients with RA and an inadequate response to csDMARD therapy and/or first TNF inhibitor. Methods. In this UK multicentre, open-label phase IIIb study, patients received TCZ-SC 162 mg once weekly for 52 weeks as monotherapy or with csDMARDs. Efficacy and safety were evaluated at baseline, weeks 2 and 4 and every 4 weeks thereafter up to week 52. Results. Of 161 patients who received at least one dose of TCZ-SC, 21 (13.0%) received TCZ-SC alone and 140 (87.0%) TCZ-SC with a csDMARD(s). From baseline to week 52, there was a mean decrease in DAS28-ESR score among all patients (!3.68), and within monotherapy (!3.75) and combination therapy (!3.67) groups. The proportion of patients who achieved DAS28 clinical remission (DAS28-ESR <2.6) at week 52 was 75.4% (95% CI 66.8, 82.8). At the same time point, "80% of patients who remained on TCZ-SC achieved DAS28 clinical remission or had low disease activity (DAS28-ESR "2.6 and #3.2). Overall, 6.2% of patients had at least one serious adverse event (10.2/ 100 patient-years), and there was one death; 11.2% of patients discontinued owing to adverse events. Conclusion. TCZ-SC was effective and tolerated in a real-world setting over 1 year. The efficacy of TCZ-SC was similar whether given as monotherapy or with csDMARDs; its safety profile was consistent with that previously establishe

Effects of short-term treatment with atorvastatin in smokers with asthma - a randomized controlled trial

&lt;b&gt;Background&lt;/b&gt; The immune modulating properties of statins may benefit smokers with asthma. We tested the hypothesis that short-term treatment with atorvastatin improves lung function or indices of asthma control in smokers with asthma.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Methods&lt;/b&gt; Seventy one smokers with mild to moderate asthma were recruited to a randomized double-blind parallel group trial comparing treatment with atorvastatin (40 mg per day) versus placebo for 4 weeks. After 4 weeks treatment inhaled beclometasone (400 ug per day) was added to both treatment arms for a further 4 weeks. The primary outcome was morning peak expiratory flow after 4 weeks treatment. Secondary outcome measures included indices of asthma control and airway inflammation.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Results&lt;/b&gt; At 4 weeks, there was no improvement in the atorvastatin group compared to the placebo group in morning peak expiratory flow [-10.67 L/min, 95% CI -38.70 to 17.37, p=0.449], but there was an improvement with atorvastatin in asthma quality of life score [0.52, 95% CI 0.17 to 0.87 p=0.005]. There was no significant improvement with atorvastatin and inhaled beclometasone compared to inhaled beclometasone alone in outcome measures at 8 weeks.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Conclusions&lt;/b&gt; Short-term treatment with atorvastatin does not alter lung function but may improve asthma quality of life in smokers with mild to moderate asthma. Clinicaltrials.gov identifier: NCT0046382

Genetically Raised Circulating Bilirubin Levels and Risk of Ten Cancers: A Mendelian Randomization Study

Bilirubin, an endogenous antioxidant, may play a protective role in cancer development. We applied two-sample Mendelian randomization to investigate whether genetically raised bilirubin levels are causally associated with the risk of ten cancers (pancreas, kidney, endometrium, ovary, breast, prostate, lung, Hodgkin's lymphoma, melanoma, and neuroblastoma). The number of cases and their matched controls of European descent ranged from 122,977 and 105,974 for breast cancer to 1200 and 6417 for Hodgkin's lymphoma, respectively. A total of 115 single-nucleotide polymorphisms (SNPs) associated (p < 5 × 10-8) with circulating total bilirubin, extracted from a genome-wide association study in the UK Biobank, were used as instrumental variables. One SNP (rs6431625) in the promoter region of the uridine-diphosphoglucuronate glucuronosyltransferase1A1 (UGT1A1) gene explained 16.9% and the remaining 114 SNPs (non-UGT1A1 SNPs) explained 3.1% of phenotypic variance in circulating bilirubin levels. A one-standarddeviation increment in circulating bilirubin (≈ 4.4 µmol/L), predicted by non-UGT1A1 SNPs, was inversely associated with risk of squamous cell lung cancer and Hodgkin's lymphoma (odds ratio (OR) 0.85, 95% confidence interval (CI) 0.73-0.99, P 0.04 and OR 0.64, 95% CI 0.42-0.99, p 0.04, respectively), which was confirmed after removing potential pleiotropic SNPs. In contrast, a positive association was observed with the risk of breast cancer after removing potential pleiotropic SNPs (OR 1.12, 95% CI 1.04-1.20, p 0.002). There was little evidence for robust associations with the other seven cancers investigated. Genetically raised bilirubin levels were inversely associated with risk of squamous cell lung cancer as well as Hodgkin's lymphoma and positively associated with risk of breast cancer. Further studies are required to investigate the utility of bilirubin as a low-cost clinical marker to improve risk prediction for certain cancers

A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing

Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of the biological events that govern the development and progression of human diseases, and the exploration of the mechanisms of survival, drug-resistance and virulence of pathogens. Next-generation sequencing (NGS) technologies are contributing to a massive expansion of transcriptomics in all fields and are reducing the cost, time and performance barriers presented by conventional approaches. However, bioinformatic tools for the analysis of the sequence data sets produced by these technologies can be daunting to researchers with limited or no expertise in bioinformatics. Here, we constructed a semi-automated, bioinformatic workflow system, and critically evaluated it for the analysis and annotation of large-scale sequence data sets generated by NGS. We demonstrated its utility for the exploration of differences in the transcriptomes among various stages and both sexes of an economically important parasitic worm (Oesophagostomum dentatum) as well as the prediction and prioritization of essential molecules (including GTPases, protein kinases and phosphatases) as novel drug target candidates. This workflow system provides a practical tool for the assembly, annotation and analysis of NGS data sets, also to researchers with a limited bioinformatic expertise. The custom-written Perl, Python and Unix shell computer scripts used can be readily modified or adapted to suit many different applications. This system is now utilized routinely for the analysis of data sets from pathogens of major socio-economic importance and can, in principle, be applied to transcriptomics data sets from any organism

A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing

Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of the biological events that govern the development and progression of human diseases, and the exploration of the mechanisms of survival, drug-resistance and virulence of pathogens. Next-generation sequencing (NGS) technologies are contributing to a massive expansion of transcriptomics in all fields and are reducing the cost, time and performance barriers presented by conventional approaches. However, bioinformatic tools for the analysis of the sequence data sets produced by these technologies can be daunting to researchers with limited or no expertise in bioinformatics. Here, we constructed a semi-automated, bioinformatic workflow system, and critically evaluated it for the analysis and annotation of large-scale sequence data sets generated by NGS. We demonstrated its utility for the exploration of differences in the transcriptomes among various stages and both sexes of an economically important parasitic worm (Oesophagostomum dentatum) as well as the prediction and prioritization of essential molecules (including GTPases, protein kinases and phosphatases) as novel drug target candidates. This workflow system provides a practical tool for the assembly, annotation and analysis of NGS data sets, also to researchers with a limited bioinformatic expertise. The custom-written Perl, Python and Unix shell computer scripts used can be readily modified or adapted to suit many different applications. This system is now utilized routinely for the analysis of data sets from pathogens of major socio-economic importance and can, in principle, be applied to transcriptomics data sets from any organism

Global patterns and environmental controls of perchlorate and nitrate co-occurrence in arid and semi-arid environments

Natural perchlorate (ClO4-) is of increasing interest due to its wide-spread occurrence on Earth and Mars, yet little information exists on the relative abundance of ClO4- compared to other major anions, its stability, or long-term variations in production that may impact the observed distributions. Our objectives were to evaluate the occurrence and fate of ClO4- in groundwater and soils/caliche in arid and semi-arid environments (southwestern United States, southern Africa, United Arab Emirates, China, Antarctica, and Chile) and the relationship of ClO4- to the more well-studied atmospherically deposited anions NO3- and Cl- as a means to understand the prevalent processes that affect the accumulation of these species over various time scales. ClO4- is globally distributed in soil and groundwater in arid and semi-arid regions on Earth at concentrations ranging from 10-1 to 106 µg/kg. Generally, the ClO4- concentration in these regions increases with aridity index, but also depends on the duration of arid conditions. In many arid and semi-arid areas, NO3- and ClO4- co-occur at molar ratios (NO3-/ClO4-) that vary between ~104 and 105. We hypothesize that atmospheric deposition ratios are largely preserved in hyper-arid areas that support little or no biological activity (e.g. plants or bacteria), but can be altered in areas with more active biological processes including N2 fixation, N mineralization, nitrification, denitrification, and microbial ClO4- reduction, as indicated in part by NO3- isotope data. In contrast, much larger ranges of Cl-/ClO4- and Cl-/NO3- ratios indicate Cl- varies independently from both ClO4- and NO3-. The general lack of correlation between Cl- and ClO4- or NO3- implies that Cl- is not a good indicator of co-deposition and should be used with care when interpreting oxyanion cycling in arid systems. The Atacama Desert appears to be unique compared to all other terrestrial locations having a NO3-/ClO4- molar ratio ~103. The relative enrichment in ClO4- compared to Cl- or NO3- and unique isotopic composition of Atacama ClO4- may reflect either additional in-situ production mechanism(s) or higher relative atmospheric production rates in that specific region or in the geological past. Elevated concentrations of ClO4- reported on the surface of Mars, and its enrichment with respect to Cl- and NO3-, could reveal important clues regarding the climatic, hydrologic, and potentially biologic evolution of that planet. Given the highly conserved ratio of NO3-/ClO4- in non-biologically active areas on Earth, it may be possible to use alterations of this ratio as a biomarker on Mars and for interpreting major anion cycles and processes on both Mars and Earth, particularly with respect to the less-conserved NO3- pool terrestrially

Global patterns and environmental controls of perchlorate and nitrate co-occurrence in arid and semi-arid environments

Natural perchlorate (ClO4-) is of increasing interest due to its wide-spread occurrence on Earth and Mars, yet little information exists on the relative abundance of ClO4- compared to other major anions, its stability, or long-term variations in production that may impact the observed distributions. Our objectives were to evaluate the occurrence and fate of ClO4- in groundwater and soils/caliche in arid and semi-arid environments (southwestern United States, southern Africa, United Arab Emirates, China, Antarctica, and Chile) and the relationship of ClO4- to the more well-studied atmospherically deposited anions NO3- and Cl- as a means to understand the prevalent processes that affect the accumulation of these species over various time scales. ClO4- is globally distributed in soil and groundwater in arid and semi-arid regions on Earth at concentrations ranging from 10-1 to 106 µg/kg. Generally, the ClO4- concentration in these regions increases with aridity index, but also depends on the duration of arid conditions. In many arid and semi-arid areas, NO3- and ClO4- co-occur at molar ratios (NO3-/ClO4-) that vary between ~104 and 105. We hypothesize that atmospheric deposition ratios are largely preserved in hyper-arid areas that support little or no biological activity (e.g. plants or bacteria), but can be altered in areas with more active biological processes including N2 fixation, N mineralization, nitrification, denitrification, and microbial ClO4- reduction, as indicated in part by NO3- isotope data. In contrast, much larger ranges of Cl-/ClO4- and Cl-/NO3- ratios indicate Cl- varies independently from both ClO4- and NO3-. The general lack of correlation between Cl- and ClO4- or NO3- implies that Cl- is not a good indicator of co-deposition and should be used with care when interpreting oxyanion cycling in arid systems. The Atacama Desert appears to be unique compared to all other terrestrial locations having a NO3-/ClO4- molar ratio ~103. The relative enrichment in ClO4- compared to Cl- or NO3- and unique isotopic composition of Atacama ClO4- may reflect either additional in-situ production mechanism(s) or higher relative atmospheric production rates in that specific region or in the geological past. Elevated concentrations of ClO4- reported on the surface of Mars, and its enrichment with respect to Cl- and NO3-, could reveal important clues regarding the climatic, hydrologic, and potentially biologic evolution of that planet. Given the highly conserved ratio of NO3-/ClO4- in non-biologically active areas on Earth, it may be possible to use alterations of this ratio as a biomarker on Mars and for interpreting major anion cycles and processes on both Mars and Earth, particularly with respect to the less-conserved NO3- pool terrestrially