Search

Oncogene amplification on extrachromosomal DNA (ecDNA) drives the evolution of tumours and their resistance to treatment, and is associated with poor outcomes for patients with cancer1–6. At present, it is unclear whether ecDNA is a later manifestation of genomic instability, or whether it can be an early event in the transition from dysplasia to cancer. Here, to better understand the development of ecDNA, we analysed whole-genome sequencing (WGS) data from patients with oesophageal adenocarcinoma (EAC) or Barrett’s oesophagus. These data included 206 biopsies in Barrett’s oesophagus surveillance and EAC cohorts from Cambridge University. We also analysed WGS and histology data from biopsies that were collected across multiple regions at 2 time points from 80 patients in a case–control study at the Fred Hutchinson Cancer Center. In the Cambridge cohorts, the frequency of ecDNA increased between Barrett’s-oesophagus-associated early-stage (24%) and late-stage (43%) EAC, suggesting that ecDNA is formed during cancer progression. In the cohort from the Fred Hutchinson Cancer Center, 33% of patients who developed EAC had at least one oesophageal biopsy with ecDNA before or at the diagnosis of EAC. In biopsies that were collected before cancer diagnosis, higher levels of ecDNA were present in samples from patients who later developed EAC than in samples from those who did not. We found that ecDNAs contained diverse collections of oncogenes and immunomodulatory genes. Furthermore, ecDNAs showed increases in copy number and structural complexity at more advanced stages of disease. Our findings show that ecDNA can develop early in the transition from high-grade dysplasia to cancer, and that ecDNAs progressively form and evolve under positive selection.

Perspective on this Article from Single Nucleotide Polymorphism–Based Genome-Wide Chromosome Copy Change, Loss of Heterozygosity, and Aneuploidy in Barrett's Esophagus Neoplastic Progression

Neoplastic progression is an evolutionary process driven by the generation of clonal diversity and natural selection on that diversity within a neoplasm. We hypothesized that clonal diversity is associated with risk of progression to cancer. We obtained molecular data from a cohort of 239 participants with Barrett's esophagus, including microsatellite shifts and loss of heterozygosity, DNA content tetraploidy and aneuploidy, methylation, and sequence mutations. Using these data, we tested all major diversity measurement methods, including genetic divergence and entropy-based measures, to determine which measures are correlated with risk of progression to esophageal adenocarcinoma. We also tested whether the use of different sets of loci and alterations to define clones (e.g., selectively advantageous versus evolutionarily neutral) improved the predictive value of the diversity indices. All diversity measures were strong and highly significant predictors of progression (Cox proportional hazards model, P < 0.001). The type of alterations evaluated had little effect on the predictive value of most of the diversity measures. In summary, diversity measures are robust predictors of progression to cancer in this cohort. Cancer Prev Res; 3(11); 1388–97. ©2010 AACR.

ROC for combined T1+T2 data. The model was trained by repeatedly using a randomly drawn 2/3 of the combined T1+T2 data for training, and testing on the reserved 1/3 of the data. The average AUC of 10,000 ROC from the reserved test data is AUC=0.86.

Supplementary Fig 1C from Single Nucleotide Polymorphism–Based Genome-Wide Chromosome Copy Change, Loss of Heterozygosity, and Aneuploidy in Barrett's Esophagus Neoplastic Progression

Perspective on This Article from A Comprehensive Survey of Clonal Diversity Measures in Barrett's Esophagus as Biomarkers of Progression to Esophageal Adenocarcinoma

PDF file 2119K, Supplementary Table S1, Cohort characteristics. Supplementary Table S2, Mean SCA and mean percent of probes with SCA per biopsy in time windows. Supplementary Table S3, SCA with similar frequency in progressors and nonprogressors in time windows before cancer or final endoscopy. Supplementary Table S4, Regions of SCA with higher frequency in progressors than in nonprogressors in time windows before cancer or final endoscopy. Supplementary Figure S1, Schematic of endoscopic landmarks and image of epithelial isolation of Barrett's epithelium. Supplementary Figure S2. Balanced gain example. Supplementary Figure S3. Individual biopsy SCA. Supplementary Figure S4, Co-selection of SCA in individual biopsies

Supplementary Figures Legend from Single Nucleotide Polymorphism–Based Genome-Wide Chromosome Copy Change, Loss of Heterozygosity, and Aneuploidy in Barrett's Esophagus Neoplastic Progression

Supplementary Methods from Assessment of Esophageal Adenocarcinoma Risk Using Somatic Chromosome Alterations in Longitudinal Samples in Barrett's Esophagus

Population characteristics of study subjects.

All cancers are believed to arise by dynamic, stochastic somatic genomic evolution with genome instability, generation of diversity, and selection of genomic alterations that underlie multistage progression to cancer. Advanced esophageal adenocarcinomas have high levels of somatic copy number alterations. Barrett's esophagus is a risk factor for developing esophageal adenocarcinoma, and somatic chromosomal alterations (SCA) are known to occur in Barrett's esophagus. The vast majority (∼95%) of individuals with Barrett's esophagus do not progress to esophageal adenocarcinoma during their lifetimes, but a small subset develop esophageal adenocarcinoma, many of which arise rapidly even in carefully monitored patients without visible endoscopic abnormalities at the index endoscopy. Using a well-designed, longitudinal case-cohort study, we characterized SCA as assessed by single-nucleotide polymorphism arrays over space and time in 79 “progressors” with Barrett's esophagus as they approach the diagnosis of cancer and 169 “nonprogressors” with Barrett's esophagus who did not progress to esophageal adenocarcinoma over more than 20,425 person-months of follow-up. The genomes of nonprogressors typically had small localized deletions involving fragile sites and 9p loss/copy neutral LOH that generate little genetic diversity and remained relatively stable over prolonged follow-up. As progressors approach the diagnosis of cancer, their genomes developed chromosome instability with initial gains and losses, genomic diversity, and selection of SCAs followed by catastrophic genome doublings. Our results support a model of differential disease dynamics in which nonprogressor genomes largely remain stable over prolonged periods, whereas progressor genomes evolve significantly increased SCA and diversity within four years of esophageal adenocarcinoma diagnosis, suggesting a window of opportunity for early detection. Cancer Prev Res; 7(1); 114–27. ©2013 AACR.

Cancers detected at a late stage are often refractory to treatments and ultimately lethal. Early detection can significantly increase survival probability, but attempts to reduce mortality by early detection have frequently increased overdiagnosis of indolent conditions that do not progress over a lifetime. Study designs that incorporate biomarker trajectories in time and space are needed to distinguish patients who progress to an early cancer from those who follow an indolent course. Esophageal adenocarcinoma is characterized by evolution of punctuated and catastrophic somatic chromosomal alterations and high levels of overall mutations but few recurrently mutated genes aside from TP53. Endoscopic surveillance of Barrett's esophagus for early cancer detection provides an opportunity for assessment of alterations for cancer risk in patients who progress to esophageal adenocarcinoma compared with nonprogressors. We investigated 1,272 longitudinally collected esophageal biopsies in a 248 Barrett's patient case–cohort study with 20,425 person-months of follow-up, including 79 who progressed to early-stage esophageal adenocarcinoma. Cancer progression risk was assessed for total chromosomal alterations, diversity, and chromosomal region-specific alterations measured with single-nucleotide polymorphism arrays in biopsies obtained over esophageal space and time. A model using 29 chromosomal features was developed for cancer risk prediction (area under receiver operator curve, 0.94). The model prediction performance was robust in two independent esophageal adenocarcinoma sets and outperformed TP53 mutation, flow cytometric DNA content, and histopathologic diagnosis of dysplasia. This study offers a strategy to reduce overdiagnosis in Barrett's esophagus and improve early detection of esophageal adenocarcinoma and potentially other cancers characterized by punctuated and catastrophic chromosomal evolution. Cancer Prev Res; 8(9); 845–56. ©2015 AACR.

Supplementary Table S1.

Barrett's esophagus (BE) is a premalignant intermediate to esophageal adenocarcinoma, which develops in the context of chronic inflammation and exposure to bile and acid. We asked whether there might be common genomic alterations that could be identified as potential clinical biomarker(s) for BE by whole genome profiling. We detected copy number alterations and/or loss of heterozygosity at 56 fragile sites in 20 patients with premalignant BE. Chromosomal fragile sites are particularly sensitive to DNA breaks and are frequent sites of rearrangement or loss in many human cancers. Seventy-eight percent of all genomic alterations detected by array-CGH were associated with fragile sites. Copy number losses in early BE were observed at particularly high frequency at FRA3B (81%), FRA9A/C (71.4%), FRA5E (52.4%), and FRA 4D (52.4%), and at lower frequencies in other fragile sites, including FRA1K (42.9%), FRAXC (42.9%), FRA 12B (33.3%), and FRA16D (33.3%). Due to the consistency of the region of copy number loss, we were able to verify these results by quantitative PCR, which detected the loss of FRA3B and FRA16D, in 83% and 40% of early molecular stage BE patients, respectively. Loss of heterozygosity in these cases was confirmed through pyrosequencing at FRA3B and FRA16D (75% and 70%, respectively). Deletion and genomic instability at FRA3B and other fragile sites could thus be a biomarker of genetic damage in BE patients and a potential biomarker of cancer risk. Mol Cancer Res; 8(8); 1084–94. ©2010 AACR.

Supplementary Table 2 from Single Nucleotide Polymorphism–Based Genome-Wide Chromosome Copy Change, Loss of Heterozygosity, and Aneuploidy in Barrett's Esophagus Neoplastic Progression

Supplementary Table 1 from Single Nucleotide Polymorphism–Based Genome-Wide Chromosome Copy Change, Loss of Heterozygosity, and Aneuploidy in Barrett's Esophagus Neoplastic Progression

Supplementary Table 1. Missing rates for three risk factors by study site in BEAGESS Supplementary Table 2. Genome-wide significant single nucleotide polymorphisms (SNPs) selected for GxE analysis. Supplementary Table 3. Odds ratios (95% confidence intervals) for risk factors in the BEACON study according to the number of minor alleles (rs2687201 or rs10419226), using a combined BE/EA case group. Inverse probability weighting techniques were used to account for the missing risk factor data in the GXE interaction analysis. The weights were computed based on a logistic regression model fit to the indicator variable of the risk factor being observed, adjusting for case control status, region (Australia, Europe, North America), age, sex, SNP genotype, and four principal components. Supplementary Table 4. Odds ratios (95% confidence intervals) for risk factors in the BEACON study according to the number of minor alleles (rs2687201 or rs10419226), using a combined BE/EA case group. Supplementary Table 5. Thirteen imputed SNPs found to interact with GERD more significantly than rs2687201 in relation to risk of Barrett's esophagus (BE). Supplementary Table 6.1 Annotations for top SNPs identified in GxE analysis (ordered by interaction P value). Supplementary Table 6.2 Genotype-Tissue Expression (GTEx) eQTL analysis of top 14 SNPs identified.

Purpose: Chromosomal instability, as assessed by many techniques, including DNA content aneuploidy, loss of heterozygosity, and comparative genomic hybridization, has consistently been reported to be common in cancer and rare in normal tissues. Recently, a panel of chromosome instability biomarkers, including loss of heterozygosity and DNA content, has been reported to identify patients at high and low risk of progression from Barrett's esophagus (BE) to esophageal adenocarcinoma (EA), but required multiple platforms for implementation. Although chromosomal instability involving amplifications and deletions of chromosome regions have been observed in nearly all cancers, copy number alterations (CNA) in premalignant tissues have not been well characterized or evaluated in cohort studies as biomarkers of cancer risk.Experimental Design: We examined CNAs in 98 patients having either BE or EA using Bacterial Artificial Chromosome (BAC) array comparative genomic hybridization to characterize CNAs at different stages of progression ranging from early BE to advanced EA.Results: CNAs were rare in early stages (less than high-grade dysplasia) but were progressively more frequent and larger in later stages (high-grade dysplasia and EA), including high-level amplifications. The number of CNAs correlated highly with DNA content aneuploidy. Patients whose biopsies contained CNAs involving >70 Mbp were at increased risk of progression to DNA content abnormalities or EA (hazards ratio, 4.9; 95% confidence interval, 1.6-14.8; P = 0.0047), and the risk increased as more of the genome was affected.Conclusions: Genome-wide analysis of CNAs provides a common platform for the evaluation of chromosome instability for cancer risk assessment as well as for the identification of common regions of alteration that can be further studied for biomarker discovery.

Supplementary Data from Chromosomal Instability and Copy Number Alterations in Barrett's Esophagus and Esophageal Adenocarcinoma

Figure legends

Supplementary Figure S1. NIH Roadmap Epigenome Atlas characterization of genomic regions flanking rs2687201.

Background: Important risk factors for esophageal adenocarcinoma and its precursor, Barrett's esophagus, include gastroesophageal reflux disease, obesity, and cigarette smoking. Recently, genome-wide association studies have identified seven germline single-nucleotide polymorphisms (SNP) that are associated with risk of Barrett's esophagus and esophageal adenocarcinoma. Whether these genetic susceptibility loci modify previously identified exposure–disease associations is unclear.Methods: We analyzed exposure and genotype data from the BEACON Consortium discovery phase GWAS, which included 1,516 esophageal adenocarcinoma case patients, 2,416 Barrett's esophagus case patients, and 2,187 control participants. We examined the seven newly identified susceptibility SNPs for interactions with body mass index, smoking status, and report of weekly heartburn or reflux. Logistic regression models were used to estimate ORs for these risk factors stratified by SNP genotype, separately for Barrett's esophagus and esophageal adenocarcinoma.Results: The odds ratio for Barrett's esophagus associated with at least weekly heartburn or reflux varied significantly with the presence of at least one minor allele of rs2687201 (nominal P = 0.0005, FDR = 0.042). ORs (95% CIs) for weekly heartburn or reflux among participants with 0, 1, or 2 minor alleles of rs2687201 were 6.17 (4.91–7.56), 3.56 (2.85–4.44), and 3.97 (2.47–6.37), respectively. No statistically significant interactions were observed for smoking status and body mass index.Conclusion: Reflux symptoms are more strongly associated with Barrett's esophagus risk among persons homozygous for the major allele of rs2687201, which lies approximately 75 kb downstream of the transcription factor gene FOXP1.Impact: The novel gene–exposure interaction discovered in this study provides new insights into the etiology of esophageal adenocarcinoma. Cancer Epidemiol Biomarkers Prev; 24(11); 1739–47. ©2015 AACR.

This paper addresses the issue of pesticide loss from agriculture and its impact on the aquatic environment. Specifically, this study assesses the transport of the relatively water-soluble polar molluscicide compound metaldehyde in a small (14 km2) water abstraction catchment in Essex, southeast England during a 14-month period (January 2019–February 2020). A rise in metaldehyde concentrations was observed at all monitoring points, to varying extents, in the months of seasonal metaldehyde applications. The highest increases in metaldehyde concentrations (up to 0.05 µg L–1) across the catchment were observed in the autumn months and in December. These findings reinforce the mobile nature of the pesticide, with surface and field drain runoff likely to be the predominant mode of transfer to surface waters. The scale of individual sources of metaldehyde influx to the Ardleigh surface storage reservoir in the catchment showed that the highest contribution to the total flux to the reservoir was from water transferred from the adjacent River Colne catchment. Atmospheric deposition of metaldehyde followed a similar seasonal pattern to that observed in metaldehyde levels in surface water and field drain runoff, and in certain months accounted for a higher input than influx from surface runoff (May, August–October 2019). Monthly values of metaldehyde mass in the reservoir ranged from 27.7 to 47.4 g. An increase in mass was associated with elevated levels of flux from individual sources. Relatively stable levels of metaldehyde total mass in the reservoir are probably due to the aqueous solubility and decreased degradation rates of metaldehyde in the aquatic environment.

BACKGROUNDOncogenes are commonly amplified on extrachromosomal DNA (ecDNA) contributing to poor outcomes for patients. Currently, the chronology of ecDNA development is not known. We studied the origination and evolution of ecDNA in patients with Barrett’s esophagus (BE) who progressed to esophageal adenocarcinoma (EAC).METHODSWe analyzed whole-genome sequencing (WGS) data from a BE surveillance cohort and EAC patients at Cambridge University UK (n=206 patients). We also analyzed WGS data from biopsies taken at two time points from multiple sites in the esophagus from 80 patients enrolled in a case-control study at the Fred Hutchinson Cancer Center (FHCC) - 40 BE patients who progressed to EAC and 40 who did not.RESULTSecDNA was detected in 24% and 43% of BE patients with BE-associated early and late-stage EAC, respectively, in the Cambridge cross-sectional cohort. ecDNA was found in 33% of all FHCC BE patients who developed cancer, either prior to, or at EAC diagnosis. ecDNA was strongly associated with patients who developed cancer, in contrast with FHCC BE patients who did not progress (odds ratio, 18.8, CI – 2.3-152, p=3.3×10-4). ecDNAs were enriched for oncogenes and immunomodulatory genes and could be detected early in the transition from high-grade dysplasia to cancer and increased in copy number and complexity over time.CONCLUSIONSecDNAs can develop before a diagnosis of cancer in BE patients and are strongly selected for during the evolution to EAC. ecDNAs promote diverse oncogene and immunomodulatory gene amplification during EAC development and progression.

Soil ecosystem service (SES) approaches evidence the importance of soil for human well-being, contribute to improving dialogue between science and decision-making and encourage the translation of scientific results into public policies. Herein, through systematic review, we assess the state of the art of SES approaches in tropical regions. Through this review, 41 publications were identified; while most of these studies considered SES, a lack of a consistent framework to define SES was apparent. Most studies measured soil natural capital and processes, while only three studies undertook monetary valuation. Although the number of publications increased (from 1 to 41), between 2001 and 2019, the total number of publications for tropical regions is still small. Countries with the largest number of publications were Brazil (n = 8), Colombia (n = 6) and Mexico (n = 4). This observation emphasizes an important knowledge gap pertaining to SES approaches and their link to tropical regions. With global momentum behind SES approaches, there is an opportunity to integrate SES approaches into policy and practice in tropical regions. The use of SES evaluation tools in tropical regions could transform how land use decisions are informed, mitigating soil degradation and protecting the ecosystems that soil underpins. Made available in DSpace on 2021-04-01T02:26:10Z (GMT). No. of bitstreams: 1 Systematic-review-of-soil-ecosystem-services-2021.pdf: 968680 bytes, checksum: c21bd70cec854956f333a7af7e80d711 (MD5) Previous issue date: 2021

Farmland soils in China have been reported to be diffusely contaminated, Cd has been recognized as a significant contributor to this issue and biochars have been reported to be effective in mitigating soil Cd pollution. However, previous studies have shown contradictory outcomes. Furthermore, in general, laboratory experiments and unrealistically large amounts of biochar (>10 t/ha) have been used. In this study, three biochars: rice straw biochar (RS), pig manure biochar (PM) and rice husk biochar (RH) were produced from readily available farm residues and characterized. These were used in a field experiment, at low applications rates of 1.8 and 3.6 t/ha, with rape (Brassica campestris L.). Batch adsorption experiments indicated Cd adsorption in the order RS biochar > PM biochar > RH biochar. Field experiment indicated biochar amendments to slightly changes in soil pH and CEC; yet led to considerable and significant decreases in extractable Cd concentrations (reductions of: 43%-51% (PM), 29%-35% (RS) and 17%-19% (RH)). Reduced extractable Cd correlated with lower Cd concentrations in rape plants. PM and RS biochars were the most effective in decreasing Cd phytoaccumulation into edible parts of rape (>68% reduction). It is highlighted that biochars were produced using a pyrolysis unit with an output of 20 ton/yr. Thus, assuming a working application rate of 2 ton/ha, the pyrolysis unit could service 10 ha/yr. While at a modest scale, this research demonstrates the genuine reality of biochar-based remediation solutions to contribute to the mitigation of diffuse Cd contamination in some of China’s impaired farmland.

Background and aims: Incorporation of biochar into the soil sequesters C for millennia, but the concomitant effects on plant rhizodepositions and nutrient (e.g., nitrogen; N) trade-offs via interactions of heterotrophic microbiota, might offset this sequestration. Methods: Ryegrass (Lolium perenne L.) with and without biochar amendment were pulse labelled in a 13CO2 atmosphere and 15N fertilizer added. Ryegrass and soils were destructively sampled at 16 and 30 days after seedling emergence. Isotope analysis was coupled with MiSeq sequencing of bacterial (16s rRNA) and fungal (ITS) genes to identify the effect of biochar on the associated microbiota involved in 13C allocation into soil aggregates and promotion of 15N uptake by L. perenne. Results: Biochar increased root biomass and 15N uptake but decreased rhizodeposited-13C recovery from large and small macroaggregates (by 12–57% and 57–72%, respectively). These changes in 13C flow and 15N uptake were accompanied by an increase in microbial biomass, and enhanced negative correlations between bacteria and fungi. O2PLS indicated members of seventeen genera that were correlated with soil stabilization of rhizodeposits in soil and plant N-uptake. For instance, Xanthomonadales (Proteobacteria) and RB41 (Acidobacteria), previously reported to be plant growth promoting rhizobacteria, were found to be positively correlated with 15N uptake by L. perenne. Conclusions: Our research explored the genera associated with biochar-modified 15N uptake by Lolium perenne and photosynthate 13C allocation into soil aggregates. Future research with SIP is required to fully assess microbial turnover, the ubiquity of similar rhizosphere microbiota and their fundamental importance for sequestration in the plant-soil-microbe-biochar systems.

Metaldehyde, a widely used molluscicide, is one of the most commonly detected pesticides in aquatic environments in the UK. In this study, metaldehyde concentrations and fluxes in stream water over a ten-year period (2008-2018) are reported for the River Colne catchment (Essex, southeast England), and the influence of hydrological conditions and application regimes are assessed. In general, peaks in metaldehyde concentration in river water occasionally exceeded 0.25 μg L-1, and concentrations did not typically exceed the European Union Drinking Water Directive (EU DWD) regulatory limit of 0.1 μg L-1. Metaldehyde concentration peaks displayed a seasonal pattern. Metaldehyde concentrations during periods when the molluscicide was not applied to agricultural land (January, July) and during the spring-summer application period (February to June) were generally low (0.01-0.03 μg L-1). Peaks in metaldehyde concentration mainly occurred during the autumn-winter application season (August to December), and were typically associated with high intensity hydrological regimes (daily rainfall ≥10 mm; stream flow up to 18 m3 s-1). Where metaldehyde concentrations exceeded the EU DWD regulatory limit, this was short-lived. The annual flux at the top of the Colne catchment (0.2-0.6 kg a-1) tended to be lower than in the middle of the catchment (0.3-1.4 kg a-1), with maximum flux values observed at the bottom of the catchment (0.5-25.8 kg a-1). Metaldehyde losses from point of application to surface water varied between 0.01 and 0.25%, with a maximum of 1.18% (2012). Annual flux was primarily controlled by the annual precipitation and stream flow (R2 = 0.9) rather than annual metaldehyde use (kg active applied). Precipitation explained 37% and 81% of variability in metaldehyde concentration and flux, respectively. Annual ranges in metaldehyde concentration were greater in the years 2012 and 2014 with an overall reduction in the range of metaldehyde concentrations evident over the period 2015-2018. It is the expectation that metaldehyde concentrations in stream water will continue to decrease following the withdrawal of metaldehyde for outdoor use in the UK from March 2022.

Current carbon pricing and trading mechanisms, despite their efficacy in reducing GHG emissions from industry, will not be sufficient to achieve Net Zero targets. Current mechanisms that redress emissions are largely economic disincentives , in effect financial penalties for emitters. In order to attain Net Zero futures, financial incentives for activities that sequester carbon from the atmosphere are needed. Herein, we present the environmental and economic co-benefits of soil re-carbonization and justify support for soil carbon remuneration. With increasing momentum to develop green economies, and projected increases in carbon price, growth in the global carbon market is inevitable. The establishment of a soil-based carbon economy, within this emerging financial space, has the potential to deliver a paradigm shift that will accelerate climate change mitigation, and concurrently realize net gains for soil health and the delivery of soil ecosystem services. Pivotal to the emergence of a global soil carbon economy will be a consensus on certification instruments used for long-term soil carbon storage, and the development of robust institutional agreements and processes to facilitate soil carbon trading.

Arsenic (As) pollution remains a major threat to the quality of global soils and drinking water. The health effects of As pollution are often severe and have been largely reported across Asia and South America. This study investigated the possibility of using unmodified biochar derived from rice husk (RB) and aspen wood (WB) at 400 °C and 700 °C to enhance the precipitation of calcium/arsenic compounds for the removal of As(III) from solution. The approach was based on utilizing calcium to precipitate arsenic in solution and adding unmodified biochar to enhance the process. Using this approach, As(III) concentration in aqueous solution decreased by 58.1% when biochar was added, compared to 25.4% in the absence of biochar. Varying the pH from acidic to alkaline enabled an investigation into the pH dependent dynamics of the approach. Results indicated that significant precipitation was only possible at near neutral pH (i.e. pH = 6.5) where calcium arsenites (i.e. Ca(AsO2)2, and CaAsO2OH•½H2O) and arsenates (i.e. Ca5(AsO4)3OH) were precipitated and deposited as aggregates in the pores of biochars. Arsenite was only slightly precipitated under acidic conditions (pH = 4.5) while no arsenite was precipitated under alkaline conditions (pH = 9.5). Arsenite desorption from wood biochar was lowest at pH 6.5 indicating that wood biochar was able to retain a large quantity of the precipitates formed at pH 6.5 compared to pH 4.5 and pH 9.5. Given that the removal of As(III) from solution is often challenging and that biochar modification invites additional cost, the study demonstrated that low cost unmodified biochar can be effective in enhancing the removal of As(III) from the environment through Ca–As precipitation.

While the genomes of normal tissues undergo dynamic changes over time, little is understood about the temporal-spatial dynamics of genomes in premalignant tissues that progress to cancer compared to those that remain cancer-free. Here we use whole genome sequencing to contrast genomic alterations in 427 longitudinal samples from 40 patients with stable Barrett’s esophagus compared to 40 Barrett’s patients who progressed to esophageal adenocarcinoma (ESAD). We show the same somatic mutational processes were active in Barrett’s tissue regardless of outcome, with high levels of mutation, ESAD gene and focal chromosomal alterations, and similar mutational signatures. The critical distinction between stable Barrett’s versus those who progress to cancer is acquisition and expansion of TP53-/- cell populations having complex structural variants and high-level amplifications, which were detectable up to six years prior to a cancer diagnosis. These findings reveal the timing of common somatic genome dynamics in stable Barrett’s esophagus and define key genomic features specific to progression to esophageal adenocarcinoma, both of which are critical for cancer prevention and early detection strategies.

The organic matter was absent prior to planetesimal formation (4.6 Gyr) but at present abundant in planetary environments. The aim of this study was to combine information about the organic inventory of the Earth, which is accompanied by the evolution of life. A variety of available free energy sources, including geochemical energy, sunlight, oxygen and fire have supported life evolution. In the meantime these energy sources have mediated the diversity and complexity of living organisms and resulted in a concomitant increase in the diversity and complexity of organic matter, including microbial-, plant-, fire-, and human derived organics. The change of the diversity and complexity of organic matter (microbial-, plant-, fire- and human-derived organics) have in-return significantly influenced Earth’s carbon cycle, planetary climate and ecosystems. Overall, energy harnessing and conservation of life entwined and expanded the evolutional histories of life and organic molecules on the planet. Considering the key role of organics on the stability of the oxygen level of the atmosphere, temperature, the tectonic rise of continents, and global habitability, the changing characters of organics over geologic time had an important shaping influence on Earth’s geochemical cycles.

Previous Mendelian randomization (MR) studies on 25-hydroxyvitamin D (25(OH)D) and cancer have typically adopted a handful of variants and found no relationship between 25(OH)D and cancer; however, issues of horizontal pleiotropy cannot be reliably addressed. Using a larger set of variants associated with 25(OH)D (74 SNPs, up from 6 previously), we perform a unified MR analysis to re-evaluate the relationship between 25(OH)D and ten cancers. Our findings are broadly consistent with previous MR studies indicating no relationship, apart from ovarian cancers (OR 0.89; 95% C.I: 0.82 to 0.96 per 1 SD change in 25(OH)D concentration) and basal cell carcinoma (OR 1.16; 95% C.I.: 1.04 to 1.28). However, after adjustment for pigmentation related variables in a multivariable MR framework, the BCC findings were attenuated. Here we report that lower 25(OH)D is unlikely to be a causal risk factor for most cancers, with our study providing more precise confidence intervals than previously possible., Studies of the genetic association between vitamin D and cancer risk have typically been underpowered. Here the authors analyse this using Mendelian Randomisation with more than 70 vitamin D variants obtained from the UK Biobank and large-scale data from various consortia, confirming null associations between vitamin D and most cancers.

Contains fulltext : 229320.pdf (Publisher’s version ) (Closed access) BACKGROUND & AIMS: Esophageal adenocarcinoma (EA) and its premalignant lesion, Barrett's esophagus (BE), are characterized by a strong and yet unexplained male predominance (with a male-to-female ratio in EA incidence of up to 6:1). Genome-wide association studies (GWAS) have identified more than 20 susceptibility loci for these conditions. However, potential sex differences in genetic associations with BE/EA remain largely unexplored. METHODS: Given strong genetic overlap, BE and EA cases were combined into a single case group for analysis. These were compared with population-based controls. We performed sex-specific GWAS of BE/EA in 3 separate studies and then used fixed-effects meta-analysis to provide summary estimates for >9 million variants for male and female individuals. A series of downstream analyses were conducted separately in male and female individuals to identify genes associated with BE/EA and the genetic correlations between BE/EA and other traits. RESULTS: We included 6758 male BE/EA cases, 7489 male controls, 1670 female BE/EA cases, and 6174 female controls. After Bonferroni correction, our meta-analysis of sex-specific GWAS identified 1 variant at chromosome 6q11.1 (rs112894788, KHDRBS2-MTRNR2L9, P(BONF) = .039) that was statistically significantly associated with BE/EA risk in male individuals only, and 1 variant at chromosome 8p23.1 (rs13259457, PRSS55-RP1L1, P(BONF) = 0.057) associated, at borderline significance, with BE/EA risk in female individuals only. We also observed strong genetic correlations of BE/EA with gastroesophageal reflux disease in male individuals and obesity in female individuals. CONCLUSIONS: The identified novel sex-specific variants associated with BE/EA could improve the understanding of the genetic architecture of the disease and the reasons for the male predominance.

The low risk of progression of Barrett’s esophagus (BE) to esophageal adenocarcinoma can lead to over-diagnosis and over-treatment of BE patients. This may be addressed through a better understanding of the dynamics surrounding BE malignant progression. Although genetic diversity has been characterized as a marker of malignant development, it is still unclear how BE arises and develops. Here we uncover the evolutionary dynamics of BE at crypt and biopsy levels in eight individuals, including four patients that experienced malignant progression. We assay eight individual crypts and the remaining epithelium by SNP array for each of 6–11 biopsies over 2 time points per patient (358 samples in total). Our results indicate that most Barrett’s segments are clonal, with similar number and inferred rates of alterations observed for crypts and biopsies. Divergence correlates with geographical location, being higher near the gastro-esophageal junction. Relaxed clock analyses show that genomic instability precedes and is enhanced by genome doubling. These results shed light on the clinically relevant evolutionary dynamics of BE., Clonal dynamics of Barrett’s esophagus (BE) leading to cancer are poorly understood. Here, they report BE segments are clonal, have frequent mutations at the gastro-esophageal junction, genomic instability precedes genome doubling/clonal expansion, and a correlation between inter- and intra-biopsy genetic diversity.