The co-evolution of the genome and epigenome in colorectal cancer.

Colorectal malignancies are a leading cause of cancer-related death1 and have undergone extensive genomic study2,3. However, DNA mutations alone do not fully explain malignant transformation4-7. Here we investigate the co-evolution of the genome and epigenome of colorectal tumours at single-clone resolution using spatial multi-omic profiling of individual glands. We collected 1,370 samples from 30 primary cancers and 8 concomitant adenomas and generated 1,207 chromatin accessibility profiles, 527 whole genomes and 297 whole transcriptomes. We found positive selection for DNA mutations in chromatin modifier genes and recurrent somatic chromatin accessibility alterations, including in regulatory regions of cancer driver genes that were otherwise devoid of genetic mutations. Genome-wide alterations in accessibility for transcription factor binding involved CTCF, downregulation of interferon and increased accessibility for SOX and HOX transcription factor families, suggesting the involvement of developmental genes during tumourigenesis. Somatic chromatin accessibility alterations were heritable and distinguished adenomas from cancers. Mutational signature analysis showed that the epigenome in turn influences the accumulation of DNA mutations. This study provides a map of genetic and epigenetic tumour heterogeneity, with fundamental implications for understanding colorectal cancer biology.

Phenotypic plasticity and genetic control in colorectal cancer evolution.

Genetic and epigenetic variation, together with transcriptional plasticity, contribute to intratumour heterogeneity1. The interplay of these biological processes and their respective contributions to tumour evolution remain unknown. Here we show that intratumour genetic ancestry only infrequently affects gene expression traits and subclonal evolution in colorectal cancer (CRC). Using spatially resolved paired whole-genome and transcriptome sequencing, we find that the majority of intratumour variation in gene expression is not strongly heritable but rather 'plastic'. Somatic expression quantitative trait loci analysis identified a number of putative genetic controls of expression by cis-acting coding and non-coding mutations, the majority of which were clonal within a tumour, alongside frequent structural alterations. Consistently, computational inference on the spatial patterning of tumour phylogenies finds that a considerable proportion of CRCs did not show evidence of subclonal selection, with only a subset of putative genetic drivers associated with subclone expansions. Spatial intermixing of clones is common, with some tumours growing exponentially and others only at the periphery. Together, our data suggest that most genetic intratumour variation in CRC has no major phenotypic consequence and that transcriptional plasticity is, instead, widespread within a tumour.

Humanized Transgenic Mice Are Resistant to Chronic Wasting Disease Prions From Norwegian Reindeer and Moose.

Chronic wasting disease (CWD) is the transmissible spongiform encephalopathy or prion disease affecting cervids. In 2016, the first cases of CWD were reported in Europe in Norwegian wild reindeer and moose. The origin and zoonotic potential of these new prion isolates remain unknown. In this study to investigate zoonotic potential we inoculated brain tissue from CWD-infected Norwegian reindeer and moose into transgenic mice overexpressing human prion protein. After prolonged postinoculation survival periods no evidence for prion transmission was seen, suggesting that the zoonotic potential of these isolates is low.

COVID-19 pandemic and tourism: The impact of health risk perception and intolerance of uncertainty on travel intentions.

Understanding tourist behavior during and after major tourism crises is essential to help destinations recover. The COVID-19 pandemic - a period of uncertainty and risk - makes it relevant to assess factors that influence travel intentions. There has been little research on tourist behavior during health crises and, in particular, on perceived health risk and uncertainty effects on travel intentions. This study was carried out at the beginning of the pandemic in Brazil and aims to investigate the role of health risk perception and intolerance of uncertainty on travel intentions for 2020 and 2021. We applied an online survey to 1150 Brazilian participants from April to May 2020. Our findings indicate that perceived COVID-19 severity, perceived probability of infection, and expected duration of the pandemic are significant predictors of travel intentions for both years. This paper contributes to a deeper understanding of crisis-resistant tourists' characteristics and provides insights for destinations' recovery.

High-level mosaic monosomy 21 in a 13-year-old girl: Case report and review of the literature.

Monosomy 21 is an exceedingly rare and fatal chromosomal anomaly. Mosaic monosomy 21, however, can be observed in living patients. There have been discussions on whether there are liveborn cases with true mosaic full monosomy 21. Here, we report the case of a 13-year-old patient with mosaic full monosomy 21 who presented with postnatal microcephaly, low weight, facial dysmorphisms, developmental delay, and severe intellectual disability. To the best of our knowledge, this is the oldest patient with mosaic full monosomy 21 described so far and the first reported in Brazil.

4-hydroxy-2-alkenals in foods: a review on risk assessment, analytical methods, formation, occurrence, mitigation and future challenges.

Undoubtedly, significant advances were performed concerning 4-hydroxy-2-alkenals research on foods, and their formation by double oxidation of polyunsaturated fatty acids. But further studies are still needed, especially on their occurrence in foods enriched with n-3 and n-6 fatty acids, as well as in foods for infants and processed foods. Major factors concerning the formation of 4-hydroxy-2-alkenals were discussed, namely the influence of fatty acids composition, time/temperature, processing conditions, salt, among others. Regarding mitigation, the most effective strategies are adding phenolic extracts to foods matrices, as well as other antioxidants, such as vitamin E. Exposure assessment studies revealed 4-hydroxy-2-alkenals values that could not be considered a risk for human health. However, these toxic compounds remain unaltered after digestion and can easily reach the systemic circulation. Therefore, it is crucial to develop in vivo research, with the inclusion of the colon phase, as well as, cell membranes of the intestinal epithelium. In conclusion, according to our review it is possible to eliminate or effectively decrease 4-hydroxy-2-alkenals in foods using simple and economic practices.

Opuntia ficus-indica (L.) Mill.: A Multi-Benefit Potential to Be Exploited.

Consumer interest in foods with enhanced nutritional quality has increased in recent years. The nutritional and bioactive characterization of fruits and their byproducts, as well as their use in the formulation of new food products, is advisable, contributing to decrease the global concerns related to food waste and food security. Moreover, the compounds present in these raw materials and the study of their biological properties can promote health and help to prevent some chronic diseases. Opuntia ficus-indica (L.) Mill. (prickly pear) is a plant that grows wild in the arid and semi-arid regions of the world, being a food source for ones and a potential for others, but not properly valued. This paper carries out an exhaustive review of the scientific literature on the nutritional composition and bioactive compounds of prickly pear and its constituents, as well as its main biological activities and applications. It is a good source of dietary fiber, vitamins and bioactive compounds. Many of its natural compounds have interesting biological activities such as anti-inflammatory, hypoglycemic and antimicrobial. The antioxidant power of prickly pear makes it a good candidate as an ingredient of new food products with fascinating properties for health promotion and/or to be used as natural extracts for food, pharmaceutic or cosmetic applications. In addition, it could be a key player in food security in many arid and semi-arid regions of the world, where there are often no more plants.

PEOPLE: PatiEnt prOstate samPLes for rEsearch, a tissue collection pathway utilizing magnetic resonance imaging data to target tumor and benign tissue in fresh radical prostatectomy specimens.

BACKGROUND: Over 1 million men are diagnosed with prostate cancer each year worldwide, with a wide range of research programs requiring access to patient tissue samples for development of improved diagnoses and treatments. A random sampling of prostate tissue is sufficient for certain research studies; however, there is growing research need to target areas of the aggressive tumor as fresh tissue. Here we set out to develop a new pathway "PEOPLE: PatiEnt prOstate samPLes for rEsearch" to collect high-quality fresh tissue for research use, using magnetic resonance imaging (MRI) to target areas of tumor and benign tissue. METHODS: Prostate tissue was sampled following robotic radical prostatectomy, using MRI data to target areas of benign and tumor tissue. Initially, 25 cases were sampled using MRI information from clinical notes. A further 59 cases were sampled using an optimized method that included specific MRI measurements of tumor location along with additional exclusion criteria. All cases were reviewed in batches with detailed clinical and histopathological data recorded. For one subset of samples, DNA was extracted and underwent quality control. Ex vivo culture was carried out using the gelatin sponge method for an additional subset. RESULTS: Tumor was successfully fully or partially targeted in 64% of the initial cohort and 70% of the optimized cohort. DNA of high quality and concentration was isolated from 39 tumor samples, and ex vivo culture was successfully carried out in three cases with tissue morphology, proliferation, and apoptosis remaining comparable before and after 72 hours culture. CONCLUSION: Here we report initial data from the PEOPLE pathway; using a method for targeting areas of tumor within prostate samples using MRI. This method operates alongside the standard clinical pathway and minimizes additional input from surgical, radiological, and pathological teams, while preserving surgical margins and diagnostic tissue.

Overview of Brazilian Requirements for Therapeutic Equivalence of Orally Inhaled and Nasal Drug Products.

Brazil has established a framework for provision of generic pharmaceuticals including for orally inhaled and nasal drug products (OINDP) to its populace. This includes the development of guidelines or "resolutions" and normative instructions describing the Brazilian medicines agency's (Anvisa) expectations for demonstrating OINDP therapeutic equivalence. The Anvisa regulatory framework for OINDP therapeutic equivalence, challenges, and comparisons with the US Food and Drug Administration and European Medicines Agency approaches are assessed and discussed.

Overexpression of endothelin B receptor in glioblastoma: a prognostic marker and therapeutic target?

BACKGROUND: Glioblastoma (GBM) is the most common malignant brain tumor with median survival of 12-15 months. Owing to uncertainty in clinical outcome, additional prognostic marker(s) apart from existing markers are needed. Since overexpression of endothelin B receptor (ETBR) has been demonstrated in gliomas, we aimed to test whether ETBR is a useful prognostic marker in GBM and examine if the clinically available endothelin receptor antagonists (ERA) could be useful in the disease treatment. METHODS: Data from The Cancer Genome Atlas and the Gene Expression Omnibus database were analyzed to assess ETBR expression. For survival analysis, glioblastoma samples from 25 Swedish patients were immunostained for ETBR, and the findings were correlated with clinical history. The druggability of ETBR was assessed by protein-protein interaction network analysis. ERAs were analyzed for toxicity in in vitro assays with GBM and breast cancer cells. RESULTS: By bioinformatics analysis, ETBR was found to be upregulated in glioblastoma patients, and its expression levels were correlated with reduced survival. ETBR interacts with key proteins involved in cancer pathogenesis, suggesting it as a druggable target. In vitro viability assays showed that ERAs may hold promise to treat glioblastoma and breast cancer. CONCLUSIONS: ETBR is overexpressed in glioblastoma and other cancers and may be a prognostic marker in glioblastoma. ERAs may be useful for treating cancer patients.

25 years of European Union (EU) quality schemes for agricultural products and foodstuffs across EU Member States.

Consumers are increasingly turning their attention to the quality and origin of products that they consume. European Union (EU) quality schemes are associated with a label, which was introduced to allow consumers to perform an informed choice and to protect producers from unfair practices. This present study provides an overview of the last 25 years of EU quality schemes [Protected Designations of Origin (PDO), Protected Geographical Indications (PGI) and Traditional Specialities Guaranteed (TSG)] on agricultural products and foodstuffs across the 28 EU Member States. According to the results, it was possible to conclude that Southern European countries have the highest number of registered products. The most used EU quality scheme is PGI, followed by PDO. Concerning the analysis of the evolution in the last 25 years, the number of registered products among EU Member States has increased significantly. The fruit, vegetables and cereals (fresh or processed) category is the one that accounts for the highest percentage (26.8%) of registered products, followed by cheeses and meat products (cooked, salted, smoked) categories, with 17.2% and 13.5%, respectively. Further investigations should address consumer preferences, knowledge and attitudes, especially Northern European countries with a lower number of registered products. Moreover, the investigation and registration of products should be encouraged among all EU Member States to allow the maintenance of important elements of the history, culture and heritage of the local areas, regions and countries. © 2017 Society of Chemical Industry.

Human cytomegalovirus microRNAs are carried by virions and dense bodies and are delivered to target cells.

Human cytomegalovirus (HCMV) infection results in the production of virions, dense bodies (DBs) and non-infectious enveloped particles, all of which incorporate proteins and RNAs that can be transferred to host cells. Here, we investigated whether virions and DBs also carry microRNAs (miRNAs) and assessed their delivery and functionality in cells. Human lung fibroblasts (MRC-5) were infected with the HCMV strain AD169, and conditioned cell culture medium was collected and centrifuged. The pellets were treated with RNase-ONE, and the virions and DBs were purified with a potassium tartrate-glycerol gradient and dialysed. The virions and DBs were incubated with micrococcal nuclease, DNA and RNA were extracted and then analysed with TaqMan PCR assays, while the proteins were examined with Western blots. To assess the delivery of miRNAs to cells and their functionality, virions and DBs were irradiated with UV light. The purity of the virions and DBs was confirmed by typical morphology, the presence of the structural protein pp65 and the HCMV genome, the ability to infect MRC-5 cells and the absence of the host genome. RNA analysis revealed the presence of 14 HCMV-encoded miRNAs (UL22A-5p, US25-1-5p, UL22A-3p, US5-2-3p, UL112-3p, US25-2-3p, US25-2-5p, US33-3p, US5-1, UL36-5p, US4-5p, UL36-3p, UL70-5p and US25-1-3p), HCMV immediate-early mRNA and long non-coding RNA2.7, moreover, two host-encoded miRNAs (hsa-miR-218-5p and hsa-miR-21-5p) and beta-2-microglobulin RNA. UV-irradiated virions and DBs delivered viral miRNAs (US25-1-5p and UL112-3p) to the host cells, and miR-US25-1-5p was functional in a luciferase reporter assay. We conclude that virions and DBs carry miRNAs that are biologically functional and can be delivered to cells, which may affect cellular processes.

Analysis of Protein Composition and Bioactivity of Neoponera villosa Venom (Hymenoptera: Formicidae).

Ants cause a series of accidents involving humans. Such accidents generate different reactions in the body, ranging from a mild irritation at the bite site to anaphylactic shock, and these reactions depend on the mechanism of action of the venom. The study of animal venom is a science known as venomics. Through venomics, the composition of the venom of several ant species has already been characterized and their biological activities described. Thus, the aim of this study was to evaluate the protein composition and biological activities (hemolytic and immunostimulatory) of the venom of Neoponera villosa (N. villosa), an ant widely distributed in South America. The protein composition was evaluated by proteomic techniques, such as two-dimensional electrophoresis. To assess the biological activity, hemolysis assay was carried out and cytokines were quantified after exposure of macrophages to the venom. The venom of N. villosa has a profile composed of 145 proteins, including structural and metabolic components (e.g., tubulin and ATPase), allergenic and immunomodulatory proteins (arginine kinase and heat shock proteins (HSPs)), protective proteins of venom (superoxide dismutase (SOD) and catalase) and tissue degradation proteins (hyaluronidase and phospholipase A2). The venom was able to induce hemolysis in human erythrocytes and also induced release of both pro-inflammatory cytokines, as the anti-inflammatory cytokine release by murine macrophages. These results allow better understanding of the composition and complexity of N. villosa venom in the human body, as well as the possible mechanisms of action after the bite.

Human cytomegalovirus gene UL76 induces IL-8 expression through activation of the DNA damage response.

Human cytomegalovirus (HCMV), a ß-herpesvirus, has evolved many strategies to subvert both innate and adaptive host immunity in order to ensure its survival and propagation within the host. Induction of IL-8 is particularly important during HCMV infection as neutrophils, primarily attracted by IL-8, play a key role in virus dissemination. Moreover, IL-8 has a positive effect in the replication of HCMV. This work has identified an HCMV gene (UL76), with the relevant property of inducing IL-8 expression at both transcriptional and protein levels. Up-regulation of IL-8 by UL76 results from activation of the NF-kB pathway as inhibition of both IKK-ß activity or degradation of Ikßα abolishes the IL-8 induction and, concomitantly, expression of UL76 is associated with the translocation of p65 to the nucleus where it binds to the IL-8 promoter. Furthermore, the UL76-mediated induction of IL-8 requires ATM and is correlated with the phosphorylation of NEMO on serine 85, indicating that UL76 activates NF-kB pathway by the DNA Damage response, similar to the impact of genotoxic drugs. More importantly, a UL76 deletion mutant virus was significantly less efficient in stimulating IL-8 production than the wild type virus. In addition, there was a significant reduction of IL-8 secretion when ATM -/- cells were infected with wild type HCMV, thus, indicating that ATM is also involved in the induction of IL-8 by HCMV. In conclusion, we demonstrate that expression of UL76 gene induces IL-8 expression as a result of the DNA damage response and that both UL76 and ATM have a role in the mechanism of IL-8 induction during HCMV infection. Hence, this work characterizes a new role of the activation of DNA Damage response in the context of host-pathogen interactions.

Genetic variation of 12 X-chromosomal STR loci in an East Timor sample.

East Timor (República Democrática de Timor Leste) is a country with a population around 1 million inhabitants located in Southeast Asia and composed of 13 districts, including the eastern half of the Timor Island, Ataúro and Jaco islands, and the coastal enclave of Oecusse-Ambeno located in West Timor. Examples of the importance of X-chromosomal short tandem repeats (STRs) analysis include parentage identification, namely in cases involving father/daughter relationships, paternity in close relative deficiency cases without access to the putative father, maternity testing, and in rape or incest cases. In this study, 149 saliva samples were collected from unrelated individuals from East Timor and 12 X-chromosomal STRs genotyped using Investigator® Argus X-12 kit (Qiagen). A total of 13 alleles not included in Investigator Argus X-12 allelic ladder (off-ladder alleles) were found, four of which never reported (alleles 34.1 and 38.1 at DXS10134, allele 17.2 at DXS10074, and allele 28.1 at DXS10146). Allele 27.3 at DXS10101 and alleles 26, 28, and 29 at DXS10148 have already been observed in other populations but their frequencies are considerably higher in East Timor population. Allele frequencies and population statistic parameters were calculated for East Timor population and data contextualized in Southeast Asia/Pacific Region.

Restriction of HIV-1 replication in primary macrophages by IL-12 and IL-18 through the upregulation of SAMHD1.

Monocyte-derived macrophages (MDM) can polarize into different subsets depending on the environment and the activation signal to which they are submitted. Differentiation into macrophages allows HIV-1 strains to infect cells of the monocytic lineage. In this study, we show that culture of monocytes with a combination of IL-12 and IL-18 led to macrophage differentiation that was resistant to HIV-1 infection. In contrast, M-CSF-derived MDM were readily infected by HIV-1. When monocytes were differentiated in the presence of M-CSF and then further treated with IL-12/IL-18, cells became resistant to infection. The restriction on HIV-1 replication was not dependent on virus entry or coreceptor expression, as vesicular stomatitis virus-pseudotyped HIV-1 replication was also blocked by IL-12/IL-18. The HIV-1 restriction factor sterile α motif and HD domain-containing protein-1 (SAMHD1) was significantly overexpressed in IL-12/IL-18 MDM compared with M-CSF MDM, and degradation of SAMHD1 by RNA interference or viral-like particles carrying the lentiviral protein Vpx restored HIV-1 infectivity of IL-12/IL-18 MDM. SAMHD1 overexpression induced by IL-12/IL-18 was not dependent on IFN-γ. Thus, we conclude that IL-12 and IL-18 may contribute to the response against HIV-1 infection through the induction of restriction factors such as SAMHD1.

Effect of UV-C radiation on bioactive compounds of pineapple (Ananas comosus L. Merr.) by-products.

BACKGROUND: The industrial processing of pineapple generates a high quantity of by-products. To reduce the environmental impact of these by-products and the inherent cost of their treatment, it is important to characterise and valorise these products, converting them into high added value products. Ultra-violet radiation is one of the main sustainable sanitation techniques for fruits. Since this radiation can induce plant stress which can promote the biosynthesis of bioactive compounds, it is important to evaluate its effect in fruits. RESULTS: The amounts of vitamins (C and E) and carotenoids (α-carotene, ß-carotene, ß-cryptoxanthin, lutein, lycopene, neoxanthin, violaxanthin and zeaxanthin) in pineapple by-products (core and rind) were analysed before and after treatment with UV radiation. All treated and untreated pineapple by-products contained ß-carotene as the main carotenoid (rind, 2537-3225 µg; and core, 960-994 µg 100 g(-1) DW). Pineapple rind also contained lutein (288-297 µg 100 g(-1) DW) and α-carotene (89-126 µg 100 g(-1) DW). CONCLUSION: The results provide evidence of the potential of pineapple by-products as a source of bioactive compounds with antioxidant activity, which can be used by pharmaceutical, cosmetics and food industries. In addition, UV-C was shown to be a treatment that can add nutritional value to pineapple by-products.

Melon peel flour: utilization as a functional ingredient in bakery products.

Food by-products are a major concern with a direct impact on the economy, society, and environment. The valorisation of these by-products could be an advantageous approach to face the increase in food waste since it can compromise environmental health and food sustainability. On the other hand, this valorisation would allow the development of new food products with health benefits for the population. Cucumis melo L. is a highly consumed fruit all over the world since it has excellent sensory and nutritional qualities, being also a good source of bioactive compounds. However, its peel and seeds are usually discarded. The aim of this study was to evaluate the potential of melon peel flour as a functional ingredient for innovative food products. For that, two different formulations containing melon peel flour were developed (a biscuit and a muffin) by replacing a conventional flour (wheat flour) in different percentages (50% and 100%, respectively). The nutritional composition, total phenolic content, and antioxidant potential of the developed products were studied, showing a high content of fibre, high levels of phenolic compounds and good sensory acceptability. These results show that it is possible to enrich different foods with melon peel flour in order to improve their nutritional properties, contributing to improving public health, simultaneously valorising a usually rejected by-product, reducing food waste and the environmental impact.

Quantitative target engagement of RIPK1 in human whole blood via the cellular thermal shift assay for potential pre-clinical and clinical applications.

The cellular thermal shift assay (CETSA®) is a target engagement method widely used for preclinical characterization of small molecule compounds. CETSA® has been used for semi-quantitative readouts in whole blood with PBMC isolation, and quantitative, plate-based readouts using cell lines. However, there has been no quantitative evaluation of CETSA® in unprocessed human whole blood, which is preferred for clinical applications. Here we report two separate assay formats - Alpha CETSA® and MSD CETSA® - that require less than 100 µL of whole blood per sample without PBMC isolation. We chose RIPK1 as a proof-of-concept target and, by measuring engagement of seven different inhibitors, demonstrate high assay sensitivity and robustness. These quantitative CETSA® platforms enable possible applications in preclinical pharmacokinetic-pharmacodynamic studies, and direct target engagement with small molecules in clinical trials.

Comparison of leafy kale populations from Italy, Portugal, and Turkey for their bioactive compound content: phenolics, glucosinolates, carotenoids, and chlorophylls.

BACKGROUND: Kales are primitive leafy Brassica oleracea L. forms, widespread in local farming systems of several European countries and employed in the preparation of traditional recipes. Kales are also potential sources of healthy bioactive phytochemical components. The present study compared the bioactive compound content of kale populations from Italy, Portugal, and Turkey, either from local sources or grown in an experimental field. RESULTS: Total phenolics, glucosinolates (GLS), carotenoids, and chlorophylls were in the ranges 8310-38 110, 755-8580, 135-2354, and 1740-16,924 mg kg(-1) dry matter, respectively. On average, locally harvested samples showed a total GLS content about twice as high as populations from the experiment. Conversely, pigments were significantly more abundant in experimental than in local kales, owing to the higher soil fertility. Portuguese samples showed higher phenolic and GLS amounts than Italian and Turkish kales, whereas some of the Italian samples were the richest in carotenoids. CONCLUSION: This paper represented the first cross-country comparison of local kale accessions with respect to bioactive compound amounts. Both geographic origin and growing environment appeared to be remarkable and discriminating factors in determining bioactive levels in leafy kales, with possible effects on their health-promoting and sensorial attributes.