Lung Cancer in Ever- and Never-Smokers: Findings from Multi-Population GWAS Studies.

BACKGROUND: Clinical, molecular, and genetic epidemiology studies displayed remarkable differences between ever- and never-smoking lung cancer. METHODS: We conducted a stratified multi-population (European, East Asian, and African descent) association study on 44,823 ever-smokers and 20,074 never-smokers to identify novel variants that were missed in the non-stratified analysis. Functional analysis including expression quantitative trait loci (eQTL) colocalization and DNA damage assays, and annotation studies were conducted to evaluate the functional roles of the variants. We further evaluated the impact of smoking quantity on lung cancer risk for the variants associated with ever-smoking lung cancer. RESULTS: Five novel independent loci, GABRA4, intergenic region 12q24.33, LRRC4C, LINC01088, and LCNL1 were identified with the association at two or three populations (P < 5 × 10-8). Further functional analysis provided multiple lines of evidence suggesting the variants affect lung cancer risk through excessive DNA damage (GABRA4) or cis-regulation of gene expression (LCNL1). The risk of variants from 12 independent regions, including the well-known CHRNA5, associated with ever-smoking lung cancer was evaluated for never-smokers, light-smokers (packyear ≤ 20), and moderate-to-heavy-smokers (packyear > 20). Different risk patterns were observed for the variants among the different groups by smoking behavior. CONCLUSIONS: We identified novel variants associated with lung cancer in only ever- or never-smoking groups that were missed by prior main-effect association studies. IMPACT: Our study highlights the genetic heterogeneity between ever- and never-smoking lung cancer and provides etiologic insights into the complicated genetic architecture of this deadly cancer.

Identification of genetically predicted DNA methylation markers associated with non-small cell lung cancer risk among 34,964 cases and 448,579 controls.

BACKGROUND: Although the associations between genetic variations and lung cancer risk have been explored, the epigenetic consequences of DNA methylation in lung cancer development are largely unknown. Here, the genetically predicted DNA methylation markers associated with non-small cell lung cancer (NSCLC) risk by a two-stage case-control design were investigated. METHODS: The genetic prediction models for methylation levels based on genetic and methylation data of 1595 subjects from the Framingham Heart Study were established. The prediction models were applied to a fixed-effect meta-analysis of screening data sets with 27,120 NSCLC cases and 27,355 controls to identify the methylation markers, which were then replicated in independent data sets with 7844 lung cancer cases and 421,224 controls. Also performed was a multi-omics functional annotation for the identified CpGs by integrating genomics, epigenomics, and transcriptomics and investigation of the potential regulation pathways. RESULTS: Of the 29,894 CpG sites passing the quality control, 39 CpGs associated with NSCLC risk (Bonferroni-corrected p ≤ 1.67 × 10-6 ) were originally identified. Of these, 16 CpGs remained significant in the validation stage (Bonferroni-corrected p ≤ 1.28 × 10-3 ), including four novel CpGs. Multi-omics functional annotation showed nine of 16 CpGs were potentially functional biomarkers for NSCLC risk. Thirty-five genes within a 1-Mb window of 12 CpGs that might be involved in regulatory pathways of NSCLC risk were identified. CONCLUSIONS: Sixteen promising DNA methylation markers associated with NSCLC were identified. Changes of the methylation level at these CpGs might influence the development of NSCLC by regulating the expression of genes nearby. PLAIN LANGUAGE SUMMARY: The epigenetic consequences of DNA methylation in lung cancer development are still largely unknown. This study used summary data of large-scale genome-wide association studies to investigate the associations between genetically predicted levels of methylation biomarkers and non-small cell lung cancer risk at the first time. This study looked at how well larotrectinib worked in adult patients with sarcomas caused by TRK fusion proteins. These findings will provide a unique insight into the epigenetic susceptibility mechanisms of lung cancer.

Immunomodulatory Effects of Natural Feed Additives for Meat Chickens.

Broiler chickens are increasingly kept in large numbers in intensive housing conditions that are stressful, potentially depleting the immune system. With the prohibition of the use of antibiotics in poultry feed spreading worldwide, it is necessary to consider the role of natural feed additives and antibiotic alternatives to stimulate the chickens' immune systems. We review the literature to describe phytogenic feed additives that have immunomodulatory benefits in broilers. We initially review the major active ingredients from plants, particularly flavonoids, resveratrol and humic acid, and then describe the major herbs, spices, and other plants and their byproducts that have immunomodulatory effects. The research reviewed demonstrates the effectiveness of many natural feed additives in improving the avian immune system and therefore broiler health. However, some, and perhaps all, additives have the potential to reduce immunocompetence if given in excessive amounts. Sometimes additives are more effective when given in combination. There is an urgent need to determine tolerance levels and optimum doses for additives deemed most suitable to replace antibiotics in the diet of broiler chickens. Effective replacement is most likely with readily available additives, such as olive oil byproducts, olive leaves and alfalfa. It is concluded that effective replacement of antibiotic function with plant-derived additives will be possible, but that further research is necessary to determine optimum doses.

Immune Infiltration in Tumor and Adjacent Non-Neoplastic Regions Codetermines Patient Clinical Outcomes in Early-Stage Lung Cancer.

INTRODUCTION: In recent years, the proportion of patients with NSCLC diagnosed at an early stage has increased continuously. METHODS: In this study, we analyzed samples and data collected from 119 samples from 67 early stage patients with NSCLC, including 52 pairs of tumor and adjacent non-neoplastic samples, and performed RNA-sequencing analysis with high sequencing depth. RESULTS: We found that immune-related genes were highly enriched among the differentially expressed genes and observed significantly higher inferred immune infiltration levels in adjacent non-neoplastic samples than in tumor samples. In survival analysis, the infiltration of certain immune cell types in tumor, but not adjacent non-neoplastic, samples were associated with overall patient survival, and excitingly, the differential infiltration between paired samples (tumor minus non-neoplastic) was more prognostic than expression in either non-neoplastic or tumor tissues. We also performed B cell receptor (BCR) and T cell receptor (TCR) repertoire analysis and observed more BCR/TCR clonotypes and increased BCR clonality in tumor than in non-neoplastic samples. Finally, we carefully quantified the fraction of the five histologic subtypes in our adenocarcinoma samples and found that higher histologic pattern complexity was associated with higher immune infiltration and low TCR clonality in the tumor-proximal regions. CONCLUSIONS: Our results indicated significantly differential immune characteristics between tumor and adjacent non-neoplastic samples and suggested that the two regions provided complementary prognostic values in early-stage NSCLCs.

Mosaic Chromosomal Alterations Are Associated With Increased Lung Cancer Risk: Insight From the INTEGRAL-ILCCO Cohort Analysis.

INTRODUCTION: Mosaic chromosomal alterations (mCAs) detected in white blood cells represent a type of clonal hematopoiesis (CH) that is understudied compared with CH-related somatic mutations. A few recent studies indicated their potential link with nonhematological cancers, especially lung cancer. METHODS: In this study, we investigated the association between mCAs and lung cancer using the high-density genotyping data from the OncoArray study of INTEGRAL-ILCCO, the largest single genetic study of lung cancer with 18,221 lung cancer cases and 14,825 cancer-free controls. RESULTS: We identified a comprehensive list of autosomal mCAs, ChrX mCAs, and mosaic ChrY (mChrY) losses from these samples. Autosomal mCAs were detected in 4.3% of subjects, in addition to ChrX mCAs in 3.6% of females and mChrY losses in 9.6% of males. Multivariable logistic regression analysis indicated that the presence of autosomal mCAs in white blood cells was associated with an increased lung cancer risk after adjusting for key confounding factors, including age, sex, smoking status, and race. This association was mainly driven by a specific type of mCAs: copy-neutral loss of heterozygosity on autosomal chromosomes. The association between autosome copy-neutral loss of heterozygosity and increased risk of lung cancer was further confirmed in two major histologic subtypes, lung adenocarcinoma and squamous cell carcinoma. In addition, we observed a significant increase of ChrX mCAs and mChrY losses in smokers compared with nonsmokers and racial differences in certain types of mCA events. CONCLUSIONS: Our study established a link between mCAs in white blood cells and increased risk of lung cancer.

InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma.

INTRODUCTION: We are conducting a multicenter study to identify classifiers predictive of disease-specific survival in patients with primary melanomas. Here we delineate the unique aspects, challenges, and best practices for optimizing a study of generally small-sized pigmented tumor samples including primary melanomas of at least 1.05mm from AJTCC TNM stage IIA-IIID patients. We also evaluated tissue-derived predictors of extracted nucleic acids' quality and success in downstream testing. This ongoing study will target 1,000 melanomas within the international InterMEL consortium. METHODS: Following a pre-established protocol, participating centers ship formalin-fixed paraffin embedded (FFPE) tissue sections to Memorial Sloan Kettering Cancer Center for the centralized handling, dermatopathology review and histology-guided coextraction of RNA and DNA. Samples are distributed for evaluation of somatic mutations using next gen sequencing (NGS) with the MSK-IMPACTTM assay, methylation-profiling (Infinium MethylationEPIC arrays), and miRNA expression (Nanostring nCounter Human v3 miRNA Expression Assay). RESULTS: Sufficient material was obtained for screening of miRNA expression in 683/685 (99%) eligible melanomas, methylation in 467 (68%), and somatic mutations in 560 (82%). In 446/685 (65%) cases, aliquots of RNA/DNA were sufficient for testing with all three platforms. Among samples evaluated by the time of this analysis, the mean NGS coverage was 249x, 59 (18.6%) samples had coverage below 100x, and 41/414 (10%) failed methylation QC due to low intensity probes or insufficient Meta-Mixed Interquartile (BMIQ)- and single sample (ss)- Noob normalizations. Six of 683 RNAs (1%) failed Nanostring QC due to the low proportion of probes above the minimum threshold. Age of the FFPE tissue blocks (p<0.001) and time elapsed from sectioning to co-extraction (p = 0.002) were associated with methylation screening failures. Melanin reduced the ability to amplify fragments of 200bp or greater (absent/lightly pigmented vs heavily pigmented, p<0.003). Conversely, heavily pigmented tumors rendered greater amounts of RNA (p<0.001), and of RNA above 200 nucleotides (p<0.001). CONCLUSION: Our experience with many archival tissues demonstrates that with careful management of tissue processing and quality control it is possible to conduct multi-omic studies in a complex multi-institutional setting for investigations involving minute quantities of FFPE tumors, as in studies of early-stage melanoma. The study describes, for the first time, the optimal strategy for obtaining archival and limited tumor tissue, the characteristics of the nucleic acids co-extracted from a unique cell lysate, and success rate in downstream applications. In addition, our findings provide an estimate of the anticipated attrition that will guide other large multicenter research and consortia.

A Comparison of the Effects of Raw and Processed Amaranth Grain on Laying Hens' Performance, Egg Physicochemical Properties, Blood Biochemistry and Egg Fatty Acids.

In order to investigate the effects of using different levels of either raw or processed amaranth (Amaranthus hybridus chlorostachys) grain on performance productivity, egg physicochemical properties, blood biochemistry and egg fatty acids, a trial was conducted using 168 Hy-line W-36 laying hens (67 week of age) in a completely randomized design with seven treatments and six replications of four birds for eight weeks. The trial treatments included the control group receiving no amaranth and the test groups receiving 5, 10 and 15% of raw or autoclaved (120 °C for 5 min) amaranth grain based on dry matter. The results showed that the use of processed amaranth up to the level of five and ten percent of the diet compared to raw amaranth resulted in a better performance than the control group (p < 0.05). The consumption of amaranth decreased blood glucose, cholesterol and triglyceride of trial birds without having a negative effect on their health and blood antioxidant status (p < 0.05). The use of different forms of amaranth in diets of laying hens had no negative effects on the physicochemical properties of eggs and led to the production of eggs with reduced yolk cholesterol and triglyceride; however, the omega-6 content in eggs and the ratio of omega-6/omega-3 increased (p < 0.05). In conclusion, the use of amaranth grain at low levels in the diet of laying hens can enhance the health of the bird and the production of quality and useful eggs.

Pathway Alterations in Stage II/III Primary Melanoma.

PURPOSE: Genomic classification of melanoma has thus far focused on the mutational status of BRAF, NRAS, and NF1. The clinical utility of this classification remains limited, and the landscape of alterations in other oncogenic signaling pathways is underexplored. METHODS: Using primary samples from the InterMEL study, a retrospective cohort of cases with specimens collected from an international consortium with participating institutions throughout the United States and Australia, with oversampling of cases who ultimately died of melanoma, we examined mutual exclusivity and co-occurrence of genomic alterations in 495 stage II/III primary melanomas across 11 cancer pathways. Somatic mutation and copy number alterations were analyzed from next-generation sequencing using a clinical sequencing panel. RESULTS: Mutations in the RTK-RAS pathway were observed in 81% of cases. Other frequently occurring pathways were TP53 (31%), Cell Cycle (30%), and PI3K (18%). These frequencies are generally lower than was observed in The Cancer Genome Atlas, where the specimens analyzed were predominantly obtained from metastases. Overall, 81% of the cases had at least one targetable mutation. The RTK-RAS pathway was the only pathway that demonstrated strong and statistically significant mutual exclusivity. However, this strong mutual exclusivity signal was evident only for the three common genes in the pathway (BRAF, NRAS, and NF1). Analysis of co-occurrence of different pathways exhibited no positive significant trends. However, interestingly, a high frequency of cases with none of these pathways represented was observed, 8.4% of cases versus 4.0% expected (P < .001). A higher frequency of RTK-RAS singletons (with no other pathway alteration) was observed compared with The Cancer Genome Atlas. Clonality analyses suggest strongly that both the cell cycle and RTK-RAS pathways represent early events in melanogenesis. CONCLUSION: Our results confirm the dominance of mutations in the RTK-RAS pathway. The presence of many mutations in several well-known, actionable pathways suggests potential avenues for targeted therapy in these early-stage cases.

Why does the X chromosome lag behind autosomes in GWAS findings?

The X-chromosome is among the largest human chromosomes. It differs from autosomes by a number of important features including hemizygosity in males, an almost complete inactivation of one copy in females, and unique patterns of recombination. We used data from the Catalog of Published Genome Wide Association Studies to compare densities of the GWAS-detected SNPs on the X-chromosome and autosomes. The density of GWAS-detected SNPs on the X-chromosome is 6-fold lower compared to the density of the GWAS-detected SNPs on autosomes. Differences between the X-chromosome and autosomes cannot be explained by differences in the overall SNP density, lower X-chromosome coverage by genotyping platforms or low call rate of X-chromosomal SNPs. Similar differences in the density of GWAS-detected SNPs were found in female-only GWASs (e.g. ovarian cancer GWASs). We hypothesized that the lower density of GWAS-detected SNPs on the X-chromosome compared to autosomes is not a result of a methodological bias, e.g. differences in coverage or call rates, but has a real underlying biological reason-a lower density of functional SNPs on the X-chromosome versus autosomes. This hypothesis is supported by the observation that (i) the overall SNP density of X-chromosome is lower compared to the SNP density on autosomes and that (ii) the density of genic SNPs on the X-chromosome is lower compared to autosomes while densities of intergenic SNPs are similar.

Methylation of nonessential genes in cutaneous melanoma - Rule Out hypothesis.

Differential methylation plays an important role in melanoma development and is associated with survival, progression and response to treatment. However, the mechanisms by which methylation promotes melanoma development are poorly understood. The traditional explanation of selective advantage provided by differential methylation postulates that hypermethylation of regulatory 5'-cytosine-phosphate-guanine-3' dinucleotides (CpGs) downregulates the expression of tumor suppressor genes and therefore promotes tumorigenesis. We believe that other (not necessarily alternative) explanations of the selective advantages of methylation are also possible. Here, we hypothesize that melanoma cells use methylation to shut down transcription of nonessential genes - those not required for cell survival and proliferation. Suppression of nonessential genes allows tumor cells to be more efficient in terms of energy and resource usage, providing them with a selective advantage over the tumor cells that transcribe and subsequently translate genes they do not need. We named the hypothesis the Rule Out (RO) hypothesis. The RO hypothesis predicts higher methylation of CpGs located in regulatory regions (CpG islands) of nonessential genes. It also predicts the higher methylation of regulatory CpGs linked to nonessential genes in melanomas compared to nevi and lower expression of nonessential genes in malignant (derived from melanoma) versus normal (derived from nonaffected skin) melanocytes. The analyses conducted using in-house and publicly available data found that all predictions derived from the RO hypothesis hold, providing observational support for the hypothesis.

Effect of Dietary Amaranth (Amaranthus hybridus chlorostachys) Supplemented with Enzyme Blend on Egg Quality, Serum Biochemistry and Antioxidant Status in Laying Hens.

A feeding trial was performed to assess the effects of dietary raw amaranth (Amaranthus hybridus chlorostachys) grain (RAG), with or without an enzyme blend, on the productive performance, blood biochemistry, and antioxidant status in laying hens. The trial was conducted following a completely randomized design by factorial method, including five levels of RAG (0, 10, 20, 30, and 40%, respectively) and two levels of enzyme blend (0 -E and 0.025 +E %). A total of 960 White Leghorn (Hy-line W-36) laying hens (56 weeks of age) were divided into 10 groups with eight repetitions, including 12 birds. The trial period was ten weeks. Results showed that RAG levels in feed (>10%) led to a significant decrease in blood total cholesterol (TC), but they also significantly decreased feed conversion ratio (FCR) (p ˂ 0.05) as measured by feed intake (FI), hen daily production (HDP), egg weight (EW), and mass (EM), leading to overall worse productivity compared to the control group. On the contrary, the addition of the enzyme blend led to an improvement in the investigated production traits (p ˂ 0.05), with the exception of HDP. The enzyme blend was also capable of recovering productive performance when combined with low concentrations of RAG (10%) (p ˂ 0.05), and RAG × enzyme blend groups showed the lowest values of TC (p ˂ 0.05). Moreover, the interaction effects for atherogenic index (LDL/HDL) indicated a significant and promising reduction in response to the addition of RAG both in the presence and absence of the enzyme blend (p ˂ 0.05), and this additive also significantly reduced levels of egg yolk cholesterol (p ˂ 0.05). In summary, the evidence gathered in this trial showed that dietary RAG had positive effects on egg quality characteristics, leading to the production of low-cholesterol eggs, and, at the same time, it may improve the health status of laying hens. Furthermore, the addition of an enzyme blend allowed feeding up to 10% RAG in the diet, leading to an optimal balance between animal productivity and the beneficial effects of RAG.

The effects of peppermint (Mentha piperita L.) and chicory (Cichorium intybus L.) in comparison with a prebiotic on productive performance, blood constituents, immunity and intestinal microflora in broiler chickens.

A total of 320 one-day-old broiler chickens were used in a 42-day feeding trial to evaluate the effects of peppermint (Mentha piperita L.) and chicory (Cichorium intybus L.) in comparison with a prebiotic on-growth performance, blood constitutes, immunity and intestinal microflora. The dietary treatments were as follows: basal diet (control); control + prebiotic (Fermacto™); control + 0.1% peppermint; control + 0.1% chicory, respectively. A significant (p < 0.05) body weight gain and feed intake was found at 21 and 42 days of growth period in broilers fed diet supplemented with 0.1% chicory compared with other groups. Feeding of prebiotic or chicory led to higher (p < 0.05) feed intake. Chickens fed control diet had higher (p < 0.05) abdominal fat compared with the other groups. Serum blood constituents indicated that broilers fed prebiotic or supplemented with peppermint or chicory had reduced (p < 0.05) levels of cholesterol, triglycerides and low-density lipoprotein than control group. Immunity-related parameters showed that chicken fed chicory had lower (p < 0.05) heterophil-to-lymphocyte ratio compared with the other groups. Intestinal microflora revealed that chickens fed prebiotic or herbals had higher count of Lactobacillus and lower E. coli than control. Thus, it can be concluded that broiler dietary supplementation with prebiotic or chicory can improve performance supporting positively health status.

Effects of in ovo feeding of vitamin E or vitamin C on egg hatchability, performance, carcass traits and immunity in broiler chickens.

The effect of in ovo feeding of different levels of vitamins C and E on egg hatchability, immune response, growth and carcass traits of broiler chickens were investigated. A total of 672 fertilized eggs were assigned to one of eight experimental groups having three replicates with 28 eggs as follows: (1) negative control (not injected); (2) positive control (injected with 0.2 mL deionized water); (3) vitamin C at 1 mg; (4) vitamin C at 3 mg; (5) vitamin C at 6 mg; (6) vitamin E at 0.5 IU; (7) vitamin E at 0.75 IU; and (8) vitamin E at 1.0 IU. At the end of incubation, the number of chicks hatched, and their individual body weight were recorded. Among hatched birds, a total of 240 mixed chicks were randomly selected (30 subject per group equally shared in three pen floors). Chicks were vaccinated against Avian Influenza, Gumboro, Bronchitis, and Newcastle disease virus. Performance parameters were weekly evaluated until 42 days of age. At days 28 and 42, broiler serum and spleen and Bursa of Fabricius relative weight were assessed as well as on day 42 the carcass traits. From results, in ovo injection with 3 mg of vitamin C or 0.75 IU of vitamin E, increased significantly (p < .05) the embryos hatchability when compared to the negative control. However, body weight at hatch and growth performance parameters showed no differences among treatments. Similarly, in ovo concentrations of vitamins C or E showed no differences on carcass traits, immunity-related organs weight or immune response for anti-Newcastle disease hemagglutination-inhibition and total immunoglobulins against sheep red blood cells (SRBC) when compared to the control groups. Based on findings, it can be concluded that in ovo feeding vitamins E and C supported positively chicken embryos hatchability demonstrating the key-role as antioxidant agents; however, further studies are currently being evaluated.

Effects of Using Processed Amaranth Grain with and without Enzyme on Performance, Egg Quality, Antioxidant Status and Lipid Profile of Blood and Yolk Cholesterol in Laying Hens.

The objective of this study was to investigate the effects of feeding Amaranthus hybridus chlorostachys grain (AG) with (+E) and without enzyme (−E) on performance, egg quality, antioxidant status and lipid profile of blood serum and yolk cholesterol in laying hens. A total of 960 white leghorn (Hy-line W-36) commercial layers (56 weeks) were divided into 10 groups with 8 replicates per group (12 birds per replicate, including 3 adjacent cages with 4 birds each). A completely randomized design was implemented with a 5 × 2 factorial arrangement of treatments consisting of five levels of AG (0, 100, 200, 300 and 400 g/kg) and two levels of multienzyme complex addition (0 −E and 0.25 +E g/kg) fed to the hens for 12 weeks (2 wk. adaptation + 10 wk. main experiment). Feed intake (FI) and percentage of hen day production (HDP) were not affected by main effect of the AG level, but egg mass (EM) and egg weight (EW) were decreased (p < 0.01), and the feed conversion ratio (FCR) was impaired (p < 0.01). EM, EW and FCR were improved by enzyme addition (p < 0.01). EM, EW and FCR were affected (p < 0.01) by the interaction of AG and enzyme addition. The highest value of EM and the lowest value of FCR were observed in hens on the diet containing 200 g/kg AG with enzyme addition. Egg yolk cholesterol content was reduced (p < 0.05) by up to 10% with increasing levels AG in experimental diets. The egg quality traits, including Haugh units of protein quality, strength and shell thickness, were not affected by the main effects or interaction of AG and enzyme consumption. Amaranth feeding led to a decrease (p < 0.05) in triglyceride (TG) and low-density lipoprotein (LDL) while also promoting increases (p < 0.05) in the high-density lipoprotein (HDL) and total antioxidant capacity (TAC) of the blood. A comparison of the effects of contrasts showed that functional parameters (except FI), yolk cholesterol, antioxidant parameters (except MDA) and blood lipid profile had differed significantly (p < 0.05) between the hens fed amaranth versus those not fed amaranth. These findings indicate that feeding a diet containing up to 200 g/kg of AG with enzyme addition can improve EW, EM and FCR. Feeding laying hens diets containing AG also positively influenced blood traits and antioxidant status in laying hens while reducing egg yolk cholesterol content.

The effects of green tea in the diet of broilers challenged with coccidiosis on their performance, carcass characteristics, intestinal mucosal morphology, blood constituents and ceca microflora.

BACKGROUND: Coccidiosis is an endemic protozoal disease of chickens normally controlled by ionophores. However, coccidiostats are also antibiotics, and evidence of resistance in both coccidia and bacteria may develop and reduce antibacterial activity in humans. This has led to a search for natural coccidiostats, such as green tea. OBJECTIVES: To study the effects of supplementing broilers with various levels and types of green tea, in comparison to use of a conventional coccidiostat or a control, unsupplemented diet. METHODS: A total of 360 male, day-old Ross 308 broilers (days 1-42) were used to evaluate the gut morphology and performance when challenged with coccidiosis and fed varying dietary levels of green tea powder or extract. Treatments were Negative control (NC, unsupplemented control diet); positive control (PC, control diet + commercial coccidiostat); control diets with 0.2, 0.3 or 0.4 g/kg green tea extract (GTE 0.2, 0.3 and 0.4); and control diets with 1, 2 or 3 g/kg green tea powder (GTP 1, 2 and 3). RESULTS: Compared with NC, PC and all green tea treatments, but particularly GTE0.4, increased feed intake and growth rate, with the best feed conversion ratio at GTE0.4. As a proportion of carcase weight, higher inclusion rates increased intestine weight and decreased abdominal fat. The duodenum, jejunum and ileum of birds fed green tea, and particularly GTE0.4, had longer, wider villi, and shallower crypts. Epithelium thickness was reduced by green tea and PC, compared to NC. Clostridium perfringens and coliform populations decreased in proportion to green tea inclusion rate and decreased in PC. Lactobacilli increased with green tea and were more for NC than PC. Green tea at the highest concentrations reduced blood glucose and LDL and VLDL cholesterol. CONCLUSIONS: Green tea offers a possible replacement for conventional ionophores to control coccidiosis in broiler chickens. The best inclusion rate was 0.4 g/kg.

Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer.

To identify new susceptibility loci to lung cancer among diverse populations, we performed cross-ancestry genome-wide association studies in European, East Asian and African populations and discovered five loci that have not been previously reported. We replicated 26 signals and identified 10 new lead associations from previously reported loci. Rare-variant associations tended to be specific to populations, but even common-variant associations influencing smoking behavior, such as those with CHRNA5 and CYP2A6, showed population specificity. Fine-mapping and expression quantitative trait locus colocalization nominated several candidate variants and susceptibility genes such as IRF4 and FUBP1. DNA damage assays of prioritized genes in lung fibroblasts indicated that a subset of these genes, including the pleiotropic gene IRF4, potentially exert effects by promoting endogenous DNA damage.

Landscape of mutations in early stage primary cutaneous melanoma: An InterMEL study.

It is unclear why some melanomas aggressively metastasize while others remain indolent. Available studies employing multi-omic profiling of melanomas are based on large primary or metastatic tumors. We examine the genomic landscape of early-stage melanomas diagnosed prior to the modern era of immunological treatments. Untreated cases with Stage II/III cutaneous melanoma were identified from institutions throughout the United States, Australia and Spain. FFPE tumor sections were profiled for mutation, methylation and microRNAs. Preliminary results from mutation profiling and clinical pathologic correlates show the distribution of four driver mutation sub-types: 31% BRAF; 18% NRAS; 21% NF1; 26% Triple Wild Type. BRAF mutant tumors had younger age at diagnosis, more associated nevi, more tumor infiltrating lymphocytes, and fewer thick tumors although at generally more advanced stage. NF1 mutant tumors were frequent on the head/neck in older patients with severe solar elastosis, thicker tumors but in earlier stages. Triple Wild Type tumors were predominantly male, frequently on the leg, with more perineural invasion. Mutations in TERT, TP53, CDKN2A and ARID2 were observed often, with TP53 mutations occurring particularly frequently in the NF1 sub-type. The InterMEL study will provide the most extensive multi-omic profiling of early-stage melanoma to date. Initial results demonstrate a nuanced understanding of the mutational and clinicopathological landscape of these early-stage tumors.

Identification of lung cancer drivers by comparison of the observed and the expected numbers of missense and nonsense mutations in individual human genes.

Largely, cancer development is driven by acquisition and positive selection of somatic mutations that increase proliferation and survival of tumor cells. As a result, genes related to cancer development tend to have an excess of somatic mutations in them. An excess of missense and/or nonsense mutations in a gene is an indicator of its cancer relevance. To identify genes with an excess of potentially functional missense or nonsense mutations one needs to compare the observed and expected numbers of mutations in the gene. We estimated the expected numbers of missense and nonsense mutations in individual human genes using (i) the number of potential sites for missense and nonsense mutations in individual transcripts and (ii) histology-specific nucleotide context-dependent mutation rates. To estimate mutation rates defined as the number of mutations per site per tumor we used silent mutations reported in the Catalog Of Somatic Mutations In Cancer (COSMIC). The estimates were nucleotide context dependent. We have identified 26 genes with an excess of missense and/or nonsense mutations for lung adenocarcinoma, 18 genes for small cell lung cancer, and 26 genes for squamous cell carcinoma of the lung. These genes include known genes and novel lung cancer gene candidates.

Biomedical evaluation of antioxidant properties of lamb meat enriched with iodine and selenium.

The article presents a study of the antioxidant properties of meat from lambs that received organic forms of iodine and selenium during growth. This meat was included in diets of laboratory animals using a model of acute toxic hepatitis. The experiments resulted in developing and testing a technique that was effective in enriching lamb with bioorganic elements of iodine and selenium and contributed to the activation metabolism in the bodies of animals consuming the meat. The purpose of the presented investigation was to compare the roles of bioorganic iodine and selenium and their combination as antioxidants in rat rations using a model of acute toxic hepatitis induced by carbon tetrachloride. The experimental studies have established a hepatoprotective effect of lamb meat enriched with selenium and iodine on rats suffering from toxic xenobiotic effects. This was confirmed by normalized hematological and biochemical measures in the blood of the experimental rats.

Genome-wide interaction analysis identified low-frequency variants with sex disparity in lung cancer risk.

Differences by sex in lung cancer incidence and mortality have been reported which cannot be fully explained by sex differences in smoking behavior, implying existence of genetic and molecular basis for sex disparity in lung cancer development. However, the information about sex dimorphism in lung cancer risk is quite limited despite the great success in lung cancer association studies. By adopting a stringent two-stage analysis strategy, we performed a genome-wide gene-sex interaction analysis using genotypes from a lung cancer cohort including ~ 47 000 individuals with European ancestry. Three low-frequency variants (minor allele frequency < 0.05), rs17662871 [odds ratio (OR) = 0.71, P = 4.29×10-8); rs79942605 (OR = 2.17, P = 2.81×10-8) and rs208908 (OR = 0.70, P = 4.54×10-8) were identified with different risk effect of lung cancer between men and women. Further expression quantitative trait loci and functional annotation analysis suggested rs208908 affects lung cancer risk through differential regulation of Coxsackie virus and adenovirus receptor gene expression in lung tissues between men and women. Our study is one of the first studies to provide novel insights about the genetic and molecular basis for sex disparity in lung cancer development.