TP63-TRIM29 axis regulates enhancer methylation and chromosomal instability in prostate cancer.

BACKGROUND: Prostate adenocarcinoma (PRAD) is the second leading cause of cancer-related deaths in men. High variability in DNA methylation and a high rate of large genomic rearrangements are often observed in PRAD. RESULTS: To investigate the reasons for such high variance, we integrated DNA methylation, RNA-seq, and copy number alterations datasets from The Cancer Genome Atlas (TCGA), focusing on PRAD, and employed weighted gene co-expression network analysis (WGCNA). Our results show that only single cluster of co-expressed genes is associated with genomic and epigenomic instability. Within this cluster, TP63 and TRIM29 are key transcription regulators and are downregulated in PRAD. We discovered that TP63 regulates the level of enhancer methylation in prostate basal epithelial cells. TRIM29 forms a complex with TP63 and together regulates the expression of genes specific to the prostate basal epithelium. In addition, TRIM29 binds DNA repair proteins and prevents the formation of the TMPRSS2:ERG gene fusion typically observed in PRAD. CONCLUSION: Our study demonstrates that TRIM29 and TP63 are important regulators in maintaining the identity of the basal epithelium under physiological conditions. Furthermore, we uncover the role of TRIM29 in PRAD development.

An improved and extended dual-index multiplexed 16S rRNA sequencing for the Illumina HiSeq and MiSeq platform.

BACKGROUND: Recent advancements in next-generation sequencing (NGS) technology have ushered in significant improvements in sequencing speed and data throughput, thereby enabling the simultaneous analysis of a greater number of samples within a single sequencing run. This technology has proven particularly valuable in the context of microbial community profiling, offering a powerful tool for characterizing the microbial composition at the species level within a given sample. This profiling process typically involves the sequencing of 16S ribosomal RNA (rRNA) gene fragments. By scaling up the analysis to accommodate a substantial number of samples, sometimes as many as 2,000, it becomes possible to achieve cost-efficiency and minimize the introduction of potential batch effects. Our study was designed with the primary objective of devising an approach capable of facilitating the comprehensive analysis of 1,711 samples sourced from diverse origins, including oropharyngeal swabs, mouth cavity swabs, dental swabs, and human fecal samples. This analysis was based on data obtained from 16S rRNA metagenomic sequencing conducted on the Illumina MiSeq and HiSeq sequencing platforms. RESULTS: We have designed a custom set of 10-base pair indices specifically tailored for the preparation of libraries from amplicons derived from the V3-V4 region of the 16S rRNA gene. These indices are instrumental in the analysis of the microbial composition in clinical samples through sequencing on the Illumina MiSeq and HiSeq platforms. The utilization of our custom index set enables the consolidation of a significant number of libraries, enabling the efficient sequencing of these libraries in a single run. CONCLUSIONS: The unique array of 10-base pair indices that we have developed, in conjunction with our sequencing methodology, will prove highly valuable to laboratories engaged in sequencing on Illumina platforms or utilizing Illumina-compatible kits.

Reconstruction and catalytic activity of hybrid Pd(100)/(111) monolayer on γ-Al2O3(100) in CH4, H2O, and O2 dissociation.

The importance of the "heterogeneity" of a Pd monolayer induced by interaction with a semi-ionic support in catalysis was evaluated. The geometry of the Pd monolayer was optimized on the (100) plane of γ-Al2O3 at fixed unit cell parameters defined by the oxide. Simulation of the deposition of a whole Pd monolayer in the flat Pd(100) form cut from the bulk led to the formation of a slightly distorted Pd(111) monolayer. The subsequent chemisorption or dissociation of CH4 or H2O on the Pd(111) layer resulted in a new hybrid Pd(100)/(111) structure containing alternating elements of (100) and (111) planes (the parallel bands of squares and triangles), which are similar for both CH4 and H2O reactions, and two isolated Pd mono-vacancies, respectively. The hybrid Pd(100)/(111) layer without chemisorbed species was found to be more stable than the initial distorted Pd(111) layer. The catalytic capabilities of these monolayer structures were investigated for the dissociation of methane and the water-gas shift reaction (WGSR) due to the lower predicted activation barriers for CH4, H2O, and O2 dissociation on the hybrid Pd(100)/(111) layer compared to that on the pure (bulk) Pd(100) surface. Moreover, the exothermic heats of these reactions were calculated to be moderate instead of endothermic heats on the Pd(100) or Pd(111) surfaces. The heats of H2O and NH3 adsorption on various monolayers were tested, revealing their dependence on Pd atomic charges. The relevance of the model of the heterogeneous Pd monolayer for explaining the maximum reaction rate experimentally observed at different Pd coverages was discussed. The transferability of the geometry and the extent of charge inhomogeneity of the hybrid monolayer without vacancies were also tested on the same γ-Al2O3(100) support for Pt, Rh, and Ag.

DNA methylation across the genome in aged human skeletal muscle tissue and muscle-derived cells: the role of HOX genes and physical activity.

Skeletal muscle tissue demonstrates global hypermethylation with age. However, methylome changes across the time-course of differentiation in aged human muscle derived cells, and larger coverage arrays in aged muscle tissue have not been undertaken. Using 850K DNA methylation arrays we compared the methylomes of young (27 ± 4.4 years) and aged (83 ± 4 years) human skeletal muscle and that of young/aged heterogenous muscle-derived human primary cells (HDMCs) over several time points of differentiation (0, 72 h, 7, 10 days). Aged muscle tissue was hypermethylated compared with young tissue, enriched for; pathways-in-cancer (including; focal adhesion, MAPK signaling, PI3K-Akt-mTOR signaling, p53 signaling, Jak-STAT signaling, TGF-beta and notch signaling), rap1-signaling, axon-guidance and hippo-signalling. Aged cells also demonstrated a hypermethylated profile in pathways; axon-guidance, adherens-junction and calcium-signaling, particularly at later timepoints of myotube formation, corresponding with reduced morphological differentiation and reductions in MyoD/Myogenin gene expression compared with young cells. While young cells showed little alterations in DNA methylation during differentiation, aged cells demonstrated extensive and significantly altered DNA methylation, particularly at 7 days of differentiation and most notably in focal adhesion and PI3K-AKT signalling pathways. While the methylomes were vastly different between muscle tissue and HDMCs, we identified a small number of CpG sites showing a hypermethylated state with age, in both muscle tissue and cells on genes KIF15, DYRK2, FHL2, MRPS33, ABCA17P. Most notably, differential methylation analysis of chromosomal regions identified three locations containing enrichment of 6-8 CpGs in the HOX family of genes altered with age. With HOXD10, HOXD9, HOXD8, HOXA3, HOXC9, HOXB1, HOXB3, HOXC-AS2 and HOXC10 all hypermethylated in aged tissue. In aged cells the same HOX genes (and additionally HOXC-AS3) displayed the most variable methylation at 7 days of differentiation versus young cells, with HOXD8, HOXC9, HOXB1 and HOXC-AS3 hypermethylated and HOXC10 and HOXC-AS2 hypomethylated. We also determined that there was an inverse relationship between DNA methylation and gene expression for HOXB1, HOXA3 and HOXC-AS3. Finally, increased physical activity in young adults was associated with oppositely regulating HOXB1 and HOXA3 methylation compared with age. Overall, we demonstrate that a considerable number of HOX genes are differentially epigenetically regulated in aged human skeletal muscle and HDMCs and increased physical activity may help prevent age-related epigenetic changes in these HOX genes.

Plasmonic nanosponges filled with silicon for enhanced white light emission.

Plasmonic nanosponges are a powerful platform for various nanophotonic applications owing to extremely high local field enhancement in metallic nanopores. The filling of the nanopores with high-refractive index semiconductors (e.g. Si, Ge, GaP, etc.) opens up opportunities for the enhancement of nonlinear effects in these materials. However, this task remains challenging due to the lack of knowledge on the integration process of metal and high-index semiconductor components in such nanoobjects. Here, we investigate metal-dielectric nanoparticles fabricated from bilayer Si/Au films by the laser printing technique via a combination of theoretical and experimental methods. We reveal that these hybrid nanoparticles represent the Au sponge-like nanostructure filled with Si nanocrystallites. We also demonstrate that the Au net provides strong near-field enhancement in the Si grains increasing the white light photoluminescence in the hybrid nanostructures compared to uniform Si nanoparticles. These results pave the way for engineering the internal structure of the sponge-like hybrid nanoparticles possessing white light luminescence and control of their optical properties on demand.

LogLoss-BERAF: An ensemble-based machine learning model for constructing highly accurate diagnostic sets of methylation sites accounting for heterogeneity in prostate cancer.

Although modern methods of whole genome DNA methylation analysis have a wide range of applications, they are not suitable for clinical diagnostics due to their high cost and complexity and due to the large amount of sample DNA required for the analysis. Therefore, it is crucial to be able to identify a relatively small number of methylation sites that provide high precision and sensitivity for the diagnosis of pathological states. We propose an algorithm for constructing limited subsamples from high-dimensional data to form diagnostic panels. We have developed a tool that utilizes different methods of selection to find an optimal, minimum necessary combination of factors using cross-entropy loss metrics (LogLoss) to identify a subset of methylation sites. We show that the algorithm can work effectively with different genome methylation patterns using ensemble-based machine learning methods. Algorithm efficiency, precision and robustness were evaluated using five genome-wide DNA methylation datasets (totaling 626 samples), and each dataset was classified into tumor and non-tumor samples. The algorithm produced an AUC of 0.97 (95% CI: 0.94-0.99, 9 sites) for prostate adenocarcinoma and an AUC of 1.0 (from 2 to 6 sites) for urothelial bladder carcinoma, two types of kidney carcinoma and colorectal carcinoma. For prostate adenocarcinoma we showed that identified differential variability methylation patterns distinguish cluster of samples with higher recurrence rate (hazard ratio for recurrence = 0.48, 95% CI: 0.05-0.92; log-rank test, p-value < 0.03). We also identified several clusters of correlated interchangeable methylation sites that can be used for the elaboration of biological interpretation of the resulting models and for further selection of the sites most suitable for designing diagnostic panels. LogLoss-BERAF is implemented as a standalone python code and open-source code is freely available from https://github.com/bioinformatics-IBCH/logloss-beraf along with the models described in this article.

CO diffusion as a re-orientation mechanism in the NaY zeolite.

Our work is devoted to DFT calculations of the relative rotational and diffusional barriers for CO motions in zeolite NaY. The diffusion jump of CO adsorbed in NaY from NaII to Na'II has been confirmed as the favored way for CO re-coordination via either the C or the O atom to the Na cations instead of the CO rotation, hence explaining the mechanism which is responsible for the CO exchange between different positions and the changes in the intensities of the vibrational IR spectra. The fine structure of the vibrational C-O bands is explained by the different CO locations of adsorbed mono- and dicarbonyl species. The calculated activation energy of intra-cage CO diffusion from NaII-CO to Na'II-OC matches the respective experimental barrier observed in the NaX zeolite.

[The concentration of cerebral natriuretic peptide in tear and blood serum.]

The natriuretic peptides regulate pressure and water metabolism in human organism. The concentration of N-thermal cerebral natriuretic propeptide (NT-proBNP) in tear and blood serum was analyzed. The sampling included 49 patients divided on three groups. The group I (main) included 14 patients with primary open-angle sub-compensated glaucoma degree I-III. The group II (comparative group) included 15 patients with age-related immature cataract. The group III (control) included volunteers without any visual organ diseases. The concentration of NT-proBNP in tear and blood serum was detected by solid-phase enzyme-linked immunosorbent assay technique using test system NT-proBNP - IFA - BEST¼ («Vektor-Best¼, Russia). The median of content of NT-proBNP in tear turned out to be less than in blood serum in all groups (р1 = 0,00763; р2 = 0,00452; р3 = 0,00029) and made up to in patients with glaucoma 41,3 pg/ml, with cataract - 37.5 pg/ml, in healthy people 0 25.0 pg/ml (inter-quartile range made up to 20-60 pg/ml, 20-65 pg/ml, 10-49,5 pg/ml correspondingly). No differences in concentration of NT-proBNP were established in all groups both for blood serum (p = 0,494) and tear (p = 0,388). The concentration of NT-proBNP in tear correlated with its concentration in blood serum (r = 0,694). However, no dependencies were established from value of intra-ocular pressure (r = 0,168). Therefore, the concentration of NTproBNP in tear is not a perspective laboratory arker for diagnostic of increased intra-ocular pressure and stratification of development of glaucoma.

[GSTP1, APC and RASSF1 gene methylation in prostate cancer samples: comparative analysis of MS-HRM method and Infinium HumanMethylation450 BeadChip beadchiparray diagnostic value]. / Status metilirovaniia genov GSTP1, APC i RASSF1 v obraztsakh raka predstatel'noi zhelezy cheloveka: sravnitel'nyi analiz diagnosticheskoi informativnosti metodov MS-HRM i gibridizatsii na DNK-chipakh illumina Infinium HumanMethylation450 BeadChip.

There is a clear need in molecular markers for prostate cancer (PC) risk stratification. Alteration of DNA methylation is one of processes that occur during ÐÑ progression. Methylation-sensitive PCR with high resolution melting curve analysis (MS-HRM) can be used for gene methylation analysis in routine laboratory practice. This method requires very small amounts of DNA for analysis. Numerous results have been accumulated on DNA methylation in PC samples analyzed by the Infinium HumanMethylation450 BeadChip (HM450). However, the consistency of MS-HRM results with chip hybridization results has not been examined yet. The aim of this study was to assess the consistency of results of GSTP1, APC and RASSF1 gene methylation analysis in ÐÑ biopsy samples obtained by MS-HRM and chip hybridization. The methylation levels of each gene determined by MS-HRM were statistically different in the group of PC tissue samples and the samples without signs of tumor growth. Chip hybridization data analysis confirmed the results obtained with the MS-HRM. Differences in methylation levels between tumor tissue and histologically intact tissue of each sample determined by MS-HRM and chip hybridization, were consistent with each other. Thus, we showed that the assessment of GSTP1, APC and RASSF1 gene methylation analysis using MS-HRM is suitable for the design of laboratory assays that will differentiate the PC tissue from the tissue without signs of tumor growth.

[Genome-wide analysis of DNA methylation in prostate cancer using the technology of Infinium HumanMethylation450 BeadChip (HM450)].

Using the technology of DNA chips Infinium HumanMethylation 450 BeadChip it was analyzed quantitative DNA methylation status in 12 paired samples of prostate adenocarcinoma, and morphologically altered tissues. Analysis of differentially methylated regions of the genome showed an association with abnormal status for 21610 and 3852 hypomethylated hyper-methylated CpG sites. Dominance in the cancer genome hypermethylated sites and their predominant localization in the regulatory regions of genes indicate their possible role in the implementation of mechanisms of gene suppression in the pathogenesis of prostate cancer (PCa). For 14 genes studied were characterized array maximum values hypermethylation in promoter region (> 50% CpG sites) in combination with a high level of methylation differences between treatment groups (> 40%). Role of hypermethylation in some of them: AOX1, KLF8, ZNF154, TMEM106A in the pathogenesis of prostate cancer has been showed previously. Hypermethylation of genes ACSS3, TAC1, TUBA4B, ZSCAN12 not previously been shown for prostate cancer, but is characterized by the association with other cancers. In turn, the differences in the levels of methylation in genes GPRASP1, NKX2-6, ARX, CYBA, EPSTI1, RHCG been documented as a result of a number of genome-research oncology, but has not been studied in detail. To assess the diagnostic potential of epigenetic markers of prostate cancer there was carried out unbiased selection of individual CpG sites most reliably discriminate against tumor samples from a group of no tumor samples. In selected diagnostic model based on logistic regression included 9 CpG sites. Validation of the model was carried out on an independent dataset of methylation of 40 paired samples from the prostate cancer project Atlas of Cancer Genome (TCGA) analyzed on the same version of the DNA chip. Summarized rates of diagnostic informativeness of a model (specificity 95%, sensitivity of 97%, the area under the curve of the diagnostic test (ROC) - 0,96), obtained after validation, allow us to consider these CpG Sites as potential markers for molecular diagnosis of prostate cancer.

[Hepatic leiomyosarcoma: a case report].

The authors present a review of pathogenesis, diagnosis and various approaches to treatment for an extremely rare tumor - primary hepatic leiomyosarcoma. This tumor is dif- ficult to be diagnosed by imaging examinations. The prevalent method of treatment is a radical resection (RO surgery). Ac- cording to literature the median survival of patients with LMSL is about one year with DFS after treatment about 10 months. Also the authors describe a case report of the successful cure of middle-aged female with primary hepatic leiomyosarcoma and Hodgkin's lymphoma in the anamnesis. She has undergone 6 cycles of neoadjuvant chemotherapy with Ifosfamide and Doxorubicin. The tumour response was estimated as partial. Then patient has undergone radical surgery in the volume of extended left hemihepatectomy with LND. Follow-up exami- nation 38 months after treatment revealed no progression of the disease.

[Metagenomic analysis of taxonomic and functional changes in gut microbiota of patients with alcoholic dependence syndrome].

Here we present the first metagenomic study of gut microbiota in patients with alcohol dependence syndrome (ADS) performed in the whole-genome ("shotgun") format. Taxonomic analysis highlighted changes in community "drivers" abundance previously associated with inflammatory processes (including increase in Ruminococcus gnavus and torques, as well as decrease in Faecalibacterium and Akkermansia). Microbiota of alcoholics manifested presence of specific opportunistic pathogens rarely detected in healthy control subjects of the world. Differential analysis of metabolic potential basing on changes in KEGG Orthology groups abundance revealed increase in pathways associated with response to oxidative stress. Analysis of two specific gene groups--alcohol metabolism and virulence factors--also showed increase in comparison with the control groups. We suggest that gut microbiota distinct in alcoholics by both taxonomic and functional composition plays role in modulating the effect of alcohol on host organism.

[The wound drainage after operation on thyroid gland].

Efficacy of active draining, promoting the most rapid reconvalescence and rehabilitation of the patients, in comparison to passive wound draining was studied up in various diseases of thyroid gland and operative intervention volume. The autors have had concluded, that suturing of operative wound without draining after hemithyroidectomy conduction is possible, as well as a thyroidectomy for nodular and multinodular goiter, if the excised volume of the lobe/gland do not exceed 15 cm3 and in nonapplication of anticoagulants.

Chemical reduction of the elastic properties of zeolites: a comparison of the formation of carbonate species versus dealumination.

The decrease in elastic moduli (Young's, bulk, and shear modulus), the variations in their asymmetries, the Poisson's ratio and the linear compressibility due to carbonate formation in NaX, have been compared to those produced by dealumination of the zeolite HY framework, from the Al-Si-Al fragment positioned in joined 4R rings. All these systems have been considered at the density functional theory (DFT) level using periodic boundary conditions. The representativeness of the models has been checked by comparison of the calculated IR spectra of carbonate and hydrocarbonate species in NaX and of hydroxyl groups in HY with the experimental equivalents. The correlation between the destabilization energy of the systems and the displacement of Na or K cations coordinated to the carbonate or hydrocarbonate species, expressed in terms of Me-O bond elongation, has been confirmed for either one or two carbonate and hydrocarbonate species per unit cell (UC). Finally, a similar reduction in elasticity in FAU zeolites has been observed, due either to carbonate/bicarbonate formation in NaX or as a step in HY dealumination.

SOD2 gene polymorphism and muscle damage markers in elite athletes.

Exercise-induced oxidative stress is a state that primarily occurs in athletes involved in high-intensity sports when pro-oxidants overwhelm the antioxidant defense system to oxidize proteins, lipids, and nucleic acids. During exercise, oxidative stress is linked to muscle metabolism and muscle damage, because exercise increases free radical production. The T allele of the Ala16Val (rs4880 C/T) polymorphism in the mitochondrial superoxide dismutase 2 (SOD2) gene has been reported to reduce SOD2 efficiency against oxidative stress. In the present study we tested the hypothesis that the SOD2 TT genotype would be underrepresented in elite athletes involved in high-intensity sports and associated with increased values of muscle and liver damage biomarkers. The study involved 2664 Caucasian (2262 Russian and 402 Polish) athletes. SOD2 genotype and allele frequencies were compared to 917 controls. Muscle and liver damage markers [creatine kinase (CK), creatinine, alanine transaminase (ALT), aspartate transaminase (AST), alkaline phosphatase (ALP)] were examined in serum from 1444 Russian athletes. The frequency of the SOD2 TT genotype (18.6%) was significantly lower in power/strength athletes (n = 524) compared to controls (25.0%, p = 0.0076) or athletes involved in low-intensity sports (n = 180; 33.9%, p < 0.0001). Furthermore, the SOD2 T allele was significantly associated with increased activity of CK (females: p = 0.0144) and creatinine level (females: p = 0.0276; males: p = 0.0135) in athletes. Our data show that the SOD2 TT genotype might be unfavorable for high-intensity athletic events.

[Variability in the relative quantity of human DNA resulted from metagenomic analysis of gut microbiota].

We conducted the comparative study of seven different methods of total DNA extraction from human feces. All these methods are recommended in protocols for metagenomic analysis of human gut microbiota. We studied the relative quantity of human DNA calculated from shotgun sequencing on a SOLiD 4 genetic analyzer of metagenomic samples. It was shown that either initial amount of feces or a method applied for total DNA extraction do not affect on final relative human DNA abundance, which is less than 1% in healthy people. Invariance of this parameter allows to consider increased abundance of human DNA in metagenomic samples as a potential marker of inflammatory bowel diseases.

Ion-exchanged binuclear Ca2OX clusters, X = 1-4, as active sites of selective oxidation over MOR and FAU zeolites.

A new series of calcium oxide clusters Ca(2)O(X) (X = 1-4) at cationic positions of mordenite (MOR) and faujasite (FAU) is studied via the isolated cluster approach. Active oxide framework fragments are represented via 8-membered window (8R) in MOR, and two 6R and 4R windows (6R+4R) possessing one common Si-O-Si moiety in FAU. Structural similarities between the Ca(2)O(X)(8R) and Ca(2)O(X)(6R+4R) moieties are considered up to X = 4. High oxidation possibilities of the Ca(2)O(2)(nR) and Ca(2)O(3)(nR) systems are demonstrated relative to CO, whose oxidation over the Ca-exchanged zeolite forms is well studied experimentally. Relevance of the oxide cluster models with respect to trapping and desorption of singlet dioxygen is discussed.

[Differentiated thyroid cancer in the Ukraine: clinical experience with treatment of 2000 patients and current world-wide tendencies].

Principal moments of recent (2006) European and USA consensus for the management of patients with differentiated thyroid cancer (DTC) are described. The situation with treatment of DTC patients in the Ukrain was analyzed. It was established that preoperative cytological investigation and express-biopsy should be possible and reliable as well as adequate primary surgery. The absence of full concordance of the Ukranean and European modes of management of DTC patients was established. To improve the situation more radical primary surgery, routine use of radioiodine ablation in high and low risk groups, elimination of radiological and laboratory limitations are strongly recommended.

[Aspects of low anterior rectum resection].

Results analysis of 162 low anterior rectum resections, carried out in the hospital during 1999-2006 years on account of upper and medial rectal ampulla adenocarcinoma is presented in the article. Method of marking rectum resection distal border with use of optical coherent tomography was worked out and put into practice. Comparative evaluation of operation results with total and partial mesorectal cellular tissue removal was carried out. It is established that local recurrence has been indexed in 14.28% of patients undergoing anterior resection with maintenance of mesorectum part in 7.89% of patients undergoing mesorectumectomy. Indications for mobilization of left bend colon and one or another type of discharge ostomy were formulated. Measures for prediction and prophylaxis of anal incontinence after rectum resection and also the new method of small pelvis cavity intraoperative drainage were offered.