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.

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.

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.

[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.

[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.

[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.

[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.

[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.

[Potentialities of laparoscopic adrenalectomy in treatment of patients with adrenal tumors].

Experiences with laparoscopic adrenalectomies in the clinic were analyzed. The laparoscopic method was used in 47 out of 252 adrenalectomies followed by only 1 mild complication and 3 conversions. A comparison of open and laparoscopic adrenalectomies has revealed advantages of the endoscopic method with respect of tolerance of the procedure, its safety and duration of the rehabilitation period. The technique and indications to adranalectomy were analyzed. The authors emphasize the advantages of the transperitoneal approach and good perspectives of laparoscopic adrenalectomy in almost all cases of benign and non-invasive adrenal tumors.

[Results of combined surgeries for cancer of the colon complicated with stomach and duodenal fistulas].

Positive results of combined surgeries in locally advanced cancer of the colon complicated with gastric fistula (3 patients) and duodenal fistula (1 patient) are presented. Effective treatment of these patients requires complex examination, good preoperative preparation, perfect anesthetic management, adequate operation and intensive postoperative (including antibacterial) therapy.

ret/PTC1 and ret/PTC3 in thyroid tumors from Chernobyl liquidators: comparison with sporadic tumors from Ukrainian and French patients.

Like children exposed to Chernobyl fallout, the workers who cleaned up after the accident, also known as liquidators, have exhibited an increased incidence of thyroid cancer. A high prevalence of ret/PTC3 rearrangement has been found in pediatric post-Chernobyl thyroid tumors, but this feature has not been investigated in liquidator thyroid tumors. In this study we analyzed the prevalence of ret/PTC1 and ret/PTC3 in thyroid tumors from 21 liquidators, 31 nonirradiated adult Ukrainian patients, and 34 nonirradiated adult French patients. ret rearrangements in carcinomas were found in 83.3% of liquidators, 64.7% of Ukrainian patients, and 42.9% of French patients. The prevalence of ret/PTC1 was statistically similar in the three groups. The prevalence of ret/PTC3 was significantly higher in liquidators than in French patients (P = 0.03) but it was also high in nonirradiated Ukrainian patients who exhibited values intermediate between liquidators and French patients. In adenomas the prevalence of rearrangement was significantly higher in all Ukrainians than in French patients (P = 0.004). Like children exposed to Chernobyl fallout, liquidators showed a high prevalence of ret/PTC3. This finding suggests that irradiation had the same effect regardless of age. However, given the high rate of ret/PTC3 in nonirradiated adult Ukrainians, the possibility of genetic susceptibility or low-level exposure to radiation in that group cannot be excluded.

[Surgical treatment of sporadic and radiation-induced thyroid cancer in young patients]. / Khirurgicheskoe lechenie sporadicheskogo i radioindutsirovannogo raka shchitovidnoi zhelezy u liudei molodogo vozrasta.

An analysis of results of treatment of sporadic thyroid cancer in 68 children and juveniles and in 119 adult patients with radio-induced carcinomas irradiated in childhood after the Chernobyl APS accident in 1986 has revealed that the sporadic thyroid cancer in children and adults with radio-induced carcinomas are highly aggressive. For all this, radio-induced carcinomas are known to have aggressive local growth that in most cases required extended operations. The surgical treatment of carcinomas allows to get survival of the absolute majority of the patients.

BRAF T1796A transversion mutation in various thyroid neoplasms.

A high prevalence of activating mutation of the B type Raf kinase (BRAF) gene was recently reported in papillary thyroid cancer (PTC). However, the frequency of this mutation in several other types of thyroid neoplasms was not thoroughly investigated. In the present study, in addition to PTC, we evaluated various thyroid tumor types for the most common BRAF T1796A mutation by direct genomic DNA sequencing. We found a high and similar frequency (45%) of the BRAF T1796A mutation in two geographically distinct PTC patient populations: one composed of sporadic cases from North America, and the other from Kiev, Ukraine, that included individuals who were exposed to the Chernobyl nuclear accident. In contrast, we found BRAF mutation in only 20% of anaplastic thyroid cancers and no mutation in medullary thyroid cancers and benign thyroid hyperplasia. We also confirmed previous reports that the BRAF T1796A mutation did not occur in benign thyroid adenomas and follicular thyroid cancers. Specific analysis of the Ukraine patients with confirmed history of radiation exposure failed to show a higher incidence of BRAF mutation. Our results suggest that frequent occurrence of BRAF mutation is inherently associated with PTC, irrespective of geographic origin, and is apparently not a radiation-susceptible mutation. The lack or low prevalence of BRAF mutation in other thyroid neoplasms is consistent with the notion that other previously defined genetic alterations on the same signaling pathway are sufficient to cause tumorigenesis in most thyroid neoplasms.

Akt activation and localisation correlate with tumour invasion and oncogene expression in thyroid cancer.

INTRODUCTION: Akt activation is involved in the pathogenesis of inherited thyroid cancer in Cowden's syndrome and in sporadic thyroid cancers. In cell culture, Akt regulates thyroid cell growth and survival; but recent data suggest that Akt also regulates cell motility in non-thyroid cell lines. We therefore sought to evaluate the role of Akt in thyroid cancer progression. METHODS: We evaluated 46 thyroid cancer, 20 thyroid follicular adenoma, and adjacent normal tissues samples by immunohistochemistry for activated Akt (pAkt), Akt 1, 2, and 3, and p27 expression. Immunoblots were performed in 14 samples. RESULTS: Akt activation was identified in 10/10 follicular cancers, 26/26 papillary cancers, and 2/10 follicular variant of papillary cancers, but in only 4/66 normal tissue samples and 2/10 typical benign follicular adenomas. Immunoactive pAkt was greatest in regions of capsular invasion; and was localised to the nucleus in follicular cancers and the cytoplasm in papillary cancers, except for invasive regions of papillary cancers where it localised to both compartments. Immunoactive Akt 1, but not Akt 2 or Akt 3, correlated with pAkt localisation, and nuclear pAkt was associated with cytoplasmic expression of p27. In vitro studies using human thyroid cancer cells demonstrated that nuclear translocation of Akt 1 and pAkt were associated with cytoplasmic p27 and cell invasion and migration. Cell migration and the localisation of Akt 1, pAkt, and p27 were inhibited by PI3 kinase, but not MEK inhibition. DISCUSSION: These data suggest an important role for nuclear activation of Akt 1 in thyroid cancer progression.

Repair of diaphyseal femoral fractures in cats using interlocking intramedullary nails: 12 cases (1996-2000).

OBJECTIVE: To determine the outcome of femoral fractures repaired with 4.0- and 4.7-mm interlocking intramedullary nails in cats. DESIGN: Retrospective study. ANIMALS: 12 cats with diaphyseal femoral fractures. PROCEDURE: Records of all cats in which the 4.0- and 4.7-mm interlocking nail system was used for repair of diaphyseal femoral fractures at the Animal Medical Center and Florida Veterinary Specialists between 1996 and 2000 were reviewed. Information included signalment, type of fracture, size of the implant, details of the surgery, intra- and postoperative complications, fracture healing, and clinical outcome. RESULTS: Femoral fractures in 12 cats were repaired. Eleven of the fractures were comminuted, with 2 of these being open. Clinical outcome was excellent in 7 cats, good in 3, and fair in 1. One resulted in a nonunion. Complications included screw breakage (1 cat) and fracture distal to the nail (1). Fracture distal to the nail occurred from a second trauma. CONCLUSION AND CLINICAL RELEVANCE: Use of the interlocking nail has been limited in cats because of the small diameter of the medullary canal. Use of the 4.0-mm nail will allow for greater application of this implant in small patients. Results of this study indicate that the 4.0- and 4.7-mm interlocking nails can be used to repair simple or comminuted diaphyseal femoral fractures in cats.

[CLinico-morphologic correlations in cases of fatal outcome following removal of acoustic nerve neuromas]. / Kliniko-morfologicheskie sopostavleniia v sluchaiakh letal'nykh iskhodov posle udaleniia nevrinom slukhovogo nerva.

The clinical findings were compared with the results of morphological examination of the brain in 32 patients who had died in different periods after surgery for removal of neurinoma of the acoustic nerve. In all cases vessels supplying the brain stem were injured during removal of the tumor. In 5 cases all three groups of arteries of the pons varolii were injured, which led to the development of infarction of half of the pons. The short circumflex pons arteries and the anterior inferior cerebellar artery were injured in 18 patients, which caused the formation of an infarct in the lateral part of pons varolii. The distal segment of the anterior inferior cerebellar artery was injured in 9 patients, as a result of which a small focus of infarction formed in the dorsolateral parts of the pons.