The association between the polymorphic GGN repeat in androgen receptor gene and prostate cancer susceptibility has been studied extensively. But the results of these polymorphisms with prostate cancer risk remain inconclusive. Previous meta-analysis showed short GGN repeats (≤16 repeats) had high risks for prostate cancer compared with longer GGN repeats (>16 repeats). Many studies have been published since the release of the previous meta-analysis. Here, we conducted an updated meta-analysis to demonstrate whether short repeats have higher risks for prostate cancer compared to long repeats. Five databases (PubMed, EMBASE, Cochrane Library, The China National Knowledge Infrastructure, and Web of Science) were last searched until January 1, 2016. Random- or fixed-effects model was performed based on the heterogeneity among studies. The potential publication bias was assessed via Begg funnel plot and Egger regression test. Twelve out of 157 studies were extracted. The result indicated that there was no significant difference between short repeat group and long repeat group in the overall analysis ( I2 = 80.6%, P = .000, odds ratio = 1.31, 95% confidence interval: 0.93-1.83). There was no association between the length of GGN repeats and the occurrence of prostate cancer in both Caucasian and African American ( I2 = 6.7%, P = .359, odds ratio = 1.11, 95% confidence interval: 0.94-1.32; and I2 = 74.1%, P = .050, odds ratio = 0.963, 95% confidence interval: 0.36-2.58). Our result demonstrated that a shorter GGN repeat polymorphism cannot increase the risk of prostate cancer compared to the longer GGN repeats. That's different with previous meta-analysis.

The aim of this study is to identify the diagnostic values of serum exosomal miRNA-34s of patients with HB in a large Asian group and explore the prognostic value of the exosomal miRNA-34s panel compared with other risk factors.

Lymphoproliferative diseases of the central nervous system are rare, diagnostics and treatment are accordingly challenging. Since the introduction of the 2008 WHO lymphoma classification, primary CNS DLBCL - also covering the associated primary ocular (vitreoretinal) lymphoma - is a separate entity. The special localization is related with a series of newly recognized genetic, genomic and immunologic features directing to the strong interaction between transformed lymphoma cells, neural tissue components and the local immune response. Histological differentiation is frequently disabled by the limited sampling opportunities and requires the application of all available hematopathologic technologies including immunohistochemistry, cytology, liquor serology, flow cytometry, fluorescence in situ hybridization and polymerase chain reaction with sequencing.

The recent advances in the field of molecular biology have enabled a more comprehensive genomic analysis in myeloid malignancies. The studies have unveiled recurrent somatic mutations in several genes illuminating the clinical heterogeneity of these diseases. In this review, we discuss the pathogenesis of de novo and secondary acute myeloid leukemia (AML) in view of recent findings. Mutational analysis of several genes are already included in the everyday diagnostic procedure of AML. The identification of these mutations enables improvements in risk-stratification strategies and provides new potential targets for treatment of AML.

Lymphoplasmacytic lymphoma is a rare low-grade B-cell lymphoma, which is composed of a mixture of small lymphocytes, plasmacytoid cells and plasma cells that typically infiltrate the bone marrow, but lymph nodes and rarely other organs can be involved as well. Waldenström macroglobulinaemia is a lymphoplasmacytic lymphoma with typical bone marrow involvement and is associated with detectable IgM paraproteins. The diagnosis of lymphoplasmacytic lymphoma/Waldenström macroglobulinaemia (LPL/WM) can be challenging, due to similarities to other small B-cell lymphomas with plasmacytic differentiation and/or with IgM paraproteins. The recently discovered MYD88 mutation may help in the diagnosis, as it is present in over 90% of LPL/WMs. This short review covers the pathology of LPL/WM and offers some insight into the new molecular findings that may help in the diagnostic procedure and in the new therapeutic choices.

In Systems Biology, network-based approaches have been extensively used to effectively study complex diseases. An important challenge is the detection of network perturbations which disrupt regular biological functions as a result of a disease. In this regard, we introduce a network based pathway analysis method which isolates casual interactions with significant regulatory roles within diseased-perturbed pathways. Specifically, we use gene expression data with Random Forest regression models to assess the interactivity strengths of genes within disease-perturbed networks, using KEGG pathway maps as a source of prior-knowledge pertaining to pathway topology. We deliver as output a network with imprinted perturbations corresponding to the biological phenomena arising in a disease-oriented experiment. The efficacy of our approach is demonstrated on a serous papillary ovarian cancer experiment and results highlight the functional roles of high impact interactions and key gene regulators which cause strong perturbations on pathway networks, in accordance with experimentally validated knowledge from recent literature.

We propose a methodology for predicting oral cancer recurrence using Dynamic Bayesian Networks. The methodology takes into consideration time series gene expression data collected at the follow-up study of patients that had or had not suffered a disease relapse. Based on that knowledge, our aim is to infer the corresponding dynamic Bayesian networks and subsequently conjecture about the causal relationships among genes within the same time-slice and between consecutive time-slices. Moreover, the proposed methodology aims to (i) assess the prognosis of patients regarding oral cancer recurrence and at the same time, (ii) provide important information about the underlying biological processes of the disease.

Multi-omic approaches offer the opportunity to characterize complex diseases such as cancer at various molecular levels. In this paper, we present transcriptomic, proteomic/glycoproteomic, glycomic, and metabolomic (TPGM) data we acquired by analysis of liver tissues from hepatocellular carcinoma (HCC) cases and patients with liver cirrhosis. We evaluated changes in the levels of transcripts, proteins, glycans, and metabolites between tumor and cirrhotic tissues by statistical methods. We demonstrated the potential of multi-omic approaches and network analysis to investigate the interactions among these biomolecules in the progression of liver cirrhosis to HCC. Also, we showed the significance of multi-omic approaches to identify pathways altered in HCC.

In this paper, a new approach based on Binary Black Hole Algorithm (BBHA) and Adaptive Boosting version Ml (AdaboostM1) is proposed for finding genes that can classify the group of cancers correctly. In this approach, BBHA is used to perform gene selection and AdaboostM1 with 10-fold cross validation is adopted as the classifier. Also, to find the relation between the biomarkers for biological point of view, decision tree algorithm (C4.5) is utilized. The proposed approach is tested on three benchmark microarrays. The experimental results show that our proposed method can select the most informative gene subsets by reducing the dimension of the data set and improve classification accuracy as compared to several recent studies.

Pan-cancer analyses attempt to discover similar features among multiple cancers to identify fundamental patterns common to cancer development and progression. A pan-cancer analysis integrating both protein expression and transcriptomic data is important because it can identify genes that are linked to proteins potentially responsible for a patient's status. This study aims to identify differentially expressed (DE) genes between early and advanced cases of multiple cancer types through the usage of RNA sequencing data. The relevance of these genes is further investigated by developing predictive models using K-nearest neighbor and linear discriminant analysis classifiers. The use of cancer-specific and non-cancer specific features resulted in several moderately performing models. Highlighted genes were further investigated to determine if they encoded for proteins identified in a previously conducted pan-cancer analysis. The results of this study suggest that a pan-cancer analysis may be highly complementary to standard analyses of individual cancers for identifying biologically relevant DE genes and can assist in developing effective predictive models for cancer progression.

Mast cell tumors are the most common malignant cutaneous tumors in dogs. Although there are several prognostic factors involved, the clinical and biological behavior of this type of tumor varies greatly, making the best choice of treatment challenging. Molecular techniques can be used to evaluate a large number of genes involved in the neoplastic process and aid in the selection of candidate genes related to prognostic and predicting factors. Identification of the genes associated with tumor development and progression can be performed through the analysis of numerical and structural changes in DNA isolated from tumor cells by array comparative genomic hybridization (aCGH). The aim of this study was to compare copy number variations (CNVs) in cutaneous mast cell tumors of dogs that survived less than six (ST<6) and >12months (ST>12) from the date of diagnosis. Ten animals were used: four from Group ST>12 and six from Group ST<6. Genomic DNA was extracted, and aCGH was performed using Agilent Canine Genome CGH Microarray 4×180 (ID-252 552 - Agilent, USA). Data analysis was carried out using Nexus program version 5.0 (Biodiscovery, USA). The group ST>12 presented 11±3.3 CNVs, while the ST<6 group presented 85±38.5 CNVs. Regions of loss in PTEN and FAS as well as regions of gains in MAPK3, WNT5B, FGF, FOXM1 and RAD51 were detected in mast cell tumors with shorter survival times, and thus, worst prognoses, allowing for the identification of potential candidate genes for more detailed studies.

Mesothelium vascular cell adhesion molecule-1 (VCAM-1) expression in the metastatic epithelial ovarian cancer (EOC) microenvironment is induced by tumor and mediates tumor cell invasion. VCAM-1 imaging suggests expression during treatment is an indicator of platinum resistance. Here, we assess the potential prognostic significance of mesothelium VCAM-1 expression and prospectively evaluate whether soluble VCAM-1 (sVCAM-1) is a surrogate for mesothelium expression.

We describe the case of a sinonasal adamantinoma-like Ewing sarcoma in a 41-year-old male. Histologically, the tumor exhibited distinctive areas of nested growth pattern with prominent stromal fibrosis and metaplastic bone formation. The tumor cells were small and uniform with minimal amount of pale eosinophilic to clear cytoplasm and round or oval nuclei with finely dispersed chromatin and small nucleoli. Approximately 20% of the tumor parenchyma comprised of small clusters of basaloid cells within an osteofibrous background resembling adamantinoma. The tumor showed strong expression of keratins, p63, CD99 and Fli-1, and EWSR1 rearrangement. The diagnosis of sinonasal Ewing family tumors is particularly problematic owing to the large number of potential mimics. For any poorly differentiated or undifferentiated head and neck tumor, cellular monotony and CD99 immunoreactivity should prompt consideration for molecular studies that include analysis of both EWSR1 and FLI1, even in the presence of strong cytokeratin expression or focal keratinization.

Acute lymphoblastic leukemia (ALL) is the most common cancer in the pediatric population; ∼80% of the cases show some translocation. Translocations that result in ALL are due to chromosome breaks. However, the exact mechanisms that cause these breaks have not been well studied. A detailed search of the breakpoints associated with ALL reported in the NCBI database shows that some are concentrated in limited regions of the chromosome, whereas others are scattered throughout. Therefore, the objective of this study was to identify the structural factors involved in chromosomal breaks in ALL.

Thymoquinone (TQ), an active component derived from the medial plant Nigella sativa, has been used for medical purposes for more than 2 000 years. Recent studies have reported that TQ blocked angiogenesis in animal model and reduced migration, adhesion, and invasion of glioblastoma cells. We have recently shown that TQ could exhibit a potent cytotoxic effect and induce apoptosis in mouse neuroblastoma (Neuro-2a) cells. In the present study, TQ treatment markedly decreased the adhesion and migration of Neuro-2a cells. TQ down-regulated MMP-2 and MMP-9 protein expression and mRNA levels and their activities. Furthermore, TQ significantly down-regulated the protein expression of transcription factor NF-κB (p65) but not significantly altered the expression of N-Myc. Taken together, our data indicated that TQ's inhibitory effect on the migration of Neuro-2a cells was mediated through the suppression of MMP-2 and MMP-9 expression, suggesting that TQ treatment can be a promising therapeutic strategy for human malignant neuroblastoma.

MicroRNAs (miRNAs) are a set of non-coding small RNA molecules that play a critical role in regulation of protein coding genes in cells. MiRNAs have been extensively studied as novel biomarkers, therapeutic targets, and new drugs in various human diseases. Breast cancer is a one of the leading tumor types significantly affecting women health worldwide. Over the past decade, a number of natural agents, such as paclitaxel and curcumin, have been applied for treatment and prevention of breast cancer due to their relatively low toxicity. However, the mechanisms of action have not been completely understood. Investigation on miRNAs is able to potentially provide a novel insight into better understanding the anticancer activities of these natural products. Given that a single miRNA can target multiple genes, theoretically, those genes involved in a certain phenotype can be clustered with one or a few miRNAs. Therefore, pleiotropic activities of natural agents should be interpreted by interactions between selected miRNAs and their targets. In this review, we summarize the latest publications related to the alterations of miRNAs by two natural agents (paclitaxel and curcumin) that are currently used in intervention of breast cancer, and conclude that the mechanism involving the regulation of miRNA expression is one of the keys to understand pleiotropic activities of natural agents.

Multiple myeloma (MM) is a plasma cell malignancy characterized by cytogenetic heterogeneity. In comparison with conventional karyotyping, fluorescence in situ hybridization (FISH) can efficiently detect various genetic changes in non-cycling plasma cells in 50-90 per cent of MM cases. The present study was undertaken in MM patients to evaluate the frequency and clinico-pathological significance of various cytogenetic abnormalities in the Indian population.

The O6-methylguanine-DNA-methyltransferase (MGMT) promoter methylation has been shown to be associated with improved outcomes in patients with glioblastoma (GBM) and may be a predictive marker of sensitivity to chemotherapy. However, determination of the MGMT promoter methylation status requires tissue obtained via surgical resection or biopsy. The aim of this study was to assess the ability of quantitative and qualitative imaging variables in predicting MGMT methylation status noninvasively.

Rhabdomyosarcomas (RMS) are rare, heterogeneous, soft tissue sarcomas and a common type of childhood malignancy with a distinct histomorphology. At the molecular level, alveolar rhabdomyosarcoma (ARMS), a subtype of RMS, harbors a signature genetic makeup characterized by specific translocations. The type of translocation and associated genetic aberrations correlate with disease progression, hence we used multiple molecular modalities including high-resolution array comparative genomic hybridization to explore the oncogenic gene fusion and associated copy number variations in a case of metastatic ARMS. We describe a case where traditional cytogenetic and molecular methods yielded inconclusive results in detecting the FOXO1 gene rearrangement. However, microarray analysis identified the essential FOXO1-PAX7 aberration and additional submicroscopic genomic alterations, including amplification of MYCN and MDM2 and deletion of RB1.

The BCR-ABL1 fusion gene derived from the Philadelphia chromosome, resulting from a classical translocation event t(9;22)(q34.13;q11.23), is responsible for the pathogenesis of chronic myeloid leukemia (CML) in more than 90% of the patients. The isoderivative chromosome 22, ider(22), and relative amplification or duplication of the BCR-ABL1 gene have been considered as one of the major reasons associated with the resistance to chemotherapy with imatinib mesylate, but the data remain unclear. GTG-banding together with FISH were performed to identify the presence of the ider(22) chromosome. Reverse transcription-polymerase chain reaction (RT-PCR) for the detection of BCR-ABL1 fusion transcripts and BCR-ABL1 kinase domain mutation analysis were carried out in this study. Conventional and molecular cytogenetic analysis on metaphase chromosomes confirmed the presence of ider(22) chromosomes in both patients. Molecular characterization revealed the presence of a 210-kDa BCR-ABL1 type b3a2 and lack of mutations at the kinase domain region on the fusion product in both patients. The occurrence of the ider(22) chromosome could be considered as an important marker correlated with the aggressive progression of CML as well as the emergence of drug-resistant cell clones.