Netrank: network-based approach for biomarker discovery.

BACKGROUND: Integrating multi-omics data is fast becoming a powerful approach for predicting disease progression and treatment outcomes. In light of that, we introduce a modified version of the NetRank algorithm, a network-based algorithm for biomarker discovery that incorporates the protein associations, co-expressions, and functions with its phenotypic association to differentiate different types of cancer. NetRank is introduced here as a robust feature selection method for biomarker selection in cancer prediction. We assess the robustness and suitability of the RNA gene expression data through scanning genomic data for 19 cancer types with more than 3000 patients from The Cancer Genome Atlas (TCGA). RESULTS: The results of evaluating different cancer type profiles from the TCGA data demonstrate the strength of our approach to identifying interpretable biomarker signatures for cancer outcome prediction. NetRank's biomarkers segregate most cancer types with an area under the curve (AUC) above 90% using compact signatures. CONCLUSION: In this paper we provide a fast and efficient implementation of NetRank, with a case study from The Cancer Genome Atlas, to assess the performance. We incorporated complete functionality for pre and post-processing for RNA-seq gene expression data with functions for building protein-protein interaction networks. The source code of NetRank is freely available (at github.com/Alfatlawi/Omics-NetRank) with an installable R library. We also deliver a comprehensive practical user manual with examples and data attached to this paper.

NetRank Recovers Known Cancer Hallmark Genes as Universal Biomarker Signature for Cancer Outcome Prediction.

Gene expression can serve as a powerful predictor for disease progression and other phenotypes. Consequently, microarrays, which capture gene expression genome-wide, have been used widely over the past two decades to derive biomarker signatures for tasks such as cancer grading, prognosticating the formation of metastases, survival, and others. Each of these signatures was selected and optimized for a very specific phenotype, tissue type, and experimental set-up. While all of these differences may naturally contribute to very heterogeneous and different biomarker signatures, all cancers share characteristics regardless of particular cell types or tissue as summarized in the hallmarks of cancer. These commonalities could give rise to biomarker signatures, which perform well across different phenotypes, cell and tissue types. Here, we explore this possibility by employing a network-based approach for pan-cancer biomarker discovery. We implement a random surfer model, which integrates interaction, expression, and phenotypic information to rank genes by their suitability for outcome prediction. To evaluate our approach, we assembled 105 high-quality microarray datasets sampled from around 13,000 patients and covering 13 cancer types. We applied our approach (NetRank) to each dataset and aggregated individual signatures into one compact signature of 50 genes. This signature stands out for two reasons. First, in contrast to other signatures of the 105 datasets, it is performant across nearly all cancer types and phenotypes. Second, It is interpretable, as the majority of genes are linked to the hallmarks of cancer in general and proliferation specifically. Many of the identified genes are cancer drivers with a known mutation burden linked to cancer. Overall, our work demonstrates the power of network-based approaches to compose robust, compact, and universal biomarker signatures for cancer outcome prediction.

Evaluation of ATAD2 as a Potential Target in Hepatocellular Carcinoma.

PURPOSE: Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death worldwide with lack of effective systemic chemotherapy. In this study, we aimed to evaluate the value of ATPase family AAA domain-containing protein 2 (ATAD2) as a biomarker and potential therapeutic target for HCC. METHODS: The expression of ATAD2 was tested in different HCC patient cohorts by immunohistochemistry and comparative transcriptional analysis. The co-expression of ATAD2 and proliferation markers was compared during liver regeneration and malignancy with different bioinformatics tools. The cellular effects of ATAD2 inactivation in liver malignancy was tested on cell cycle, apoptosis, and colony formation ability as well as tumor formation using RNA interference. The genes affected by ATAD2 inactivation in three different HCC cell lines were identified by global gene expression profiling and bioinformatics tools. RESULTS: ATAD2 overexpression is closely correlated with HCC tumor stage. There was gradual increase from dysplasia, well-differentiated and poorly-differentiated HCC, respectively. We also observed transient upregulation of ATAD2 expression during rat liver regeneration in parallel to changes in Ki-67 expression. ATAD2 knockdown resulted in apoptosis and decreased cell survival in vitro and decreased tumor formation in some HCC cell lines. However, three other HCC cell lines tested were not affected. Similarly, gene expression response to ATAD2 inactivation in different HCC cell lines was highly heterogeneous. CONCLUSIONS: ATAD2 is a potential proliferation marker for liver regeneration and HCC. It may also serve as a therapeutic target despite heterogeneous response of malignant cells.

Benzoxazines as new human topoisomerase I inhibitors and potential poisons.

BACKGROUND: The numbers of topoisomerase I targeted drugs on the market are very limited although they are used clinically for treatment of solid tumors. Hence, studies about finding new chemical structures which specifically target topoisomerase I are still remarkable. OBJECTIVES: In this present study, we tested previously synthesized 3,4-dihydro-2H-1,4-benzoxazin-3-one derivatives to reveal their human DNA topoisomerase I inhibitory potentials. METHODS: We investigated inhibitory activities of 3,4-dihydro-2H-1,4-benzoxazin-3-one derivatives on human topoisomerase I by relaxation assay to clarify inhibition mechanisms of effective derivatives with EMSA and T4 DNA ligase based intercalation assay. With SAR study, it was tried to find out effective groups in the ring system. RESULTS: While 10 compounds showed catalytic inhibitory activity, 8 compounds were found to be potential topoisomerase poisons. 4 of them also exhibited both activities. 2-hydroxy-3,4-dihydro-2H-1,4-benzoxazin-3-one (BONC-001) was the most effective catalytic inhibitor (IC50:8.34 mM) and ethyl 6-chloro-4-methyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-acetate (BONC-013) was the strongest potential poison (IC50:0.0006 mM). BONC-013 was much more poisonous than camptothecin (IC50:0.034 mM). Intercalation assay showed that BONC-013 was not an intercalator and BONC-001 most probably prevented enzyme-substrate binding in an unknown way. Another important result of this study was that OH group instead of ethoxycarbonylmethyl group at R position of benzoxazine ring was important for hTopo I catalytic inhibition while the attachment of a methyl group of R1 position at R2 position were play a role for increasing of its poisonous effect. CONCLUSION: As a result, we presented new DNA topoisomerase I inhibitors which might serve novel constructs for future anticancer agent designs. Graphical abstract.

Vasculoprotective Effects of Pomegranate (Punica granatum L.).

Pomegranate (Punica granatum L.), one of the oldest known edible fruits, is nowadays broadly consumed throughout the world. Its fruits and seeds as well as other anatomical compartments (e.g., flowers and leaves) are rich in numerous bioactive compounds and therefore, the scientific interest in this plant has been constantly growing in recent years. It has been shown that pomegranate and its extracts exhibit potent antioxidative, antimicrobial, and anticarcinogenic properties. The present review summarizes some recent studies on pomegranate, highlighting mainly its vasculoprotective role attributed to the presence of hydrolyzable tannins ellagitannins and ellagic acid, as well as other compounds (e.g., anthocyanins and flavonoids). These in vitro and in vivo studies showed that substances derived from pomegranate reduce oxidative stress and platelet aggregation, diminish lipid uptake by macrophages, positively influence endothelial cell function, and are involved in blood pressure regulation. Clinical studies demonstrated that daily intake of pomegranate juice lessens hypertension and attenuates atherosclerosis in humans. Altogether, the reviewed studies point out the potential benefits of a broader use of pomegranate and its constituents as dietary supplements or as adjuvants in therapy of vascular diseases, such as hypertension, coronary artery disease, and peripheral artery disease.

Thiazolidinedione or Rhodanine: A Study on Synthesis and Anticancer Activity Comparison of Novel Thiazole Derivatives.

PURPOSE: A new series of thiazolyl-2,4-thiazolidinedione / rhodanine compounds T1-T23 was synthesized and tested for their anticancer activities. Hepatocellular carcinoma cell lines were chosen due to their strong drug resistance to test the new compounds. METHODS: All compounds were synthesized via Knoevenagel Condensation reaction and thiazolidinedione ester compounds (T3,T9,T15,T20) were hydrolyzed for obtaining the acidic compounds (T6,T12,T17,T23). All compounds were firstly screened for their anticancer activity against two hepatocellular carcinoma (HCC) cell lines, Huh7 and Plc/Prf/5 (Plc) cell lines by sulforhodamine B assay. Further IC50 values were calculated for three candidates (T4, T15, T21) in five different HCC (Huh7, Plc, Snu449, HepG2, Hep3B) and one breast cancer (Mcf7) cell line. RESULTS: Compounds T4, T15, T21 had very strong anticancer effects even though their 10 µM concentration in Huh7 cell line. According to IC50 values, T21 was the most effective compound with IC50 values in a range from 2 to 16 µM in 6 cancer cell lines. In terms of cytotoxicity T21 mostly affected Huh7 and interestingly it was less effective against Plc. CONCLUSIONS: Considering these results it can be suggested that compounds T4, T15 and T21 may lead to the development of more potent anticancer drugs in the future. This article is open to POST-PUBLICATION REVIEW. Registered readers (see "For Readers") may comment by clicking on ABSTRACT on the issue's contents page.

Synthesis and bio-molecular study of (+)-N-Acetyl-α-amino acid dehydroabietylamine derivative for the selective therapy of hepatocellular carcinoma.

BACKGROUND: The purpose of present work is to synthesize novel (+)-Dehydroabietylamine derivatives (DAAD) using N-acetyl-α-amino acid conjugates and determine its cytotoxic effects on hepatocellular carcinoma cells. METHODS: An analytical study was conducted to explore cytotoxic activity of DAAD on hepatocellular carcinoma cell lines. The cytotoxicity effect was recorded using sulforhodamine B technique. Cell cycle analysis was performed using Propidium Iodide (PI) staining. Based on cell morphology, anti growth activity and microarray findings of DAAD2 treatment, Comet assay, Annexin V/PI staining, Immunoperoxidase assay and western blots were performed accoringly. RESULTS: Hep3B cells were found to be the most sensitive with IC50 of 2.00 ± 0.4 µM against (+)-N-(N-Acetyl-L-Cysteine)-dehydroabietylamine as DAAD2. In compliance to time dependent morphological changes of low cellular confluence, detachment and rounding of DAAD2 treated cells; noticeable changes in G2/M phase were recorded may be leading to cell cycle cessation. Up-regulation (5folds) of TUBA1A gene in Hep3B cells was determined in microarray experiments. Apoptotic mode of cell death was evaluated using standardized staining procedures including comet assay and annexin V/PI staining, Immuno-peroxidase assay. Using western blotting technique, caspase dependant apoptotic mode of cell death was recorded against Hep3B cell line. CONCLUSION: It is concluded that a novel DAAD2 with IC50 values less than 8 µM can induce massive cell attenuation following caspase dependent apoptotic cell death in Hep3B cells. Moreover, the corelation study indicated that DAAD2 may have vital influence on cell prolifration properties.

Schizophrenia and gastroesophageal reflux symptoms.

BACKGROUND: Psychological factors and psychiatric disorders play a role in a variety of gastrointestinal illnesses, including esophageal diseases. AIM: The aim of the present study was to evaluate the frequency of gastroesophageal reflux disease symptoms in patients with schizophrenia in Turkey. PATIENTS AND METHODS: Ninety-eight patients with schizophrenia and one hundred control individuals were enrolled in the study, which was undertaken at the Manisa State Hospital for Mental Health and Neurological Disorders and Celal Bayar University Gastroenterology Department. Case and control subjects alike underwent 30-45 min oral interviews conducted by a designated study coordinator (E.K.). The coordinator gathered information about demographic characteristics, social habits, and a large variety of symptoms suggestive of reflux disease or other gastrointestinal conditions. RESULTS: In terms of reflux symptoms, cough was the only significant association in schizophrenic patients than controls. Heartburn and regurgitation were more frequent in schizophrenic patients who smoked than in controls who were smokers. However, the prevalence of reflux symptoms in cigarette smokers versus nonsmoker patients with schizophrenia was similar. Heartburn and/or regurgitation occurred more frequently in patients with schizophrenic than controls with alcohol use. CONCLUSIONS: Psychiatric disorders might indirectly affect esophageal physiology through increased consumption of alcohol and nicotine.

Reliability and Validity of the Turkish Version of Abdel-Khalek's Death Anxiety Scale among College Students.

INTRODUCTION: Although death anxiety is considered a universal phenomenon, attitudes toward death may vary across populations that differ in terms of religion and culture. Abdel-Khalek's Death Anxiety Scale (ASDA) was developed on the basis of the rationale that there are specific concepts related to death and after death in Muslim populations. This study aims to translate and adapt ASDA in the Turkish population, examine its validity and reliability, and to compare its psychometric properties with the widely used Templer's Death Anxiety Scale (DAS). METHODS: A total of 220 medical students were included in the study. The Turkish version of ASDA, DAS, and Hospital Anxiety and Depression Scale were used for data collection. RESULTS: Cronbach's alpha coefficients were .86 for ASDA and .66 for DAS. Analysis by principal components with varimax rotation produced five factors for ASDA that explained 65.6% of total variance. ASDA and DAS were highly correlated with each other (r=.68, p<.001). CONCLUSION: The results of this study indicate that the Turkish version of Abdel-Khalek's Death Anxiety Scale is a reliable and valid instrument. The Turkish version of ASDA revealed better psychometric properties than DAS. This finding may reflect specific cultural and religious attitudes toward death or may result from more comprehensible language use in ASDA.

Comparative evaluation of in vitro cytotoxic effects among parent abietyl alcohol and novel fatty acid ester derivatives against MCF7 and hepatocellular carcinoma cell lines.

Synthesis of twelve hitherto unreported esters of abietyl alcohol and screening of these esters against four cancer cell lines including one breast cancer line MCF7 and four hepatocellular carcinoma cell lines (HCC) Huh7, Hep3B, Snu449 and Plc has been determined using SRB assay. The Cell cycle progression showed changes in cellular behaviour after 48 and 72 hours in MCF7 and Huh7 cell lines. Abietyl alcohol was obtained from the reduction of abietic acid, a tricyclic diterpene, isolated from oleoresin of Pinus longifolia Roxberghii.

Synthesis and characterization of amino acid conjugates of oleanolic acid and their in vitro cytotoxic effect on HCC cell lines.

Oleanolic acid (3ß-hydroxy-olean-12-en-28-oic acid; OA-01), a pentacyclic triterpene, exhibit a wide range of pharmacological and biological activities. We have isolated oleanolic acid from methanolic extract of Periploca aphylla, collected from surroundings of Karachi in the month of February. Furthermore, four known and two new C-28 amino acid conjugates of oleanolic acid were prepared to explore potential of these compounds on HCCs and one breast cancer cell line. Cytotoxic effects revealed that as compare to parent compound (OA-01), two derivatives OA-04 (p<0.0001) and OA-06 (p<0.01) showed significantly increased/higher inhibition rates.

[Closed reduction of zygoma tripod and isolated arch fractures with Volkmann bone hook]. / Zigoma tripod ve izole ark kiriklarinin Volkmann kemik kancasi ile kapali redüksiyonu.

OBJECTIVES: This study aims to investigate the effectiveness of closed reduction technique for the management of zygoma tripod or arch fractures without internal fixation. PATIENTS AND METHODS: Between June 2011 - December 2013, medical data of seven patients (2 females, 5 males; mean age 49.1 years; range 34 to 76 years) who were treated using closed reduction technique with Volkman bone hook due to zygoma tripod and isolated arch fractures were retrospectively analyzed. Symmetry and functional findings of the patients were assessed at three and six months postoperatively. RESULTS: No complication related to the closed reduction technique was observed. Inadequate reduction was seen in one patient with isolated zygoma arch fracture who was admitted in late-stage. CONCLUSION: Closed reduction using a bone hook can be safely applied in the management of isolated zygoma arch fractures and non-complicated zygoma tripod fractures without fixation.

Genome-wide transcriptional reorganization associated with senescence-to-immortality switch during human hepatocellular carcinogenesis.

Senescence is a permanent proliferation arrest in response to cell stress such as DNA damage. It contributes strongly to tissue aging and serves as a major barrier against tumor development. Most tumor cells are believed to bypass the senescence barrier (become "immortal") by inactivating growth control genes such as TP53 and CDKN2A. They also reactivate telomerase reverse transcriptase. Senescence-to-immortality transition is accompanied by major phenotypic and biochemical changes mediated by genome-wide transcriptional modifications. This appears to happen during hepatocellular carcinoma (HCC) development in patients with liver cirrhosis, however, the accompanying transcriptional changes are virtually unknown. We investigated genome-wide transcriptional changes related to the senescence-to-immortality switch during hepatocellular carcinogenesis. Initially, we performed transcriptome analysis of senescent and immortal clones of Huh7 HCC cell line, and identified genes with significant differential expression to establish a senescence-related gene list. Through the analysis of senescence-related gene expression in different liver tissues we showed that cirrhosis and HCC display expression patterns compatible with senescent and immortal phenotypes, respectively; dysplasia being a transitional state. Gene set enrichment analysis revealed that cirrhosis/senescence-associated genes were preferentially expressed in non-tumor tissues, less malignant tumors, and differentiated or senescent cells. In contrast, HCC/immortality genes were up-regulated in tumor tissues, or more malignant tumors and progenitor cells. In HCC tumors and immortal cells genes involved in DNA repair, cell cycle, telomere extension and branched chain amino acid metabolism were up-regulated, whereas genes involved in cell signaling, as well as in drug, lipid, retinoid and glycolytic metabolism were down-regulated. Based on these distinctive gene expression features we developed a 15-gene hepatocellular immortality signature test that discriminated HCC from cirrhosis with high accuracy. Our findings demonstrate that senescence bypass plays a central role in hepatocellular carcinogenesis engendering systematic changes in the transcription of genes regulating DNA repair, proliferation, differentiation and metabolism.

Genetics and epigenetics of liver cancer.

Hepatocellular carcinoma (HCC) represents a major form of primary liver cancer in adults. Chronic infections with hepatitis B (HBV) and C (HCV) viruses and alcohol abuse are the major factors leading to HCC. This deadly cancer affects more than 500,000 people worldwide and it is quite resistant to conventional chemo- and radiotherapy. Genetic and epigenetic studies on HCC may help to understand better its mechanisms and provide new tools for early diagnosis and therapy. Recent literature on whole genome analysis of HCC indicated a high number of mutated genes in addition to well-known genes such as TP53, CTNNB1, AXIN1 and CDKN2A, but their frequencies are much lower. Apart from CTNNB1 mutations, most of the other mutations appear to result in loss-of-function. Thus, HCC-associated mutations cannot be easily targeted for therapy. Epigenetic aberrations that appear to occur quite frequently may serve as new targets. Global DNA hypomethylation, promoter methylation, aberrant expression of non-coding RNAs and dysregulated expression of other epigenetic regulatory genes such as EZH2 are the best-known epigenetic abnormalities. Future research in this direction may help to identify novel biomarkers and therapeutic targets for HCC.

Depression, anxiety, health-related quality of life, and disability in patients with overt and subclinical thyroid dysfunction.

BACKGROUND: Thyroid dysfunction may impair the quality of life (QoL) and may cause psychological symptoms. The aim of this study is to investigate prospectively the effects of thyroid dysfunction on quality of life, levels of depression/anxiety and the changes in these variables after treatment. METHODS: A total of 160 subjects, consisting of an overt hypothyroidism group (n = 33), a subclinical hypothyroidism group (n = 43), an overt hyperthyroidism group (n = 51), a subclinical hyperthyroidism group (n = 13), and a healthy control group (n = 20) were included in the study. All groups were evaluated with the Hamilton Depression Rating Scale (HDRS), Hamilton Anxiety Rating Scale (HARS), Short Form-36 (SF-36), and Brief Disability Questionnaire (BDQ). Health-related quality of life (HRQL) was measured by SF-36. RESULTS: Anxiety and depressive symptoms were more severe in patients with overt hypo- and hyperthyroidism (p <0.001). The QoL was worse in overt or subclinical hyper- and hypothyroidism groups than in the control group [p = 0.013 for physical composite score (PCS); p = 0.002 for mental composite score (MCS)]. Psychological symptoms and QoL were improved in overt and subclinical hypothyroidism and overt hyperthyroidism groups as a result of the treatment. The overt hyper- and hypothyroidism groups showed more improvement than the subclinical groups. CONCLUSIONS: This study suggests that restoration of euthyroidism is accompanied by improvement on QoL and psychological symptoms in all groups except the subclinical hyperthyroidism group. Controlled, randomized studies in larger groups are, however, necessary.