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.

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.

Electronic supplementary material

The online version of this article (doi:10.1186/s12885-016-2942-5) contains supplementary material, which is available to authorized users.

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.

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 (3β-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.

Evaluation of inhibitory effects of benzothiazole and 3-amino-benzothiazolium derivatives on DNA topoisomerase II by molecular modeling studies

There has been considerable interest in DNA topoisomerases over the last decade, as they have been shown to be one of the major cellular targets in anticancer drug development. Previously we synthesized some benzothiazole derivatives and corresponding benzothiazolium forms, and tested their DNA inhibitory activity to develop novel antitumor agents. Among the 12 prepared compounds, compound BM3 (3-aminobenzothiazole-3-ium 4-methylbenzene sulfonate) exhibited extreme topoisomerase II inhibitory activity compared with the reference drug etoposide. We also tried to determine the DNA and enzyme binding abilities of BM3 and found that BM3 acted on topoisomerase II first at low doses, while it had also showed DNA minor groove binding properties at higher doses. In this study the interactions between DNA topoisomerase II and the compounds were examined in detail by molecular modelling studies such as molecular docking and pharmacophore analysis performed using Discovery Studio 3.5. As a result, it was found that benzothiazolium compounds exhibited a totally different mechanism than benzothiazoles by binding to the different amino acids at the active site of the protein molecule. 3-Aminobenzothiazoliums are worthy of carrying onto anticancer studies; BM3 especially would be a good anticancer candidate for preclinical studies.

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.

Vaccination of dairy cows with recombinant Streptococcus uberis adhesion molecule induces antibodies that reduce adherence to and internalization of S. uberis into bovine mammary epithelial cells

Streptococcus uberis is an important environmental mastitis pathogen that causes subclinical and clinical mastitis in lactating and nonlactating cows and heifers throughout the world. Previous work from our laboratory suggests that S. uberis adhesion molecule (SUAM) is involved in S. uberis pathogenesis and may be an excellent target for vaccine development. The objective of this study was to evaluate the antibody response of cattle vaccinated with recombinant SUAM (rSUAM). Uninfected primiparous dairy cows (n=30) in late lactation were divided randomly into three groups of 10 cows each: control, 200 μg rSUAM, and 400 μg rSUAM. Cows in groups vaccinated with 200 μg and 400 μg rSUAM received an emulsion containing adjuvant, phosphate-buffered saline (PBS) and affinity purified rSUAM. Cows in the control group received an emulsion containing adjuvant and PBS. Cows were vaccinated subcutaneously in the neck region at drying off (D-0), 28 d after drying off (D+28) and within 7 d after calving. Serum was collected at D-0, D+28, at calving (C-0), calving vaccination (CV), and during early lactation (CV+14). Serum antibody responses were measured by an ELISA against rSUAM. Following the first vaccination a significant increase in anti-rSUAM antibodies was detected at D+28 in cows from groups vaccinated with 200 μg and 400 μg rSUAM when compared to the control group. This increase in anti-rSUAM antibodies continued following the second immunization at D+28; reaching the highest levels in the post-parturient sampling period (C0), after which antibodies appeared to plateau. S. uberis UT888 pretreated with several dilutions of heat-inactivated serum from cows vaccinated with rSUAM, affinity purified antibodies against rSUAM, and to a 17 amino acid long peptide from the N terminus of SUAM (pep-SUAM) were co-cultured with bovine mammary epithelial cells and adherence to and internalization of S. uberis into epithelial cells was measured. Compared to untreated controls, opsonization of two strains of S. uberis with sera from cows vaccinated with rSUAM, with affinity purified rSUAM antibodies, or with affinity purified pep-SUAM antibodies significantly reduced adherence to and internalization of this pathogen into bovine mammary epithelial cells. In conclusion, subcutaneous vaccination of dairy cows with rSUAM during physiological transitions of the mammary gland either from or to a state of active milk synthesis induced antibodies in serum and milk and these antibodies reduced adherence to and internalization of S. uberis into mammary epithelial cells under in vitro conditions. SUAM appears to be an excellent candidate for vaccine development.

Spin- and parity-resolved level densities from the fine structure of giant resonances

Level densities of J pi=2+ and 2- states extracted from high-resolution studies of E2 and M2 giant resonances in 58Ni and 90Zr are used to test recent predictions of a possible parity dependence. The experimental results are compared to a combinatorial approach based on the Hartree-Fock-Bogoliubov model and to shell-model Monte Carlo calculations including both spin and parity projection. No parity dependence is observed experimentally, which is in agreement for 90Zr but in contrast with the model predictions for 58Ni.

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.