Induction of senescence in cancer cells by 5′-Aza-2′-deoxycytidine: Bioinformatics and experimental insights to its targets

5′-Aza-2′-deoxycytidine (5-Aza-dC) is a demethylating drug that causes genome-wide hypomethylation resulting in the expression of several tumor suppressor genes causing growth arrest of cancer cells. Cancer is well established as a multifactorial disease and requires multi-module therapeutics. Search for new drugs and their approval by FDA takes a long time. Keeping this in view, research on new functions of FDA-approved anticancer drugs is desired to expand the list of multi-module functioning drugs for cancer therapy. In this study, we conducted an analysis for new functions of 5-Aza-dC by applying bio-chemo-informatics approach. The potential of 5-Aza-dC bioactivity was analyzed by PASS online and Molinspiration. Target proteins were predicted by SuperPred. The protein networks and biological processes were analyzed by Biological Networks using Gene Ontology tool, BINGO, based on BIOGRID database. Interactions between 5-Aza-dC and targeted proteins were examined by Autodoc Vina integrated into pyrx software. Induction of p53 by 5-Aza-dC was tested in vitro using cancer cells. Bioinformatics analyses predicted that 5-Aza-dC functions as a p53 inducer, radiosensitizer, and inhibitor of some enzymes. It was predicted to target proteins including MDM2, POLA1, POLB, and CXCR4 that are involved in the induction of DNA damage response and p53-HDM2-p21 signaling. In this study, we provide experimental evidence showing HDM2 is one of the targets of 5-AZA-dC leading to activation of p53 pathway and growth arrest of cells. Furthermore, we found that the combinatorial treatment of 5-AZA-dC with three other drugs caused drug resistance. We discuss that 5-Aza-dC-induced senescence is a multi-module drug that controls cell proliferation phenotype not only by proteins but also by noncoding miRNAs. Further studies are warranted to dissect these mechanisms and establish 5-Aza-dC as an effective multi-module anticancer reagent.     

Discovering DNA methylation patterns for long non-coding RNAs associated with cancer subtypes

Despite growing evidence demonstrates that the long non-coding ribonucleic acids (lncRNAs) are critical modulators for cancers, the knowledge about the DNA methylation patterns of lncRNAs is quite limited. We develop a systematic analysis pipeline to discover DNA methylation patterns for lncRNAs across multiple cancer subtypes from probe, gene and network levels. By using The Cancer Genome Atlas (TCGA) breast cancer methylation data, the pipeline discovers various DNA methylation patterns for lncRNAs across four major subtypes such as luminal A, luminal B, her2-enriched as well as basal-like. On the probe and gene level, we find that both differentially methylated probes and lncRNAs are subtype specific, while the lncRNAs are not as specific as probes. On the network level, the pipeline constructs differential co-methylation lncRNA network for each subtype. Then, it identifies both subtype specific and common lncRNA modules by simultaneously analyzing multiple networks. We show that the lncRNAs in subtype specific and common modules differ greatly in terms of topological structure, sequence conservation as well as expression. Furthermore, the subtype specific lncRNA modules serve as biomarkers to improve significantly the accuracy of breast cancer subtypes prediction. Finally, the common lncRNA modules associate with survival time of patients, which is critical for cancer therapy.     

Photodynamic Therapy: Past,Present and Future

Though we crossed many milestones in the field of medicine and health care in eradicating some deadly diseases over the past decades, cancer remained a challenge taking the lives of millions of people and having adverse effects on the quality of life of survivors. Chemotherapy and radiotherapy, the two existing major treatment modalities, have severe side effects and patients undergoing these treatments experience unbearable pain. Consequently, clinicians and researchers are working for the alternate treatment regimens, which can provide complete cure with minimum or no side effects. To this end, the present review highlights the major advances and future promises of photodynamic therapy, an emerging and promising therapeutic modality for combating cancer. We delve on various important aspects of photodynamic therapy including principle, mechanism of action, brief history and development of photosensitizers from first generation to the existing third generation, delivery strategies, development or suppression of immunity, combination therapy and future prospects.     

In situ spectral imaging of marker proteins in gastric cancer with near-infrared and visible quantum dots probes

This study presents the investigation of bioconjugating ability of near-infrared (NIR) CdSeTe/ZnS quantum dots (QDs) (710 nm) and visible CdSe QDs (595 nm) in immunofluorescent staining for cancer biomarkers in gastric cancer tissues probed with the homemade Hadamard transform (HT) spectral imaging microscope and a commercial multispectral imaging system. The results show that imunostaining ability of NIR QDs probes is stronger than that of visible QDs when the two kinds of QDs are simultaneously used to probe the cancer biomarkers such as cytokeratin 20 (CK20) and proliferating cell nuclear antigen (PCNA) in gastric cancer tissues. Moreover, when the two QDs probes are used for immunostaining successively for the same target molecules, staining order has great influences on the final results due to their different conjugating ability to the marker proteins. The results imply that NIR QDs hold more promise for real-time imaging of tumor tissues due to its higher sensitivity and contrast. In addition, the results also demonstrate the potential of Hadamard transform spectral imaging as a useful tool in biomedical analysis and quantitative evaluation for tumor tissues.     

Evaluation of photodynamic therapy (PDT) procedures using microfluidic system

A hybrid PDMS/glass microfluidic system for evaluation of the efficiency of photodynamic therapy is presented. 5-aminolevulinic acid (ALA) was used as a precursor of photosensitizer. The geometry of the microdevice presented in this paper enables to test different concentrations of the photosensitizer in a single assay. The viability of the A549 cells was determined 24 h after PDT procedure (irradiation with light which induced a photosensitizer accumulated in carcinoma cells, λ = 625 nm). The presented results confirmed the possibility to perform the photodynamic therapy process in vitro in microscale and the possibility to assess its effectiveness. Moreover, because two identical microstructures on a single chip were performed, the microchip can be used for examination simultaneously various cell lines (carcinoma and normal) or various photosensitizers.     

On the maximum total sample size of a group sequential test about bivariate binomial proportions

For testing “univariate” binomial proportions, it has been proven that, under mild conditions, there exist group sequential designs which satisfy the pre-specified Type I error and power of the single-stage design while the sample size is bounded above by that of the single-stage design (Kepner and Chang, 2003). In this article, we extend this result and prove the existence of such group sequential designs for various decision rules in the space of bivariate binomial variables. We also demonstrate how to obtain the actual group sequential designs for detecting changes in bivariate binomial variables.     

Evaluating shielding effectiveness for reducing space radiation cancer risks

We discuss calculations of probability distribution functions (PDF) representing uncertainties in projecting fatal cancer risk from galactic cosmic rays (GCR) and solar particle events (SPE). The PDFs are used in significance tests for evaluating the effectiveness of potential radiation shielding approaches. Uncertainties in risk coefficients determined from epidemiology data, dose and dose–rate reduction factors, quality factors, and physics models of radiation environments are considered in models of cancer risk PDFs. Competing mortality risks and functional correlations in radiation quality factor uncertainties are included in the calculations. We show that the cancer risk uncertainty, defined as the ratio of the upper value of 95% confidence interval (CI) to the point estimate is about 4-fold for lunar and Mars mission risk projections. For short-stay lunar missions (), SPEs present the most significant risk, however one that is mitigated effectively by shielding, especially for carbon composites structures with high hydrogen content. In contrast, for long duration lunar () or Mars missions, GCR risks may exceed radiation risk limits that are based on acceptable levels of risk. For example, the upper 95% CI exceeding 10% fatal risk for males and females on a Mars mission. For reducing GCR cancer risks, shielding materials are marginally effective because of the penetrating nature of GCR and secondary radiation produced in tissue by relativistic particles. At the present time, polyethylene or carbon composite shielding cannot be shown to significantly reduce risk compared to aluminum shielding based on a significance test that accounts for radiobiology uncertainties in GCR risk projection.     

Bayesian analysis of lymphatic spreading patterns in cancer of the thoracic esophagus

For the treatment of patients with cancer of the thoracic esophagus, lymphatic spreading is one important factor to infer how advanced their cancer is. We introduced a one-dimensional scale based on lymphatic spreading patterns, the stage of cancer, to express how advanced their cancer is, and we proposed a method to infer each patient's stage from his lymphatic spreading pattern by applying a Bayesian model. Our Bayesian model was built based on the assumption that lymphatic spreading in cancer could be explained as what was brought about by the advance of stage. In the modeling, we introduced the probability of what stage each patient was in as a prior distribution. We also introduced distribution functions of Weibull distributions to express the relation between the advance of stage and the increase of the probability of metastasis. Our model was applied to the data of nodal involvement obtained from 103 patients with cancer of the thoracic esophagus and the parameters were estimated with the maximum likelihood method. AIC was used to check that the data had enough information to be divided into the stages of a clinically reasonable number. With the estimated parameters, we inferred the probability of metastasis to each lymph node in each stage and calculated by Bayes' theorem with 31 new patients the probability of what stage they were in. The results well represented some characteristics of the lymphatic spreading and suggested the appropriateness of our approach.The present study was carried out under the ISM Cooperative Research Program (91-ISM·CRP-18).     

Preliminary report on detection of papillomaviruses types 6, 11, 16, and 18 in laryngeal benign and malignant lesions

Recently, clinicians have observed an increase in the incidence of laryngeal papilloma coincident with the rising incidence of venereal warts. The lesions occur in young adults of professional singing age. Different types of human papillomavirus (HPV) are presented. Gynecologic exam revealed cervical tumors, involving 18 HPV in benign and malignant lesions. Thirty patients with the following pathologic conditions were studied: 10 papillomas, 10 severe dysplasias, and 10 invasive cancers. All the lesions were located on the free edge of the vocal folds or the anterior commissure involving the epithelium. The results are as follows: 11 patients (33%) had virus infection, of which four had HPV 6 or HPV 11 on laryngeal papilloma, three had HPV 16 or HPV 18 on severe dysplasia, four had HPV 16 or HPV 18 on carcinoma; and 19 (66%) had no virus infection. Gynecologic research in this field is more advanced. However, this preliminary report raises interesting research questions in laryngology.     

In Light of Recent Developments,Application of Fluorescence Spectral Analysis in Tumor Diagnosis

Abstract

This paper reviews the background to cancer tumors. Fluorescence spectral analysis has been quantitatively applied to the detection of protoporphyrin IX (Pp‐IX) in transplanted squamous cell carcinoma (SCC) tissue and intra‐operative brain astrocytoma (glioblastoma) tissue after the administration of 5‐aminolevulinic acid (5‐ALA). Coincidence with the emission spectra of Pp‐IX incorporated into the tumor tissues (cryo‐sections) and a standard Pp‐IX in the miceller solution was confirmed. A calibration curve of the fluorescence intensity of Pp‐IX against a known concentration standard of Pp‐IX was established. From the fluorescence detection method (calibration curve), it was found that the longer alkyl‐chain length (methyl‐ and hexyl‐) 5‐ALA induced Pp‐IX in the SCC tissue. Furthermore, an ultrasound treatment enhanced the uptake of Pp‐IX during the topical administration of 5‐ALA derivatives. In the case of intra‐operative observation for the fluorescence intensity of Pp‐IX in the brain astrocytoma tissue, this quantitative detection in the cryo‐section demonstrated the intra‐operative observation for the fluorescence intensities (?, +/?, +, ++, +++) diagnosis was correlated closely with the grades of astrocytoma. The intensity increased exponentially with the cancer grades. In future, fluorescence spectral diagnosis of Pp‐IX in the tumor will be very useful for other clinical diagnosis of tumors using 5‐ALA.