Discovering biomarkers from gene expression data for predicting cancer subgroups using neural networks and relational fuzzy clustering

Background  

The four heterogeneous childhood cancers, neuroblastoma, non-Hodgkin lymphoma, rhabdomyosarcoma, and Ewing sarcoma present a similar histology of small round blue cell tumor (SRBCT) and thus often leads to misdiagnosis. Identification of biomarkers for distinguishing these cancers is a well studied problem. Existing methods typically evaluate each gene separately and do not take into account the nonlinear interaction between genes and the tools that are used to design the diagnostic prediction system. Consequently, more genes are usually identified as necessary for prediction. We propose a general scheme for finding a small set of biomarkers to design a diagnostic system for accurate classification of the cancer subgroups. We use multilayer networks with online gene selection ability and relational fuzzy clustering to identify a small set of biomarkers for accurate classification of the training and blind test cases of a well studied data set.     

Expression profiling of genes regulated by TGF-beta: Differential regulation in normal and tumour cells

Background

The normalization of DNA microarrays allows comparison among samples by adjusting for individual hybridization intensities. The approaches most commonly used are global normalization methods that are based on the expression of all genes on the slide and on the modulation of a small proportion of genes. Alternative approaches must be developed for microarrays where the proportion of modulated genes and their distribution are unknown and they may be biased towards up- or down-modulated trends.

Results

The aim of the work is to study the use of spike-in controls to normalize low-density microarrays. Our test-array was designed to analyze gene modulation in response to hypoxia (a condition of low oxygen tension) in a macrophage cell line. RNA was extracted from controls and cells exposed to hypoxia, mixed with spike RNA, labeled and hybridized to our test-array. We used eight bacterial RNAs as source of spikes. The test-array contained the oligonucleotides specific for 178 mouse genes and those specific for the eight spikes. We assessed the quality of the spike signals, the reproducibility of the results and, in general, the nature of the variability. The small values of the coefficients of variation revealed high reproducibility of our platform either in replicated spots or in technical replicates. We demonstrated that the spike-in system was suitable for normalizing our platform and determining the threshold for discriminating the hypoxia modulated genes. We assessed the application of the spike-in normalization method to microarrays in which the distribution of the expression values was symmetric or asymmetric. We found that this system is accurate, reproducible and comparable to other normalization methods when the distribution of the expression values is symmetric. In contrast, we found that the use of the spike-in normalization method is superior and necessary when the distribution of the gene expression is asymmetric and biased towards up-regulated genes.

Conclusion

We demonstrate that spike-in controls based normalization is a reliable and reproducible method that has the major advantage to be applicable also to biased platform where the distribution of the up- and down-regulated genes is asymmetric as it may occur in diagnostic chips.     

Facility Death Review of Maternal and Neonatal Deaths in Bangladesh

Objectives

To explore the experiences, acceptance, and effects of conducting facility death review (FDR) of maternal and neonatal deaths and stillbirths at or below the district level in Bangladesh.

Methods

This was a qualitative study with healthcare providers involved in FDRs. Two districts were studied: Thakurgaon district (a pilot district) and Jamalpur district (randomly selected from three follow-on study districts). Data were collected between January and November 2011. Data were collected from focus group discussions, in-depth interviews, and document review. Hospital administrators, obstetrics and gynecology consultants, and pediatric consultants and nurses employed in the same departments of the respective facilities participated in the study. Content and thematic analyses were performed.

Results

FDR for maternal and neonatal deaths and stillbirths can be performed in upazila health complexes at sub-district and district hospital levels. Senior staff nurses took responsibility for notifying each death and conducting death reviews with the support of doctors. Doctors reviewed the FDRs to assign causes of death. Review meetings with doctors, nurses, and health managers at the upazila and district levels supported the preparation of remedial action plans based on FDR findings, and interventions were planned accordingly. There were excellent examples of improved quality of care at facilities as a result of FDR. FDR also identified gaps and challenges to overcome in the near future to improve maternal and newborn health.

Discussion

FDR of maternal and neonatal deaths is feasible in district and upazila health facilities. FDR not only identifies the medical causes of a maternal or neonatal death but also explores remediable gaps and challenges in the facility. FDR creates an enabled environment in the facility to explore medical causes of deaths, including the gaps and challenges that influence mortality. FDRs mobilize health managers at upazila and district levels to forward plan and improve healthcare delivery.     

Improvement of photoluminescence of Cu+ ion in Li2SO4

The synthesis of the Li₂SO₄: Cu phosphor using a wet chemical method is reported here. The XRD technique showed the crystalline nature of the prepared material. The presence of Na and K in the host affected the observed photoluminescence characteristics of Li₂SO₄: Cu. Photoluminsecent emission spectra of Li₂SO₄: Cu phosphor showed a very strong prominet peak at 387 nm in the indigo region due to 3d⁹ 4 s¹ ? 3d¹⁰ transition of the Cu⁺ ion. The increase in peak intensity of the PL spectrum suggests that Cu⁺ acts as the luminescence center in the present matrix. Copyright © 2010 John Wiley & Sons, Ltd.     

Role of PKCα-p(38)MAPK-G(i)α axis in NADPH oxidase derived O(2)(·-)-mediated activation of cPLA(2) under U46619 stimulation in pulmonary artery smooth muscle cells

We have recently reported that treatment of bovine pulmonary artery smooth muscle cells with the thromboxane A(2) mimetic, U46619 stimulated NADPH oxidase derived O(2)(·-) level, which subsequently caused marked increase in [Ca(2+)](i)[17]. Herein, we demonstrated that O(2)(·-)-mediated increase in [Ca(2+)](i) stimulates an aprotinin sensitive proteinase activity, which proteolytically activates PKC-α under U46619 treatment to the cells. The activated PKC-α then phosphorylates p(38)MAPK and that subsequently caused G(i)α phosphorylation leading to stimulation of cPLA(2) activity in the cell membrane.     

Correlation of HER1/EGFR expression and degree of radiosensitizing effect of the HER1/EGFR-tyrosine kinase inhibitor erlotinib

Epidermal growth factor receptor (HER1/EGFR)-mediated signal transduction pathways are important in cellular response to ionizing radiation. High HER1/EGFR expression on cancer cells may contribute to radioresistance. In this pre-clinical study, we evaluated the radiosensitizing effect of erlotinib, a small molecule HER1/EGFR inhibitor in three human cancer cell lines with different HER1/EGFR expression--A431 (very high expression), H157 (moderate expression) and H460 (low expression). Our results demonstrated that A431 was the most radioresistant, while H460 was the most radiosensitive. However, A431 cells were the most sensitive to erlotinib (IC50 = 300 nM) and H460 cells the most resistant (IC50 = 8 microM). H157 had intermediate sensitivity to radiation and erlotinib (IC50 = 3 microM). With 300 nM erlotinib, the radiation dose enhancement ratios (DER) were 1.40, 1.17 and 1.04 in A431, H157 and H460, respectively. Treatment with erlotinib for 24 hr at 300 nM increased G1 arrest by 18.6, 2.0 and 4.8% in A431, H157 and H460, respectively. Erlotinib-induced apoptosis was augmented by radiation in A431 cells only. In conclusion, high HER1/EGFR expression may result in a high degree of radiosensitization with erlotinib combined with radiation. The extent of erlotinib-induced radiosensitization was proportional to HER1/EGFR expression, as well as autophosphorylation of the human epidermal growth factor receptor (HER1/EGFR).     

Homologous recombination: ends as the means

Broken chromosomal ends in somatic cells of higher plants frequently heal by the ligation of DNA ends to unrelated sequences or to sequences with micro-homologies. This pathway of DNA-strand-break repair is the bane of gene-targeting attempts in plants. However, there is a second somatic pathway of chromosome repair, which is driven by DNA-sequence homology. Observations from yeast, fly and plants of homologous-recombination mechanisms point towards new strategies of gene targeting in plants.