Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

Therapy development for adult diffuse glioma is hindered by incomplete knowledge of somatic glioma driving alterations and suboptimal disease classification. We defined the complete set of genes associated with 1,122 diffuse grade II-III-IV gliomas from The Cancer Genome Atlas and used molecular profiles to improve disease classification, identify molecular correlations, and provide insights into the progression from low- to high-grade disease. Whole-genome sequencing data analysis determined that ATRX but not TERT promoter mutations are associated with increased telomere length. Recent advances in glioma classification based on IDH mutation and 1p/19q co-deletion status were recapitulated through analysis of DNA methylation profiles, which identified clinically relevant molecular subsets. A subtype of IDH mutant glioma was associated with DNA demethylation and poor outcome; a group of IDH-wild-type diffuse glioma showed molecular similarity to pilocytic astrocytoma and relatively favorable survival. Understanding of cohesive disease groups may aid improved clinical outcomes

Assessment of C++ object-oriented mutation operators: A selective mutation approach

Mutation testing is an effective but costly testing technique. Several studies have observed that some mutants can be redundant and therefore removed without affecting its effectiveness. Similarly, some mutants may be more effective than others in guiding the tester on the creation of high‐quality test cases. On the basis of these findings, we present an assessment of C++ class mutation operators by classifying them into 2 rankings: the first ranking sorts the operators on the basis of their degree of redundancy and the second regarding the quality of the tests they help to design. Both rankings are used in a selective mutation study analysing the trade‐off between the reduction achieved and the effectiveness when using a subset of mutants. Experimental results consistently show that leveraging the operators at the top of the 2 rankings, which are different, lead to a significant reduction in the number of mutants with a minimum loss of effectiveness

Generating compact classifier systems using a simple artificial immune system

Current artificial immune system (AIS) classifiers have two major problems: 1) their populations of B-cells can grow to huge proportions, and 2) optimizing one B-cell (part of the classifier) at a time does not necessarily guarantee that the B-cell pool (the whole classifier) will be optimized. In this paper, the design of a new AIS algorithm and classifier system called simple AIS is described. It is different from traditional AIS classifiers in that it takes only one B-cell, instead of a B-cell pool, to represent the classifier. This approach ensures global optimization of the whole system, and in addition, no population control mechanism is needed. The classifier was tested on seven benchmark data sets using different classification techniques and was found to be very competitive when compared to other classifiers

Search-Based Mutant Selection for Efficient Test Suite Improvement: Evaluation and Results

Context: Search-based techniques have been applied to almost all areas in software engineering, especially to software testing, seeking to solve hard optimization problems. However, the problem of selecting mutants to improve the test suite at a lower cost has not been explored to the same extent as other problems, such as mutant selection for test suite evaluation or test data generation. Objective: In this paper, we apply search-based mutant selection to enhance the quality of test suites efficiently. Namely, we use the technique known as Evolutionary Mutation Testing (EMT), which allows reducing the number of mutants while preserving the power to refine the test suite. Despite reported benefits of its application, the existing empirical results were derived from a limited number of case studies, a particular set of mutation operators and a vague measure, which currently makes it difficult to determine the real performance of this technique. Method: This paper addresses the shortcomings of previous studies, providing a new methodology to evaluate EMT on the basis of the actual improvement of the test suite achieved by using the evolutionary strategy. We make use of that methodology in new experiments with a carefully selected set of real-world C++ case studies. Results: EMT shows a good performance for most case studies and levels of demand of test suite improvement (around 45% less mutants than random selection in the best case). The results reveal that even a reduced subset of mutants selected with EMT can serve to increase confidence in the test suite, especially in programs with a large set of mutants. Conclusions: These results support the use of search-based techniques to solve the problem of mutant selection for a more efficient test suite refinement. Additionally, we identify some aspects that could foreseeably help enhance EMT

A Systematics for Discovering the Fundamental Units of Bacterial Diversity

Bacterial systematists face unique challenges when trying to identify ecologically meaningful units of biological diversity. Whereas plant and animal systematists are guided by a theory-based concept of species, microbiologists have yet to agree upon a set of ecological and evolutionary properties that will serve to define a bacterial species. Advances in molecular techniques have given us a glimpse of the tremendous diversity present within the microbial world, but significant work remains to be done in order to understand the ecological and evolutionary dynamics that can account for the origin, maintenance, and distribution of that diversity. We have developed a conceptual framework that uses ecological and evolutionary theory to identify the DNA sequence clusters most likely corresponding to the fundamental units of bacterial diversity. Taking into account diverse models of bacterial evolution, we argue that bacterial systematics should seek to identify ecologically distinct groups with evidence of a history of coexistence, as based on interpretation of sequence clusters. This would establish a theory-based species unit that holds the dynamic properties broadly attributed to species outside of microbiology

TNF-insulin crosstalk at the transcription factor GATA6 is revealed by a model that links signaling and transcriptomic data tensors

Signal -transduction networks coordinate transcriptional programs activated by diverse extracellular stimuli, such as growth factors and cytokines. Cells receive multiple stimuli simultaneously, and mapping how activation of the integrated signaling network affects gene expression is a challenge. We stimulated colon adenocarcinoma cells with various combinations of the cytokine tumor necrosis factor (TNF) and the growth factors insulin and epidermal growth factor (EGF) to investigate signal integration and transcriptional crosstalk. We quantitatively linked the proteomic and transcriptomic data sets by implementing a structured computational approach called tensor partial least squares regression. This statistical model accurately predicted transcriptional signatures from signaling arising from single and combined stimuli and also predicted time-dependent contributions of signaling events. Specifically, the model predicted that an early-phase, Akt-associated signal downstream of insulin repressed a set of transcripts induced by TNF. Through bioinformatics and cell-based experiments, we identified the Akt-repressed signal as glycogen synthase kinase 3 (GSK3)–catalyzed phosphorylation of Ser37 on the long form of the transcription factor GATA6. Phosphorylation of GATA6 on Ser37 promoted its degradation, thereby preventing GATA6 from repressing transcripts that are induced by TNF and attenuated by insulin. Our analysis showed that predictive tensor modeling of proteomic and transcriptomic data sets can uncover pathway crosstalk that produces specific patterns of gene expression in cells receiving multiple stimuli

Identifying aging-related genes in mouse hippocampus using gateway nodes

BACKGROUND: High-throughput studies continue to produce volumes of metadata representing valuable sources of information to better guide biological research. With a stronger focus on data generation, analysis models that can readily identify actual signals have not received the same level of attention. This is due in part to high levels of noise and data heterogeneity, along with a lack of sophisticated algorithms for mining useful information. Networks have emerged as a powerful tool for modeling high-throughput data because they are capable of representing not only individual biological elements but also different types of relationships en masse. Moreover, well-established graph theoretic methodology can be applied to network models to increase efficiency and speed of analysis. In this project, we propose a network model that examines temporal data from mouse hippocampus at the transcriptional level via correlation of gene expression. Using this model, we formally define the concept of “gateway” nodes, loosely defined as nodes representing genes co-expressed in multiple states. We show that the proposed network model allows us to identify target genes implicated in hippocampal aging-related processes. RESULTS: By mining gateway genes related to hippocampal aging from networks made from gene expression in young and middle-aged mice, we provide a proof-of-concept of existence and importance of gateway nodes. Additionally, these results highlight how network analysis can act as a supplement to traditional statistical analysis of differentially expressed genes. Finally, we use the gateway nodes identified by our method as well as functional databases and literature to propose new targets for study of aging in the mouse hippocampus. CONCLUSIONS: This research highlights the need for methods of temporal comparison using network models and provides a systems biology approach to extract information from correlation networks of gene expression. Our results identify a number of genes previously implicated in the aging mouse hippocampus related to synaptic plasticity and apoptosis. Additionally, this model identifies a novel set of aging genes previously uncharacterized in the hippocampus. This research can be viewed as a first-step for identifying the processes behind comparative experiments in aging that is applicable to any type of temporal multi-state network