1,721,011 research outputs found
The integration of gene and miRNA expression using pathway topology: a case study on Epithelial Ovarian Cancer
Get PDFPathways are formal descriptions of the biological processes involving finely regulated structures by which a cell converts molecules or processes signals. The study of gene expression in terms of pathways is defined as pathway analysis and aims at identifying groups of functionally related genes that show coordinated expression changes. Recently, pathway analysis moved from algorithms using merely gene list to ones exploiting the topology that define gene connections. A crucial, and unfortunately limiting step for these novel methods are the availability of the pathways as gene networks in which nodes are genes and edges are the relations between two elements.
To this aim, we develop a pathway data interpreter, called graphite, able to uniformly store, process and convert pathway information into gene networks. graphite has been made publicly available as R package within the Bioconductor platform. In the field of the topological pathway analysis, graphite fills the existing gap lying between technical and methodological aspects. graphite i) allows performing more informative analysis on omics data and ii) allows developing new methods based on the increased accessibil- ity of biological knowledge. However, the pathways of the four main public resources integrated into graphite (KEGG, Reactome, Biocarta and PID), still lack of crucial interactors: the microRNAs.
The microRNAs are small non-coding RNAs that post-transcriptionally regulate gene expression, their function on the messenger target is repressive but their effect on the transcription is dependent of the topology of the pathway in which the miRNA is involved. In the last decade, many targets have been discovered and experimentally validated, dedicated databases are available providing these information. Thus, I worked on an extension of graphite package able to integrate microRNAs in pathway topology, i) linking the non-coding RNAs to their validated target genes, ii) providing integrated networks suitable for the topological pathway analyses. The feasibility of this approach has been validated on a specific biological context, the early stage of Epithelial Ovarian Cancer (EOC).
EOC has long been considered as a single disease. The emerging opinion, however, sees ovarian cancer as a general term that encloses a group of histo-pathological subtypes sharing a common anatomic location. In collaboration with the Mario Negri institute, 257 stage I EOC tumour biopsies were collected and stratified into training and validation sets. miRNA microarray data was used to generate the most highly reproducible signatures for each histotype through a dedicated resampling inferential strategy. qRT- PCR was used to validate the results in both the training and validation set. The results indicate that the clear cell histotype is characterized by high expression levels of miR- 30a and miR-30a*, while mucinous patients by high levels of miR-192 and miR-194, interestingly as well as mucinous non-ovarian tissues. Then, the integrative approach that combines mRNA and miRNA profiles using graphite has been applied to identify the mucinous specific regulatory circuits. Taken together our findings demonstrate that EOC histotypes have discriminant regulatory circuits that drive the differentiation of the tumour environment. Our approach successfully guides us towards important biological results with interesting therapeutic implications in EOC
metaGraphite - a new layer of pathway annotation to get metabolite networks
No full textMetabolomics is an emerging 'omics' science involving the characterization of metabolites and metabolism in biological systems. Few bioinformatic tools have been developed for the visualization, exploration and analysis of metabolomic data within the context of metabolic pathways: some of them became rapidly obsolete and are no longer supported, others are based on a single database. A systematic collection of existing annotations has the potential of considerably boosting the investigation and contextualization of metabolomic measurements
Integration analysis of microRNA and mRNA expression profiles in human peripheral blood lymphocytes cultured in modeled microgravity
Get PDFWe analyzed miRNA and mRNA expression profiles in human peripheral blood lymphocytes (PBLs) incubated in microgravity condition, simulated by a ground-based rotating wall vessel (RWV) bioreactor.Our results show that 42 miRNAs were differentially expressed in MMG-incubated PBLs compared with 1 g incubated ones. Among these, miR-9-5p, miR-9-3p, miR-155-5p, miR-150-3p, and miR-378-3p were the most dysregulated. To improve the detection of functional miRNA-mRNA pairs, we performed
gene expression profiles on the same samples assayed for miRNA profiling and we integrated miRNA and mRNA expression data. The functional classification of miRNA-correlated genes evidenced significant enrichment in the biological processes of immune/inflammatory response, signal transduction, regulation of response to stress, regulation of programmed cell death, and regulation of cell proliferation. We identified the correlation of miR-9-3p, miR-155-5p, miR-150-3p, and miR-378-3p expression
with that of genes involved in immune/inflammatory response (e.g., IFNG and IL17F), apoptosis (e.g., PDCD4 and PTEN), and cell proliferation (e.g., NKX3-1 and GADD45A). Experimental assays of cell viability and apoptosis induction validated the results obtained by bioinformatics analyses demonstrating that in human PBLs the exposure to reduced gravitational force increases the frequency of apoptosis and decreases cell proliferation
Graphite Web: Web tool for gene set analysis exploiting pathway topology.
No full textGraphite web is a novel web tool for pathway analyses and network visualization for gene expres-sion data of both microarray and RNA-seq experi-ments. Several pathway analyses have been proposed either in the univariate or in the global and multivariate context to tackle the complexity and the interpretation of expression results. These methods can be further divided into ‘topological’ and ‘non-topological ’ methods according to their ability to gain power from pathway topology. Biological pathways are, in fact, not only gene lists but can be represented through a network where genes and connections are, respectively, nodes and edges. To this day, the most used approaches are non-topological and univariate although they miss the relationship among genes. On the contrary, topological and multivariate approaches are more powerful, but difficult to be used by re-searchers without bioinformatic skills. Here we present Graphite web, the first public web server for pathway analysis on gene expression data that combines topological and multivariate pathway analyses with an efficient system of interactive network visualizations for easy results interpret-ation. Specifically, Graphite web implements five different gene set analyses on three model organ-isms and two pathway databases. Graphite Web is freely available a
Wiring miRNAs to pathways: a topological approach to integrate miRNA and mRNA expression profiles.
No full textg<monospace>raphite</monospace> - a Bioconductor package to convert pathway topology to gene network
Get PDFAbstract Background Gene set analysis is moving towards considering pathway topology as a crucial feature. Pathway elements are complex entities such as protein complexes, gene family members and chemical compounds. The conversion of pathway topology to a gene/protein networks (where nodes are a simple element like a gene/protein) is a critical and challenging task that enables topology-based gene set analyses. Unfortunately, currently available R/Bioconductor packages provide pathway networks only from single databases. They do not propagate signals through chemical compounds and do not differentiate between complexes and gene families. Results Here we present graphite, a Bioconductor package addressing these issues. Pathway information from four different databases is interpreted following specific biologically-driven rules that allow the reconstruction of gene-gene networks taking into account protein complexes, gene families and sensibly removing chemical compounds from the final graphs. The resulting networks represent a uniform resource for pathway analyses. Indeed, graphite provides easy access to three recently proposed topological methods. The graphite package is available as part of the Bioconductor software suite. Conclusions graphite is an innovative package able to gather and make easily available the contents of the four major pathway databases. In the field of topological analysis graphite acts as a provider of biological information by reducing the pathway complexity considering the biological meaning of the pathway elements.</p
Identification and validation of microRNAs targeting genes of DNA-Damage Response in human lymphocytes irradiated with γ-rays
No full textIonizing radiation (IR) used in radiotherapy to treat cancer cells is a source of DNA damage, among which double-strand breaks (DSBs) represent the most deleterious lesions. The major problems encountered when treating cancer patients with radiotherapy are toxic side effects and lack of efficacy owing to radioresistance. Many human tumors have a strong DNA repair capacity and so radiation therapy has low efficacy against cancer cells displaying radioresistant phenotypes. Therefore, the possibility to inhibit DNA repair pathways, and in particular DSB repair, may represent an efficient way to sensitize human cells to IR induced killing. In presence of DSBs eukaryotic cells activate a highly regulated system pathway-the DNA-Damage Response (DDR)-which encompasses damage sensors, mediators, signal transducers and effectors of cell cycle progression/arrest, DNA repair and apoptosis. The expression of DDR genes is modulated by microRNAs (miRNAs), small non-coding RNAs that act as post-transcriptional regulators of gene expression by direct association with target transcripts.
The aim of our study is to assess the potential applicability of miRNA delivery in combination with ionizing radiation to increase the cytotoxic effects of IR in cancer cells. Indeed, the delivery into cancer cells of synthetic miRNAs that mimic endogenous miRNAs targeting genes of DDR pathway should perturb such process, making cells more sensitive to IR. To this purpose we are identifying and validating miRNAs targeting genes of DNA repair in human peripheral blood lymphocytes (PBLs) irradiated with γ-rays. We identified miRNA expression changes at two different times after irradiation (4 and 24h), with two different doses of radiation (0.2 and 2Gy). To improve the detection of target genes of radio-responsive miRNAs we analyzed mRNA expression profiles in irradiated PBLs and we integrated the transcriptome and microRNome to identify miRNAs modulating the expression of DDR genes. Our results show that few miRNA species are candidate to be essential regulators of genes of DDR, in particular, miRNAs targeting ATM, BAX, STAT5A, and genes of DNA repair DDB2, XPC, GADD45A, FANCF, LIG1. The in vitro validation with quantitative real-time PCR (qRT-PCR) and luciferase reporter assay confirmed several of the miRNA-mRNA interactions identified
Systems biology approach to the dissection of the complexity of regulatory networks in the S. scrofa cardiocirculatory system.
Get PDFGenome-wide experiments are routinely used to increase the understanding of the biological processes involved in the development and maintenance of a variety of pathologies. Although the technical feasibility of this type of experiment has improved in recent years, data analysis remains challenging. In this context, gene set analysis has emerged as a fundamental tool for the interpretation of the results. Here, we review strategies used in the gene set approach, and using datasets for the pig cardiocirculatory system as a case study, we demonstrate how the use of a combination of these strategies can enhance the interpretation of results. Gene set analyses are able to distinguish vessels from the heart and arteries from veins in a manner that is consistent with the different cellular composition of smooth muscle cells. By integrating microRNA elements in the regulatory circuits identified, we find that vessel specificity is maintained through specific miRNAs, such as miR-133a and miR-143, which show anti-correlated expression with their mRNA targets
A pan-cancer landscape of pathogenic somatic copy number variations
Get PDFObjective: Copy number variations (CNVs) play crucial roles in physiological and pathological processes, including cancer. However, the functional implications of somatic CNVs in tumor progression and evolution remain unclear. This study focuses on identifying CNV alterations with high pathogenic potential that drive and sustain tumorigenesis, distinguishing them from passenger alterations that accumulate during tumor growth. Our goal is to explore the variability of CNVs across different tumor types and infer their impact on tumor cell functions.Methods: Starting from 7352 copy number profiles across 33 different cancer types, we infer the pathogenicity of each CNV and perform both intra-and inter-tumor analyses to predict the functional impact of different genomic patterns. We evaluate the actionability of genes belonging to altered regions and we correlate the presence of pathogenic regions with genome instability patterns and patients' survival.Results: Our analysis uncovered large heterogeneity among different tumors suggesting in many cases distinct genetic drivers of tumorigenesis. Recurrent genomic alterations frequently coincide with dysfunctional homologous recombination pathways and negative regulation of the immune system. In certain tumors, the number of pathogenic CNVs emerged as a prognostic biomarker, highlighting their significance in cancer progression.Conclusion: This study contributes to elucidate the functional impact of pathogenic CNVs in tumor progression and sheds light on their potential as prognostic markers in specific cancer types
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