A5023495931- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- MicroRNA in disease regulation
- Cell Image Analysis Techniques
- Advanced Electron Microscopy Techniques and Applications
- Cancer-related molecular mechanisms research
- Enzyme function and inhibition
- Metabolomics and Mass Spectrometry Studies
- Gene expression and cancer classification
- Glutathione Transferases and Polymorphisms
- Advanced Radiotherapy Techniques
- Biomedical Text Mining and Ontologies
- Alzheimer's disease research and treatments
- RNA Research and Splicing
- Epigenetics and DNA Methylation
- Circular RNAs in diseases
- Synthesis and biological activity
- Cancer Cells and Metastasis
- Melanoma and MAPK Pathways
- RNA and protein synthesis mechanisms
- Gene Regulatory Network Analysis
- Semantic Web and Ontologies
- Chronic Obstructive Pulmonary Disease (COPD) Research
- Management of metastatic bone disease
- Genomics, phytochemicals, and oxidative stress
National Research Council
2017-2024
Istituto di Analisi dei Sistemi ed Informatica Antonio Ruberti
2016-2024
Sapienza University of Rome
2014-2022
Institute for Systems Analysis
2019
National Academies of Sciences, Engineering, and Medicine
2019
University of Turin
1979-2005
Abstract Background miRNAs regulate the expression of several genes with one miRNA able to target multiple and gene be simultaneously targeted by more than miRNA. Therefore, it has become indispensable shorten long list miRNA-target interactions put in spotlight order gain insight into understanding regulatory mechanism orchestrated various cellular processes. A reasonable solution is certainly prioritize maximize effectiveness downstream analysis. Results We propose a new easy-to-use web...
The metabolic state represents a major hurdle for an effective adoptive T cell therapy (ACT). Indeed, specific lipids can harm CD8+ (CTL) mitochondrial integrity, leading to defective antitumor responses. However, the extent which affect CTL functions and fate remains unexplored. Here, we show that linoleic acid (LA) is positive regulator of activity by improving fitness, preventing exhaustion, stimulating memory-like phenotype with superior effector functions. We report LA treatment...
Several studies in recent times have linked gut microbiome (GM) diversity to the pathogenesis of cancer and its role disease progression through immune response, inflammation metabolism modulation. This study focused on use network analysis weighted gene co-expression (WGCNA) identify biological interaction between ecosystem metabolites that could impact immunotherapy response non-small cell lung (NSCLC) patients undergoing second-line treatment with anti-PD1. Metabolomic data were merged...
Recent findings have identified competing endogenous RNAs (ceRNAs) as the drivers in many disease conditions, including cancers. The ceRNAs indirectly regulate each other by reducing amount of microRNAs (miRNAs) available to target messenger (mRNAs). ceRNA interactions mediated miRNAs are modulated a titration mechanism, i.e. large changes expression levels either overcome, or relieve, miRNA repression on RNAs; similarly, very overexpression may abolish competition. also called "decoys"...
The novelty of new human coronavirus COVID-19/SARS-CoV-2 and the lack effective drugs vaccines gave rise to a wide variety strategies employed fight this worldwide pandemic. Many these rely on repositioning existing that could shorten time reduce cost compared de novo drug discovery. In study, we presented network-based algorithm for repositioning, called SAveRUNNER (Searching off-lAbel dRUg aNd NEtwoRk), which predicts drug–disease associations by quantifying interplay between targets...
Abstract In this study, we integrate the outcomes of co-expression network analysis with human interactome to predict novel putative disease genes and modules. We first apply SWItch Miner (SWIM) methodology, which predicts important (switch) within that regulate state transitions, then map them protein–protein interaction (PPI, or interactome) disease–disease relationships (i.e., a SWIM-informed diseasome). Although relevance switch an observed phenotype has been recently assessed, their...
Glioblastoma, the most malignant brain cancer, contains self-renewing, stem-like cells that sustain tumor growth and therapeutic resistance. Identifying genes promoting cell differentiation might unveil targets for novel treatments. To detect them, here we apply SWIM - a software able to (named switch genes) involved in drastic changes of phenotype public datasets gene expression profiles from human glioblastoma cells. By analyzing matched pairs differentiated cells, identified 336 genes,...
Abstract Chronic obstructive pulmonary disease (COPD) is a complex and heterogeneous syndrome. Network-based analysis implemented by SWIM software can be exploited to identify key molecular switches - called “switch genes” for the disease. Genes contributing common biological processes or defining given cell types are usually co-regulated co-expressed, forming expression network modules. Consistently, we found that COPD correlation built consists of three well-characterized modules: one...
Abstract Obesity is the main risk factor for many non-communicable diseases. In clinical practice, unspecific markers are used determination of metabolic alterations and inflammation, without allowing characterization subjects at higher complications. Circulating microRNAs represent an attractive approach early screening to identify affected by obesity more developing connected pathologies. The aim this study was identification circulating free extracellular vesicles (EVs)-embedded able...
Abstract Cancer stem-like cells (CSCs) have self-renewal abilities responsible for cancer progression, therapy resistance, and metastatic growth. The glioblastoma are the most studied among CSC populations. A recent study identified four transcription factors (SOX2, SALL2, OLIG2, POU3F2) as minimal core sufficient to reprogram differentiated (GBM) into cells. Transcriptomic data of GBM tissues cell lines from two different datasets were then analyzed by SWItch Miner (SWIM), a network-based...
Abstract Despite advances in modern medicine that led to improvements cardiovascular outcomes, disease (CVD) remains the leading cause of mortality and morbidity globally. Thus, there is an urgent need for new approaches improve CVD drug treatments. As development time cost discovery clinical application are excessive, alternate strategies warranted. Among these included computational based on omics data repositioning, which have attracted increasing attention. In this work, we developed...
It is well-known that glioblastoma contains self-renewing, stem-like subpopulation with the ability to sustain tumor growth. These cells - called cancer share certain phenotypic characteristics untransformed stem and are resistant many conventional therapies, which might explain limitations in curing human malignancies. Thus, identification of genes controlling differentiation these becoming a successful therapeutic strategy, owing promise novel targets for treating malignancies.Recently, we...
ABSTRACT Extracellular vesicles (EVs) are mediators of a range pathological conditions. However, their role in bone loss disease has not been well understood. In this study we characterized plasma EVs 54 osteoporotic (OP) postmenopausal women compared to 48 osteopenic (OPN) and 44 healthy controls (CN), investigated effects on osteoclasts osteoblasts. We found no differences between the three groups terms anthropometric measurements biochemical evaluation serum calcium, phosphate,...
We monitored radon anomalies before, during and after the recent paroxysmal eruptions of Stromboli. Major eruptive events are preceded by relative minima in emissions at stations located base cone, whereas three summit reached peak values (∼20,000 Bq/m 3 or higher) 12 to 14 days before major eruptions, nearly coeval with earth tides. Radon at/or above such high threshold proposed result from dynamic response fracture network due degassing processes associated magma ascent. Relative recorded...
Insulin resistance is the common denominator of several diseases including type 2 diabetes and cancer, investigating mechanisms responsible for insulin signaling impairment primary importance. A mathematical model network (ISN) proposed used to investigate dose-response curves components this network. Experimental data C2C12 myoblasts with phosphatase tensin homologue (PTEN) suppressed L6 myotubes induced have been analyzed by model. We focused particularly on single double Akt...
The transcriptional regulatory structure of plant genomes is still relatively unexplored, and little known about factors that influence expression variation in plants. We used a genetic system consisting 10 heterozygous grape varieties with high consanguinity haplotypic diversity to: (i) identify regions haplotype sharing through whole-genome resequencing single-nucleotide polymorphism (SNP) genotyping; (ii) analyse gene RNA-seq four stages berry development; (iii) associate epigenetic...
Breast cancer (BC) is a heterogeneous and complex disease as witnessed by the existence of different subtypes clinical characteristics that poses significant challenges in management. The complexity this tumor may rely on highly interconnected nature various biological processes stated new paradigm Network Medicine. We explored Cancer Genome Atlas (TCGA)-BRCA data set, applying network-based algorithm named SWItch Miner, mapping findings human interactome to capture molecular...
The SARS-CoV-2 pandemic is a worldwide public health emergency. Despite the beginning of vaccination campaign, search for new drugs to appropriately treat COVID-19 patients remains priority. Drug repurposing represents faster and cheaper method than de novo drug discovery. In this study, we examined three different network-based approaches identify potentially repurposable COVID-19. We analyzed transcriptomic data from whole blood cells with 21 other related conditions, as compared those...