Search results for "BIOINFORMATICS"
showing 10 items of 1632 documents
A multicenter study benchmarks software tools for label-free proteome quantification
2016
The consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from SWATH-MS (sequential window acquisition of all theoretical fragment ion spectra), a method that uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test datasets from hybrid proteome samples of defined quantitative composition acquired on two different MS instrument…
Does iris(in) bring bad news or good news?
2017
Irisin, a novel myokine produced in response to physical activity, promotes white-to-brown fat transdifferentiation. The name irisin referred to the ancient Greek goddess Iris, the messenger who delivered (bad) news from the gods. In mice, it has been demonstrated that irisin plays a key role in metabolic regulation, energy expenditure and glucose homeostasis. New findings from various studies carried out in both animals and humans suggest that irisin might also have other favorable effects, such as increasing bone cortical mass, preventing hepatic lipid accumulation, and improving cognitive functions, thus mediating many exercise-induced health benefits. However, data on the role and funct…
Molecular differential diagnosis of uterine leiomyomas and leiomyosarcomas.
2018
Abstract Uterine leiomyomas (LM) and leiomyosarcomas (LMS) are considered biologically unrelated tumors due to their cytogenetic and molecular disparity. Yet, these tumors share morphological and molecular characteristics that cannot be differentiated through current clinical diagnostic tests, and thus cannot be definitively classified as benign or malignant until surgery. Newer approaches are needed for the identification of these tumors, as has been done for other tissues. The application of next generation sequencing enables the detection of new mutations that, when coupled to machine learning bioinformatic tools, advances our understanding of chromosomal instability. These approaches in…
Neurodegeneration in tauopathies and synucleinopathies.
2016
International audience; While increasing life expectancy is a major achievement, the global aging of societies raises a number of medical issues, such as the development of age-related disorders, including neurodegenerative diseases. The three main disease groups constituting the majority of neurodegenerative diseases are tauopathies, alpha-synucleinopathies and diseases due to repetitions of glutamine (including Huntington's disease). In each neurodegenerative disease, the accumulation of one or more aggregated proteins has been identified as the molecular signature of the disease (as seen, for example, in Alzheimer's disease, Parkinson's disease, dementia with Lewy bodies, amyotrophic lat…
Determinants of fibrosis progression and regression in NASH
2017
Cirrhosis has become the major liver-related clinical endpoint in non-alcoholic steatohepatitis (NASH). However, progression to cirrhosis is less predictable in NASH than in other chronic liver diseases. This is due to the complex and multifactorial aetiology of NASH, which is determined by lifestyle and nutrition, multiple genetic and epigenetic factors, and a prominent role of hepatic and extrahepatic comorbidities. Thus, modest changes in these cofactors can also induce fibrosis regression, at least in patients with precirrhotic liver disease. Fibrogenesis in NASH correlates with, but is indirectly coupled to, classical inflammation, since fibrosis progression is driven by repetitive per…
Profile of the Roche cobas® EGFR mutation test v2 for non-small cell lung cancer
2017
Abstract: Introduction: The discovery of driver mutations in non-small cell lung cancer (NSCLC) has led to the development of genome-based personalized medicine. Fifteen to 20% of adenocarcinomas harbor an epidermal growth factor receptor (EGFR) activating mutation associated with responses to EGFR tyrosine kinase inhibitors (TKIs). Individual laboratories' expertise and the availability of appropriate equipment are valuable assets in predictive molecular pathology, although the choice of methods should be determined by the nature of the samples to be tested and whether the detection of only well-characterized EGFR mutations or rather, of all detectable mutations, is required.Areas covered:…
Molecular similarities and differences from human pulmonary fibrosis and corresponding mouse model: MALDI imaging mass spectrometry in comparative me…
2017
Animal models can reproduce some model-specific aspects of human diseases, but some animal models translate poorly or fail to translate to the corresponding human disease. Here, we develop a strategy to systematically compare human and mouse tissues, and conduct a proof-of-concept experiment to identify molecular similarities and differences using patients with idiopathic pulmonary fibrosis and a bleomycin-induced fibrosis mouse model. Our novel approach employs high-throughput tissue microarrays (TMAs) of humans and mice, high-resolution matrix-assisted laser desorption/ionization-Fourier transform-ion cyclotron resonance-mass spectrometry imaging (MALDI-FT-ICR-MSI) to spatially resolve ma…
Integrated analysis of colorectal cancer microRNA datasets: Identification of microRNAs associated with tumor development
2018
Colorectal cancer (CRC) is one of the leading cause of cancer death worldwide. Currently, no effective early diagnostic biomarkers are available for colorectal carcinoma. Therefore, there is a need to discover new molecules able to identify pre-cancerous lesions. Recently, microRNAs (miRNAs) have been associated with the onset of specific pathologies, thus the identification of miRNAs associated to colorectal cancer may be used to detect this pathology at early stages. On these bases, the expression levels of miRNAs were analyzed to compare the miRNAs expression levels of colorectal cancer samples and normal tissues in several miRNA datasets. This analysis revealed a group of 19 differentia…
The role of microRNAs in oral lichenoid disorders. Systematic review
2017
Background: Certain changes in the microRNA expression are considered to be associated with chronic inflammatory processes and with the malignant transformation of oral potentially malignant disorders. The purpose of this systematic review is to update the existing data on the aberrant microRNA expression profiles identified in oral lichenoid disease (OLD).