Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2012.2.1.1-3 | Award Amount: 4.68M | Year: 2012
High-throughput sequencing (HTS) is a powerful and rapidly evolving family of technologies with a multitude of applications. They include genetics of rare and common diseases, understanding of disease mechanism and progression through transcriptome and epigenome profiling, cancer stratification, personalised medicine and molecular systems biology of gene regulation. The genome, epigenome, transcriptome and interactome are all intricately connected, and modern HTS technology can probe all of these -omic levels. Statistical analysis is a crucial component of many experiments and studies, and the quality and efficiency of the analysis often determines the success of a project. In this collaborative project we will develop a range of new statistical analysis tools to solve open problems in HTS data analysis, ranging from low-level processing of sequence reads up to systems-level modelling of disease associated and cellular processes. We will provide to a wide audience an integrated computational framework for HTS data analysis and interpretation that is robust, efficient and user-friendly. We will establish improved procedures for the publishing of statistical software as an integral part of the scientific publication process, within the framework of the Bioconductor project. We will provide tools to benchmark experimental protocols and statistical methods, and we will provide training materials and a extensive training programme to rapidly disseminate these new tools to the broader biomedical community. SME partners will integrate these new tools within their analysis pipelines with associated user-friendly commercial software providing access to their additional proprietary tools. SMEs will benefit from basic methodology development done in a public, pre-competitive arena and will be able to use these technologies to enhance their products and services.
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2013.2.2.1-5 | Award Amount: 7.88M | Year: 2014
So far, there are no effective treatments for neuropathic pain (NP), and current treatments suffer from serious unwanted side effects. The NGF ligand-receptor system has recently emerged as a novel target for NP of great therapeutic potential, a master regulator, controlling both neuropathic and inflammatory components. Besides being a multi-component system, it also modulates the endocannabinoid (EC) signalling. Blocking the NGF signaling system is therefore a rational and thoroughly validated approach to pain therapy. Extensive evidence for potent analgesic efficacy of antiNGF mAbs has been obtained in preclinical models and in clinical trials,showing remarkable analgesic efficacy and creating great expectations for this new class of analgesic compounds.However, potential safety concerns related to off-target side effects have been raised and recently the FDA called for more preclinical research. To fully exploit the huge therapeutic potential of NGF system, we built a consortium of leading researchers in the NGF, EC and pain scientific arena.The innovative proposal will investigate new strategies for the treatment of different NP forms, based on the NGF system and its interplay with EC signalling, focussing at different levels of the pain transmission and perception systems. The project results will provide solid, mechanism-based grounds for the development of already identified second-generation therapeutics, based on the NGF target system, as well as for the identification and validation of new druggable targets emerging from the elucidated mechanisms. It will also identify biomarkers for NP, validated in animal models and clinical samples, that could result in future clinical benefits, for the stratification of patients suffering from different neuropathies and their treatment. The project will contribute to the understanding and controlling NP mechanisms, with an interdisciplinary approach, leading to the development of next-generation NGF targeting drugs.
Merelli I.,National Research Council Italy |
Guffanti A.,Genomnia SrL |
Fabbri M.,European Commission - Joint Research Center Ispra |
Cocito A.,FIRC Institute of Molecular Oncology Foundation |
And 5 more authors.
Nucleic Acids Research | Year: 2010
Recombination signal sequences (RSSs) flanking V, D and J gene segments are recognized and cut by the VDJ recombinase during development of B and T lymphocytes. All RSSs are composed of seven conserved nucleotides, followed by a spacer (containing either 12 ± 1 or 23 ± 1 poorly conserved nucleotides) and a conserved nonamer. Errors in V(D)J recombination, including cleavage of cryptic RSS outside the immunoglobulin and T cell receptor loci, are associated with oncogenic translocations observed in some lymphoid malignancies. We present in this paper the RSSsite web server, which is available from the address http://www.itb.cnr.it/rss. RSSsite consists of a web-accessible database, RSSdb, for the identification of precomputed potential RSSs, and of the related search tool, DnaGrab, which allows the scoring of potential RSSs in user-supplied sequences. This latter algorithm makes use of probability models, which can be recasted to Bayesian network, taking into account correlations between groups of positions of a sequence, developed starting from specific reference sets of RSSs. In validation laboratory experiments, we selected 33 predicted cryptic RSSs (cRSSs) from 11 chromosomal regions outside the immunoglobulin and TCR loci for functional testing. © The Author(s) 2010. Published by Oxford University Press.
Soreq L.,Hebrew University of Jerusalem |
Guffanti A.,Hebrew University of Jerusalem |
Guffanti A.,Genomnia srl |
Salomonis N.,Cincinnati Childrens Hospital Medical Center |
And 4 more authors.
PLoS Computational Biology | Year: 2014
The continuously prolonged human lifespan is accompanied by increase in neurodegenerative diseases incidence, calling for the development of inexpensive blood-based diagnostics. Analyzing blood cell transcripts by RNA-Seq is a robust means to identify novel biomarkers that rapidly becomes a commonplace. However, there is lack of tools to discover novel exons, junctions and splicing events and to precisely and sensitively assess differential splicing through RNA-Seq data analysis and across RNA-Seq platforms. Here, we present a new and comprehensive computational workflow for whole-transcriptome RNA-Seq analysis, using an updated version of the software AltAnalyze, to identify both known and novel high-confidence alternative splicing events, and to integrate them with both protein-domains and microRNA binding annotations. We applied the novel workflow on RNA-Seq data from Parkinson's disease (PD) patients' leukocytes pre- and post- Deep Brain Stimulation (DBS) treatment and compared to healthy controls. Disease-mediated changes included decreased usage of alternative promoters and N-termini, 5′-end variations and mutually-exclusive exons. The PD regulated FUS and HNRNP A/B included prion-like domains regulated regions. We also present here a workflow to identify and analyze long non-coding RNAs (lncRNAs) via RNA-Seq data. We identified reduced lncRNA expression and selective PD-induced changes in 13 of over 6,000 detected leukocyte lncRNAs, four of which were inversely altered post-DBS. These included the U1 spliceosomal lncRNA and RP11-462G22.1, each entailing sequence complementarity to numerous microRNAs. Analysis of RNA-Seq from PD and unaffected controls brains revealed over 7,000 brain-expressed lncRNAs, of which 3,495 were co-expressed in the leukocytes including U1, which showed both leukocyte and brain increases. Furthermore, qRT-PCR validations confirmed these co-increases in PD leukocytes and two brain regions, the amygdala and substantia-nigra, compared to controls. This novel workflow allows deep multi-level inspection of RNA-Seq datasets and provides a comprehensive new resource for understanding disease transcriptome modifications in PD and other neurodegenerative diseases. © 2014 Soreq et al.
Bashamboo A.,Institute Pasteur Paris |
Brauner R.,University of Paris Descartes |
Bignon-Topalovic J.,Institute Pasteur Paris |
Lortat-Jacob S.,Assistance Publique Hopitaux de Paris |
And 4 more authors.
Human Molecular Genetics | Year: 2014
In recent years, considerable advances have been made in our understanding of genetics of mammalian gonad development; however, the underlying genetic aetiology in the majority of patients with 46,XY disorders of sex development (DSD) still remains unknown. Based onmouse models, it has been hypothesized that haploinsufficiency of the Friend ofGATA2 (FOG2) gene could lead to 46,XY gonadal dysgenesis on specific inbred genetic backgrounds. Using whole exome sequencing, we identified independent missense mutations in FOG2 in two patients with 46,XY gonadal dysgenesis. One patient carried a non-synonymous heterozygous mutation (p.S402R), while the other patient carried a heterozygous p.R260Q mutation and a homozygous p.M544I mutation. Functional studies indicated that the failure of testis development in these cases could be explained by the impaired ability of the mutant FOG2 proteins to interact with a known regulator of early testis development, GATA4. This is the first example of mutations in the coding sequence of FOG2 associated with 46,XY DSD in human and adds to the list of genes in the human known to be associated with DSD. © The Author 2014. Published by Oxford University Press. All rights reserved.
Cattoglio C.,Italian Institute of Technology |
Pellin D.,Vita-Salute San Raffaele University |
Rizzi E.,National Research Council Italy |
Maruggi G.,University of Modena and Reggio Emilia |
And 10 more authors.
Blood | Year: 2010
Integration of retroviral vectors in the human genome follows nonrandom patterns that favor insertional deregulation of gene expression and increase the risk of their use in clinical gene therapy. The molecular basis of retroviral target site selection is still poorly understood. We used deep sequencing technology to build genomewide, high-definition maps of > 60 000 integration sites of Moloney murine leukemia virus (MLV)-and HIV-based retroviral vectors in the genome of human CD34+ multipotent hematopoietic progenitor cells (HPCs) and used gene expression profiling, chromatin immunoprecipitation, and bioinformatics to associate integration to genetic and epigenetic features of the HPC genome. Clusters of recurrent MLV integrations identify regulatory elements (alternative promoters, enhancers, evolutionarily conserved noncoding regions) within or around protein-coding genes and microRNAs with crucial functions in HPC growth and differentiation, bearing epigenetic marks of active or poised transcription (H3K4me1, H3K4me2, H3K4me3, H3K9Ac, Pol II) and specialized chromatin configurations (H2A.Z). Overall, we mapped 3500 high-frequency integration clusters, which represent a new resource for the identification of transcriptionally active regulatory elements. High-definition MLV integration maps provide a rational basis for predicting genotoxic risks in gene therapy and a new tool for genomewide identification of promoters and regulatory elements controlling hematopoietic stem and progenitor cell functions. © 2010 by The American Society of Hematology.
Voellenkle C.,Laboratorio Of Cardiologia Molecolare |
Van Rooij J.,Laboratorio Of Cardiologia Molecolare |
Guffanti A.,Genomnia Srl |
Brini E.,Genomnia Srl |
And 8 more authors.
RNA | Year: 2012
In order to understand the role of microRNAs (miRNAs) in vascular physiopathology, we took advantage of deep-sequencing techniques to accurately and comprehensively profile the entire miRNA population expressed by endothelial cells exposed to hypoxia. SOLiD sequencing of small RNAs derived from human umbilical vein endothelial cells (HUVECs) exposed to 1% O 2 or normoxia for 24 h yielded more than 22 million reads per library. A customized bioinformatic pipeline identified more than 400 annotated microRNA/ microRNA*species with a broad abundance range: miR-21 and miR-126 totaled almost 40% of all miRNAs. A complex repertoire of isomiRs was found, displaying also 5′ variations, potentially affecting target recognition. Highstringency bioinformatic analysis identified microRNA candidates, whose predicted pre-miRNAs folded into a stable hairpin. Validation of a subset by qPCR identified 18 high-confidence novel miRNAs as detectable in independent HUVEC cultures and associated to the RISC complex. The expression of two novel miRNAs was significantly down-modulated by hypoxia, while miR- 210 was significantly induced. Gene ontology analysis of their predicted targets revealed a significant association to hypoxiainducible factor signaling, cardiovascular diseases, and cancer. Overexpression of the novel miRNAs in hypoxic endothelial cells affected cell growth and confirmed the biological relevance of their down-modulation. In conclusion, deep-sequencing accurately profiled known, variant, and novel microRNAs expressed by endothelial cells in normoxia and hypoxia.
Falcone G.,CNR Institute of Neuroscience |
Felsani A.,CNR Institute of Neuroscience |
Felsani A.,Genomnia Srl |
D'Agnano I.,CNR Institute of Neuroscience
Journal of Experimental and Clinical Cancer Research | Year: 2015
A class of small non-coding RNAs, the microRNAs (miRNAs), have recently attracted great attention in cancer research since they play a central role in regulation of gene-expression and miRNA aberrant expression is found in almost all types of human cancer. The discovery of circulating miRNAs in body fluids and the finding that they are often tumor specific and can be detected early in tumorigenesis has soon led to the evaluation of their possible use as cancer biomarkers and treatment-response predictors. The evidence that tumor cells communicate via the secretion and delivery of miRNAs packed into tumor-released microvesicles has prompted to investigate miRNA contribution as signaling molecules to the establishment and maintenance of the tumor microenvironment and the metastatic niche in cancer. In this review we highlight the recent advances on the role of exosomal miRNAs as mediators of cancer cell-to-cell communication. © 2015 Falcone et al.; licensee BioMed Central.
Agency: European Commission | Branch: H2020 | Program: SME-1 | Phase: PHC-12-2015-1 | Award Amount: 71.43K | Year: 2016
Fine needle aspiration cytology (FNAC) is the best procedure for a timely and reliable diagnosis of either a benign or malignant thyroid lesion. However, the management of patients with indeterminate cytology (10-26%) is a frequent clinical and social problem, as this cytological category is associated with a 15 to 30% prevalence of malignancy, forcing most of these patients to diagnostic surgery. However, for the 80% of these patients the surgery is unnecessary as the postoperative histology reveal a benign lesion. The negative social and financial consequences of this approach are relevant in Europe (44000/year thyroidectomy only in Italy) as well as the adverse influences on the quality of life of the patients due to surgical complications and hormone replacement. We will introduce in the market the first clinically validated CE-IVD targeted Next Generation Sequencing diagnostic kit ThyroTrust for the correct diagnosis of thyroid nodules with indeterminate cytology. Our kit is the first to include a considerable number of variations in 47 genes, 66 types of rearrangements and 8 gene expression level measured at the same time and associated with malignant outcome. This will avoid diagnostic surgery if a risk of malignancy <5%. In the scope of the feasibility study we will assess: - Technology innovation opportunity and business idea - Development planning and partner search - IPR, quality, organization and manufacturing route - GO-TO-MARKET strategy and business plan 740,000 FNA are performed in Europe, so the addressable market, with an end-user price/kit of 300, is over 50 Million/year. Prudentially, market estimation considers only FNA results classified as indeterminate cytology. The same approach could be evaluated and adopted for other cancer diagnostics, proposing a similar gene panel kit on the market. The positive effect resulting from such diagnostic tool can virtually lead to the abolishment of 90% of unnecessary surgeries and related cos
Genomnia S.r.l. | Date: 2011-10-05
An artificial heart, including a pump comprising:- a casing internally defining a substantially spherical cavity (10) ;- a rotating shutter (12), housed within the substantially spherical cavity (10) and secured thereto so as to be rotatable about an own rotation axis;- an oscillating shutter (14), also housed within the substantially spherical cavity (10) and secured to the rotating shutter (12) so as to be rotatable relative to the latter about a rotation axis transversal to the rotation axis of the rotating shutter relative to the casing;- a guide ring (18, 18), secured to the oscillating shutter (14) so as to allow the latter to rotate relative to the same guide ring (18), wherein the guide ring is arranged to move within a seat formed in the substantially spherical cavity (10) while lying in a plane substantially slanting relative to the rotation axis of the rotating shutter (12) and making thereby the rotating shutter (12) rotate,said artificial heart being characterized in that it is arranged to be connected to a driver so that the latter operates either the rotating shutter (12) through the guide ring (18) or the oscillating shutter (14) through the rotating shutter (12), wherein the driver includes a muscle or muscle fibres.