Highly Sensitive and Specific Method for Detection of Clinically Relevant Fusion Genes across Cancer

Gene fusions are strong driver mutations in cancer and can be used as a diagnostic tool to predict different tumour phenotypes and treatments. Several fusion detection algorithms for RNA-Seq data have been developed, but all of them report a consistently high number of false positive events. Therefore, new methods are crucial to accurately identify potential fusions that may be key drivers of oncogenesis. We developed Fusion Validator, a new filtering tool able to discriminate false positive fusion transcripts from real fusions and significantly reduce the number of candidates to assess for experimental validation. Fusion Validator perform a local realignment of reads on each fusion transcript sequence and tries to close the gap around the fusion breakpoint using both a de novo assembly and a seed-extend algorithm. If the algorithm fails to reconstruct the fusion transcript around the breakpoint, the fusion is considered as false positive and is discarded. Additional filtering steps are used to remove fusions with breakpoints mapping on low complexity or homologous regions and to find correct fusion partners for promiscuous gene fusion events. A final ranking score based on fusion annotation is created for each validated event to help distinguish real driver fusions from passengers one. We tested Fusion Validator on simulated datasets of different coverage, read length and breakpoint positions, and on four published breast cancer Cell Lines, highlighting the massive increase in sensisitivity, precision and specificity of our algorithm, in comparison to other fusion-detection software. Using this tool, we successfully detected 97.95% of PCR-validated kinase recurrent fusions in 190 pan cancer samples, removing approximately 79.95% of false positives. Particularly in haematological disorders and childhood sarcomas, gene fusions are critical as diagnostic and prognostic factors. Therefore, development of this novel tool to increase the efficiency of detecting driver fusions is critical in disease detection and treatment

Spleen histology in children with sickle cell disease and hereditary spherocytosis: Hints on the disease pathophysiology

open2Hereditary spherocytosis (HS) and sickle cell disease (SCD) are associated with splenomegaly and spleen dysfunction in pediatric patients. Scant data exist on possible correlations between spleen morphology and function in HS and SCD. This study aimed to assess the histological and morphometric features of HS and SCD spleens, in order to get possible correlations with disease pathophysiology. In a large series of spleens from SCD, HS and control patients the following parameters were considered: (i) macroscopic features; (ii) lymphoid follicle (LF) density; (iii) presence of peri-follicular marginal zones (MZs); (iv) presence of Gamna-Gandy bodies; (v) density of CD8-positive sinusoids; (vi) density of CD34-positive microvessels; (vii) presence/distribution of fibrosis and SMA-positive myoid cells; (viii) density of CD68-positive macrophages. SCD and HS spleens have similar macroscopic features. SCD spleens had lower LF density and fewer MZs than HS spleens and controls. SCD also showed lower CD8-positive sinusoid density, increased CD34-positive microvessel density and SMA-positive myoid cells, and higher prevalence of fibrosis and Gamna-Gandy bodies. HS had lower LF and CD8-positive sinusoid density than controls. No significant differences were noted in red pulp macrophages. By multivariate analysis, the majority of HS spleens clustered with controls, while SCD grouped separately. A multi-parametric score could predict the degree of spleen changes irrespective of the underlying disease. In conclusion, SCD spleens display greater histologic effacement than HS and SCD-related changes suggest impaired function due to vascular damage. These observations may contribute to guide the clinical management of patients.embargoed_20161128Alaggio, RitaAlaggio, Rita; Gamba, Piergiorgi

Correction: Whole exome sequencing reveals mutations in FAT1 tumor suppressor gene clinically impacting on peripheral T-cell lymphoma not otherwise specified.

An amendment to this paper has been published and can be accessed via a link at the top of the paper

Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer.

Disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription, coordinated secondary pathway alterations, and increased transcriptional noise. To catalog the rules governing how somatic mutation exerts direct transcriptional effects, we developed an exhaustive pipeline for analyzing RNA sequencing data, which we integrated with whole genomes from 23 breast cancers. Using X-inactivation analyses, we found that cancer cells are more transcriptionally active than intermixed stromal cells. This is especially true in estrogen receptor (ER)-negative tumors. Overall, 59% of substitutions were expressed. Nonsense mutations showed lower expression levels than expected, with patterns characteristic of nonsense-mediated decay. 14% of 4,234 rearrangements caused transcriptional abnormalities, including exon skips, exon reusage, fusions, and premature polyadenylation. We found productive, stable transcription from sense-to-antisense gene fusions and gene-to-intergenic rearrangements, suggesting that these mutation classes drive more transcriptional disruption than previously suspected. Systematic integration of transcriptome with genome data reveals the rules by which transcriptional machinery interprets somatic mutation

Diversity of Bifidobacteria within the Infant Gut Microbiota

Background The human gastrointestinal tract (GIT) represents one of the most densely populated microbial ecosystems studied to date. Although this microbial consortium has been recognized to have a crucial impact on human health, its precise composition is still subject to intense investigation. Among the GIT microbiota, bifidobacteria represent an important commensal group, being among the first microbial colonizers of the gut. However, the prevalence and diversity of members of the genus Bifidobacterium in the infant intestinal microbiota has not yet been fully characterized, while some inconsistencies exist in literature regarding the abundance of this genus. Methods/Principal Findings In the current report, we assessed the complexity of the infant intestinal bifidobacterial population by analysis of pyrosequencing data of PCR amplicons derived from two hypervariable regions of the 16 S rRNA gene. Eleven faecal samples were collected from healthy infants of different geographical origins (Italy, Spain or Ireland), feeding type (breast milk or formula) and mode of delivery (vaginal or caesarean delivery), while in four cases, faecal samples of corresponding mothers were also analyzed. Conclusions In contrast to several previously published culture-independent studies, our analysis revealed a predominance of bifidobacteria in the infant gut as well as a profile of co-occurrence of bifidobacterial species in the infant’s intestine

Intermolecular versus intramolecular C–H activation reaction in the thermolysis of [Ru(Me)Cp*(PMe2Ph)2] (Cp* = η5-C5Me5): formation and crystallographic characterisation of [Ru(Ph)Cp*(PMe2Ph)2]

Thermolysis of the ruthenium complex [Ru(Me)Cp*(PMe 2Ph)2] (1) (Cp* = η5-C 5Me5) in benzene gives methane and [Ru(Ph) Cp*(PMe2Ph)2] (2), which is converted slowly to [Ru(C6H4PMe2)Cp*(PMe2Ph)] (3) through the loss of benzene. 2 was structurally characterised by single-crystal X-ray diffraction experiments. DFT calculations were performed in order to understand the behaviour of the ruthenium complex 1 towards inter- or intra-molecular C-H bond activation reactions

Second neoplasm in cutaneous T-cell lymphoma patients: a marker of worse prognosis?

Epidemiologic studies have shown that cutaneous T-cell lymphoma (CTCL) patients have an increased risk of the development of a second neoplasm (SN). The aim of our study was to evaluate the risk of SN and to correlate any possible change in CTCL course after the diagnosis of a subsequent neoplasm

Reduction of the NO+ ligand in half-sandwich ruthenium derivatives

The reduction of the tetrafluoroborate salts of the ruthenium nitrosyl dicationic [Ru(η5-C5R5) (NO)(L)2]2+ (R=Me, L=PMe3, 1a; PMe2Ph, 1b; R=H, L=PPh3, 2d) and monocationic complexes [Ru(Me)Cp*(NO)L]+ (L=PMe3, 3a; PMe2Ph, 3b (Cpz.ast;=η5- C5Me5) has been studied by electrochemical and spectroscopic (IR, NMR, EPR) techniques. The nitrosyl complexes 1a, 1b and 2d exhibit two successive one-electron cathodic processes due to the sequential reduction of coordinated NO+ to NO and NO-, respectively. Chemical reduction yields products of rearrangement of the intermediates which have been spectroscopically characterized. EPR studies and theoretical calculations show that in the first one-electron reduction product the electron interacts with the NO nitrogen atom and that the RuNO moiety presents significant distortion from linearity. The X-ray structure of the related [Ir(Me)2Cpz.ast;(NO)]BF4 has been determined