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

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

Vascular endothelial growth factor A (VEGFA) expression in mycosis fungoides

AIMS:High levels of vascular endothelial growth factor (VEGF) seem to herald a worse prognosis in mycosis fungoides (MF). METHODS AND RESULTS:Firstly, we compared VEGF mRNA levels in MF and in normal T-lymphocytes samples. Notably, significantly higher VEGF levels were found in MF. Then, we studied VEGF gene expression in different normal T-cell subsets, focusing on CD4+, CD8+, resting and activated T-lymphocytes. Furthermore, we applied the gene signatures of the normal T-cell subsets to MF samples and found that activated T-lymphocytes represented the closest normal counterpart of the tumour. However, VEGF mRNA levels turned out to be significantly higher in MF than in activated normal T-cells suggesting that VEGF over-expression in MF represents an attribute acquired during neoplastic transformation. Notably, no significant VEGF expression differences were recorded between early and advanced stages. Gene expression profile results were supported by immunohistochemistry in routine sections from 27 MF cases. CONCLUSIONS:For the first time, we demonstrated VEGF expression in MF cells, suggesting that the VEGF pathway may be implicated in MF pathogenesis and can represent a novel therapeutic target

Protein kinase CK2 is widely expressed in follicular, Burkitt and diffuse large B-cell lymphomas and propels malignant B-cell growth

Serine-threonine kinase CK2 is highly expressed and pivotal for survival and proliferation in multiple myeloma, chronic lymphocytic leukemia and mantle cell lymphoma. Here, we investigated the expression of \u3b1 catalytic and \u3b2 regulatory CK2 subunits by immunohistochemistry in 57 follicular (FL), 18 Burkitt (BL), 52 diffuse large B-cell (DLBCL) non-Hodgkin lymphomas (NHL) and in normal reactive follicles. In silico evaluation of available Gene Expression Profile (GEP) data sets from patients and Western blot (WB) analysis in NHL cell-lines were also performed. Moreover, the novel, clinical-grade, ATP-competitive CK2-inhibitor CX-4945 (Silmitasertib) was assayed on lymphoma cells. CK2 was detected in 98.4% of cases with a trend towards a stronger CK2\u3b1 immunostain in BL compared to FL and DLBCL. No significant differences were observed between Germinal Center B (GCB) and non-GCB DLBCL types. GEP data and WB confirmed elevated CK2 mRNA and protein levels as well as active phosphorylation of specific targets in NHL cells. CX-4945 caused a dose-dependent growth-arresting effect on GCB, non-GCB DLBCL and BL cell-lines and it efficiently shut off phosphorylation of NF-\u3baB RelA and CDC37 on CK2 target sites. Thus, CK2 is highly expressed and could represent a suitable therapeutic target in BL, FL and DLBCL NHL