Giulia Paciello
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View article: FUNGI: FUsioN Gene Integration toolset
FUNGI: FUsioN Gene Integration toolset Open
Motivation Fusion genes are both useful cancer biomarkers and important drug targets. Finding relevant fusion genes is challenging due to genomic instability resulting in a high number of passenger events. To reveal and prioritize relevant…
View article: Novel and Rare Fusion Transcripts Involving Transcription Factors and Tumor Suppressor Genes in Acute Myeloid Leukemia
Novel and Rare Fusion Transcripts Involving Transcription Factors and Tumor Suppressor Genes in Acute Myeloid Leukemia Open
Approximately 18% of acute myeloid leukemia (AML) cases express a fusion transcript. However, few fusions are recurrent across AML and the identification of these rare chimeras is of interest to characterize AML patients. Here, we studied …
View article: PS1437 SETD2 NON‐GENOMIC LOSS OF FUNCTION IN ADVANCED SYSTEMIC MASTOCYTOSIS (SM): PATHOGENETIC AND THERAPEUTIC IMPLICATIONS
PS1437 SETD2 NON‐GENOMIC LOSS OF FUNCTION IN ADVANCED SYSTEMIC MASTOCYTOSIS (SM): PATHOGENETIC AND THERAPEUTIC IMPLICATIONS Open
Background: We have recently found that advanced SM patients (pts) and the HMC‐1.1 and −1.2 MCL cell lines display histone H3 Lys36 trimethylation (H3K36Me3) deficiency as a result of non‐genomic loss of function of the SETD2 methyltransfe…
View article: MDM2 and Aurora Kinase a Contribute to SETD2 Loss of Function in Advanced Systemic Mastocytosis: Implications for Pathogenesis and Treatment
MDM2 and Aurora Kinase a Contribute to SETD2 Loss of Function in Advanced Systemic Mastocytosis: Implications for Pathogenesis and Treatment Open
The SETD2 gene encodes the only methyltransferase responsible for histone H3 lysine 36 trimethylation (H3K36Me3) in humans. H3K36me3 play a key role in preserving the fidelity of transcription elongation and splicing. In addition, SETD2/H3…
View article: geneEx - A Novel Tool to Assess Differential Expression from Gene and Exon Sequencing Data
geneEx - A Novel Tool to Assess Differential Expression from Gene and Exon Sequencing Data Open
The widespread of Next Generation Sequencing technologies accounted in recent years for the possibility to evaluate gene expression with great accuracy.Moreover, it allowed assessing differential gene expression among biological conditions…
View article: RALE051: a novel established cell line of sporadic Burkitt lymphoma
RALE051: a novel established cell line of sporadic Burkitt lymphoma Open
To date, the lack of chemo-naive cell models limited exploratory studies to define novel therapies for Burkitt lymphoma (BL). To obtain a useful tool for biological and translational studies for this tumor, we established the RALE051 cell …
View article: FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples
FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples Open
FuGePrior performance has been assessed on two publicly available paired-end RNA-Seq datasets: The first by Edgren and colleagues includes four breast cancer cell lines and a normal breast sample, whereas the second by Ren and colleagues c…
View article: supplemental Tables Burkitt Lymphoma cell line
supplemental Tables Burkitt Lymphoma cell line Open
Copy number results from SNP array analysis, chimeric fusion transcripts identification and mutational analyses of Burkitt Lymphoma cell line.
View article: isomiR-SEA: miRNA and isomiR expression level detection in seven RNA-Seq datasets
isomiR-SEA: miRNA and isomiR expression level detection in seven RNA-Seq datasets Open
Background: Massive parallel sequencing of transcriptomes revealed the presence of miRNA variants named isomiRs. The sequence variations identified within isomiR molecules can affect their targeting activity, with consequences in gene expr…
View article: The Genomic and Transcriptomic Landscape of Systemic Mastocytosis
The Genomic and Transcriptomic Landscape of Systemic Mastocytosis Open
Background and Aim Systemic mastocytosis (SM) is characterized by a heterogeneous spectrum of disease variants with different clinical features and prognosis. In indolent SM (ISM), the clinical course is usually stable and patients (pts) h…
View article: Abstract 113: Novel fusion transcripts identified by RNAseq cooperate with somatic mutations in the pathogenesis of acute myeloid leukemia
Abstract 113: Novel fusion transcripts identified by RNAseq cooperate with somatic mutations in the pathogenesis of acute myeloid leukemia Open
Acute Myeloid Leukemia (AML) is a highly heterogeneous disease and somatic mutations and fusion genes have a crucial diagnostic, prognostic and therapeutic role in AML. However, the leukemogenic potential of the fusions, their cooperation …
View article: isomiR-SEA: an RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation
isomiR-SEA: an RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation Open
View article: VDJSeq-Solver: In Silico V(D)J Recombination Detection Tool
VDJSeq-Solver: In Silico V(D)J Recombination Detection Tool Open
In this paper we present VDJSeq-Solver, a methodology and tool to identify clonal lymphocyte populations from paired-end RNA Sequencing reads derived from the sequencing of mRNA neoplastic cells. The tool detects the main clone that charac…
View article: On the relevance of a complete characterisation of miRNAs, isomiRs and miRNA-mRNA interaction sites through miRNA-specific alignment tools
On the relevance of a complete characterisation of miRNAs, isomiRs and miRNA-mRNA interaction sites through miRNA-specific alignment tools Open
The advent of NGS dramatically changed the characterisation of multifactorial pathologies such as cancer. The high molecular variability of cancer makes essential the identification of biomarkers able to explain the differences among cance…