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SELENE MALLIA

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Pubblicazioni

2022 - The Response to Oxidative Damage Correlates with Driver Mutations and Clinical Outcome in Patients with Myelofibrosis [Articolo su rivista]
Genovese, E.; Mirabile, M.; Rontauroli, S.; Sartini, S.; Fantini, S.; Tavernari, L.; Maccaferri, M.; Guglielmelli, P.; Bianchi, E.; Parenti, S.; Carretta, C.; Mallia, S.; Castellano, S.; Colasante, C.; Balliu, M.; Bartalucci, N.; Palmieri, R.; Ottone, T.; Mora, B.; Potenza, L.; Passamonti, F.; Voso, M. T.; Luppi, M.; Vannucchi, A. M.; Tagliafico, E.; Manfredini, R.
abstract

Myelofibrosis (MF) is the Philadelphia-negative myeloproliferative neoplasm characterized by the worst prognosis and no response to conventional therapy. Driver mutations in JAK2 and CALR impact on JAK-STAT pathway activation but also on the production of reactive oxygen species (ROS). ROS play a pivotal role in inflammation-induced oxidative damage to cellular components including DNA, therefore leading to greater genomic instability and promoting cell transformation. In order to unveil the role of driver mutations in oxidative stress, we assessed ROS levels in CD34+ hematopoietic stem/progenitor cells of MF patients. Our results demonstrated that ROS production in CD34+ cells from CALR-mutated MF patients is far greater compared with patients harboring JAK2 mutation, and this leads to increased oxidative DNA damage. Moreover, CALR-mutant cells show less superoxide dismutase (SOD) antioxidant activity than JAK2-mutated ones. Here, we show that high plasma levels of total antioxidant capacity (TAC) correlate with detrimental clinical features, such as high levels of lactate dehydrogenase (LDH) and circulating CD34+ cells. Moreover, in JAK2-mutated patients, high plasma level of TAC is also associated with a poor overall survival (OS), and multivariate analysis demonstrated that high TAC classification is an independent prognostic factor allowing the identification of patients with inferior OS in both DIPSS lowest and highest categories. Altogether, our data suggest that a different capability to respond to oxidative stress can be one of the mechanisms underlying disease progression of myelofibrosis.

2021 - Characterization of new ATM deletion associated with hereditary breast cancer [Articolo su rivista]
Parenti, S.; Rabacchi, C.; Marino, M.; Tenedini, E.; Artuso, L.; Castellano, S.; Carretta, C.; Mallia, S.; Cortesi, L.; Toss, A.; Barbieri, E.; Manfredini, R.; Luppi, M.; Trenti, T.; Tagliafico, E.
abstract

Next-generation sequencing (NGS)-based cancer risk screening with multigene panels has become the most successful method for programming cancer prevention strategies. ATM germ-line heterozygosity has been described to increase tumor susceptibility. In particular, families carrying heterozygous germ-line variants of ATM gene have a 5-to 9-fold risk of developing breast cancer. Recent studies identified ATM as the second most mutated gene after CHEK2 in BRCA-negative patients. Nowadays, more than 170 missense variants and several truncating mutations have been identified in ATM gene. Here, we present the molecular characterization of a new ATM deletion, identified thanks to the CNV algorithm implemented in the NGS analysis pipeline. An automated workflow implementing the SOPHiA Genetics’ Hereditary Cancer Solution (HCS) protocol was used to generate NGS libraries that were sequenced on Illumina MiSeq Platform. NGS data analysis allowed us to identify a new inactivating deletion of exons 19–27 of ATM gene. The deletion was characterized both at the DNA and RNA level.

2021 - Gene expression profile correlates with molecular and clinical features in patients with myelofibrosis [Articolo su rivista]
Rontauroli, S.; Castellano, S.; Guglielmelli, P.; Zini, R.; Bianchi, E.; Genovese, E.; Carretta, C.; Parenti, S.; Fantini, S.; Mallia, S.; Tavernari, L.; Sartini, S.; Mirabile, M.; Mannarelli, C.; Gesullo, F.; Pacilli, A.; Pietra, D.; Rumi, E.; Salmoiraghi, S.; Mora, B.; Villani, L.; Grilli, A.; Rosti, V.; Barosi, G.; Passamonti, F.; Rambaldi, A.; Malcovati, L.; Cazzola, M.; Bicciato, S.; Tagliafico, E.; Vannucchi, A. M.; Manfredini, R.
abstract

Myelofibrosis (MF) belongs to the family of classic Philadelphia-negative myeloproliferative neoplasms (MPNs). It can be primary myelofibrosis (PMF) or secondary myelofibrosis (SMF) evolving from polycythemia vera (PV) or essential thrombocythemia (ET). Despite the differences, PMF and SMF patients are currently managed in the same way, and prediction of survival is based on the same clinical and genetic features. In the last few years, interest has grown concerning the ability of gene expression profiles (GEPs) to provide valuable prognostic information. Here, we studied the GEPs of granulocytes from 114 patients with MF, using a microarray platform to identify correlations with patient characteristics and outcomes. Cox regression analysis led to the identification of 201 survival-related transcripts characterizing patients who are at high risk for death. High-risk patients identified by this gene signature displayed an inferior overall survival and leukemia-free survival, together with clinical and molecular detrimental features included in contemporary prognostic models, such as the presence of high molecular risk mutations. The high-risk group was enriched in post-PV and post-ET MF and JAK2V617F homozygous patients, whereas pre-PMF was more frequent in the low-risk group. These results demonstrate that GEPs in MF patients correlate with their molecular and clinical features, particularly their survival, and represent the proof of concept that GEPs might provide complementary prognostic information to be applied in clinical decision making.

2021 - Mutated clones driving leukemic transformation are already detectable at the single-cell level in CD34-positive cells in the chronic phase of primary myelofibrosis [Articolo su rivista]
Parenti, Sandra; Rontauroli, Sebastiano; Carretta, Chiara; Mallia, Selene; Genovese, Elena; Chiereghin, Chiara; Peano, Clelia; Tavernari, Lara; Bianchi, Elisa; Fantini, Sebastian; Sartini, Stefano; Romano, Oriana; Bicciato, Silvio; Tagliafico, Enrico; Della Porta, Matteo; Manfredini, Rossella
abstract

Disease progression of myeloproliferative neoplasms is the result of increased genomic complexity. Since the ability to predict disease evolution is crucial for clinical decisions, we studied single-cell genomics and transcriptomics of CD34-positive cells from a primary myelofibrosis (PMF) patient who progressed to acute myeloid leukemia (AML) while receiving Ruxolitinib. Single-cell genomics allowed the reconstruction of clonal hierarchy and demonstrated that TET2 was the first mutated gene while FLT3 was the last one. Disease evolution was accompanied by increased clonal heterogeneity and mutational rate, but clones carrying TP53 and FLT3 mutations were already present in the chronic phase. Single-cell transcriptomics unraveled repression of interferon signaling suggesting an immunosuppressive effect exerted by Ruxolitinib. Moreover, AML transformation was associated with a differentiative block and immune escape. These results suggest that single-cell analysis can unmask tumor heterogeneity and provide meaningful insights about PMF progression that might guide personalized therapy.

2020 - Genomic analysis of hematopoietic stem cell at the single-cell level: Optimization of cell fixation and whole genome amplification (WGA) protocol [Articolo su rivista]
Carretta, C.; Mallia, S.; Genovese, E.; Parenti, S.; Rontauroli, S.; Bianchi, E.; Fantini, S.; Sartini, S.; Tavernari, L.; Tagliafico, E.; Manfredini, R.
abstract

Single-cell genomics has become the method of choice for the study of heterogeneous cell populations and represents an elective application in defining the architecture and clonal evolution in hematological neoplasms. Reconstructing the clonal evolution of a neoplastic population therefore represents the main way to understand more deeply the pathogenesis of the neoplasm, but it is also a potential tool to understand the evolution of the tumor population with respect to its response to therapy. Pre-analytical phase for single-cell genomics analysis is crucial to obtain a cell population suitable for single-cell sorting, and whole genome amplification is required to obtain the necessary amount of DNA from a single cell in order to proceed with sequencing. Here, we evaluated the impact of different methods of cellular immunostaining, fixation and whole genome amplification on the efficiency and yield of single-cell sequencing.