The impact of polymorphisms in P-gp, DNA repair and folic acid metabolism genes in newly diagnosed multiple myeloma patients treated with thalidomide plus dexamethasone, with or without bortezomib

The principle aim of this study was to investigate biological predictors of response and resistance to multiple myeloma treatment. Two hypothesis had been proposed as responsible of responsiveness: SNPs in DNA repair and Folate pathway, and P-gp dependent efflux. As a first objective, panel of SNPs in DNA repair and Folate pathway genes, were analyzed. It was a retrospective study in a group of 454, previously untreated, MM patients enrolled in a randomized phase III open-label study. Results show that some SNPs in Folate pathway are correlated with response to MM treatment. MTR genotype was associated with favorable response in the overall population of MM patients. However, this relation, disappear after adjustment for treatment response. When poor responder includes very good partial response, partial response and stable/progressive disease MTFHR rs1801131 genotype was associated with poor response to therapy. This relation - unlike in MTR – was still significant after adjustment for treatment response. Identification of this genetic variant in MM patients could be used as an independent prognostic factor for therapeutic outcome in the clinical practice. In the second objective, basic disposition characteristics of bortezomib was investigated. We demonstrated that bortezomib is a P-gp substrate in a bi-directional transport study. We obtain apparent permeability rate values that together with solubility values can have a crucial implication in better understanding of bortezomib pharmacokinetics with respect to the importance of membrane transporters. Subsequently, in view of the importance of P-gp for bortezomib responsiveness a panel of SNPs in ABCB1 gene - coding for P-gp - were analyzed. In particular we analyzed five SNPs, none of them however correlated with treatment responsiveness. However, we found a significant association between ABCB1 variants and cytogenetic abnormalities. In particular, deletion of chromosome 17 and t(4;14) translocation were present in patients harboring rs60023214 and rs2038502 variants respectively.

Effetti dell'inibizione di Tanchirasi in linee cellulari di Medulloblastoma umano

Tanchirasi (TNKS) è un membro della superfamiglia delle PARP (Poli ADP-Ribosio Polimerasi). TNKS è coinvolta nella stabilizzazione della subunità catalitca del complesso proteico DNA-PK (protein chinasi DNA-dipendente), la DNA-PKcs. Questa proteina è fondamentale per il corretto funzionamento del meccanismo di riparo del DNA chiamato "Saldatura Non Omologa delle Estremità" (NHEJ). La deplezione di TNKS induce una degradazione della DNA-PKcs e una maggiore sensibilità alle radiazioni ionizzanti (RI). TNKS è inoltre un regolatore negativo di axina e di conseguenza un attivatore del pathway di WNT; l'inibizione quindi di TNKS induce anche una inibizione del pathway di WNT. Alterazioni in questo signalling si riscontrano frequentemente nel Medulloblastoma (MB), il tumore cerebrale embrionale più comune dell'infanzia. La radioterapia post-operatoria risulta essere molto efficacia in questa neoplasia, ma causa gravi effetti collaterali e un terzo dei pazienti presenta radioresistenza intrinseca. Un'importante sfida per la ricerca è quindi l'aumento della radiosensibilità tumorale. In questo lavoro, abbiamo studiato gli effetti dell'inibizione farmacologica di TNKS in linee cellulari di MB umano, mediante la small molecule XAV939, potente e specifico inibitore di TNKS. Il trattamento con XAV939 induce una consistente inibizione della capacità proliferativa e clonogenica, non correlata ad un aumento della mortalità cellulare, indicando una bassa tossicità legata alla molecola. Il co-trattamento di XAV939 e RI (γ-ray, dose 2 Gy) causa una ulteriore inibizione della proliferazione cellulare e della capacità di formare colonie. Abbiamo inoltre constatato, mediante Neutral Comet Assay, una minore efficacia nel riparo del DNA in cellule irradiate trattate con XAV939, indicando un effettivo aumento della radiosensibilità in cellule di MB trattate con l'inibitore di TNKS. L'aumentata mortalità cellulare in cellule tumorali trattate con XAV939 e RI ha confermato la nostra ipotesi. Il nostro studio in vitro indica come TNKS possa essere un utile target terapeutico per rendere più efficace l'attuale terapia contro il MB.

p300/CBP tyrosine phosphorylation in response to dna damage activated by c-Abl tyrosine kinase

The nuclear signaling that is triggered in response to DNA damage entails the recruitment and assembly of repair proteins and the induction of genes involved in the activation of cell cycle checkpoint, apoptosis or senescence. The extensive changes in chromatin structure underlying these processes suggest that chromatin-modifying enzymes could be relevant targets of DNA damage-activated signaling. The acetyltransferases p300 and CBP participate in DNA damage-activated responses, including local histone hyperacetylation, cell cycle regulation, and co-activation of DNA damage activated proteins, such as p53, p73 and BRCA1. However, the link between DNA damage and p300/CBP activation has not been identified.We have detected p300 tyrosine phosphorylation in response to DNA damage. We show that the DNA damage-activated cAbl tyrosine kinase enters the nuclei of cells exposed to genotoxic agents and phosphorylates p300 on a tyrosine residue within the bromodomain that is conserved in p300, CBP and many other bromodomain-containing proteins. Antibodies against tyrosine phosphorylated p300/CBP show a DNA damage-inducible nuclear staining, suggesting that p300 tyrosine phosphorylation is an event linking DNA damage and chromatin modifications.

Transcriptional functions of DNA Topoisomerases at a genome-wide scale and a single gene levels

The DNA topology is an important modifier of DNA functions. Torsional stress is generated when right handed DNA is either over- or underwound, producing structural deformations which drive or are driven by processes such as replication, transcription, recombination and repair. DNA topoisomerases are molecular machines that regulate the topological state of the DNA in the cell. These enzymes accomplish this task by either passing one strand of the DNA through a break in the opposing strand or by passing a region of the duplex from the same or a different molecule through a double-stranded cut generated in the DNA. Because of their ability to cut one or two strands of DNA they are also target for some of the most successful anticancer drugs used in standard combination therapies of human cancers. An effective anticancer drug is Camptothecin (CPT) that specifically targets DNA topoisomerase 1 (TOP 1). The research project of the present thesis has been focused on the role of human TOP 1 during transcription and on the transcriptional consequences associated with TOP 1 inhibition by CPT in human cell lines. Previous findings demonstrate that TOP 1 inhibition by CPT perturbs RNA polymerase (RNAP II) density at promoters and along transcribed genes suggesting an involvement of TOP 1 in RNAP II promoter proximal pausing site. Within the transcription cycle, promoter pausing is a fundamental step the importance of which has been well established as a means of coupling elongation to RNA maturation. By measuring nascent RNA transcripts bound to chromatin, we demonstrated that TOP 1 inhibition by CPT can enhance RNAP II escape from promoter proximal pausing site of the human Hypoxia Inducible Factor 1 (HIF-1) and c-MYC genes in a dose dependent manner. This effect is dependent from Cdk7/Cdk9 activities since it can be reversed by the kinases inhibitor DRB. Since CPT affects RNAP II by promoting the hyperphosphorylation of its Rpb1 subunit the findings suggest that TOP 1inhibition by CPT may increase the activity of Cdks which in turn phosphorylate the Rpb1 subunit of RNAP II enhancing its escape from pausing. Interestingly, the transcriptional consequences of CPT induced topological stress are wider than expected. CPT increased co-transcriptional splicing of exon1 and 2 and markedly affected alternative splicing at exon 11. Surprisingly despite its well-established transcription inhibitory activity, CPT can trigger the production of a novel long RNA (5’aHIF-1) antisense to the human HIF-1 mRNA and a known antisense RNA at the 3’ end of the gene, while decreasing mRNA levels. The effects require TOP 1 and are independent from CPT induced DNA damage. Thus, when the supercoiling imbalance promoted by CPT occurs at promoter, it may trigger deregulation of the RNAP II pausing, increased chromatin accessibility and activation/derepression of antisense transcripts in a Cdks dependent manner. A changed balance of antisense transcripts and mRNAs may regulate the activity of HIF-1 and contribute to the control of tumor progression After focusing our TOP 1 investigations at a single gene level, we have extended the study to the whole genome by developing the “Topo-Seq” approach which generates a map of genome-wide distribution of sites of TOP 1 activity sites in human cells. The preliminary data revealed that TOP 1 preferentially localizes at intragenic regions and in particular at 5’ and 3’ ends of genes. Surprisingly upon TOP 1 downregulation, which impairs protein expression by 80%, TOP 1 molecules are mostly localized around 3’ ends of genes, thus suggesting that its activity is essential at these regions and can be compensate at 5’ ends. The developed procedure is a pioneer tool for the detection of TOP 1 cleavage sites across the genome and can open the way to further investigations of the enzyme roles in different nuclear processes.