LONG NON-CODING RNAs IN CANCER

for mutated forms of p53 protein that cause both a loss of wild-type p53 (wt_p53) function and a gain of pro-tumorigenic features to mutant p53 (mut_p53), so called gain of function (GOF). Several studies demonstrated that mut_p53 GOF promotes tumor invasiveness and metastasis. However, the molecular mechanisms underneath are not fully characterized. Non-coding RNAs, particularly lncRNAs (long non-coding RNAs), are central players of gene regulation including wt_p53 pathway, but up today there are not reports that investigate the role of lncRNAs in the pro-invasive phenotype of mut_p53. Therefore, to better understand the mechanism of mut_p53 oncogenic functions, in this PhD thesis, we aim to investigate whether lncRNAs participate to mut_p53 gain of function, precisely in HGSOC and BC cell models. To do this, we evaluated changes in in vitro invasiveness assays (mesothelial clearance and 3D colony assay) in TP53_silenced HGSOC and BC cell lines. To profile the expression of lncRNAs in TP53_silenced cells, we used a RNA deep-sequencing analysis of nuclear long RNAs. Next, we validated deep-sequencing results in mut_p53 and wt_p53 cell models. We observed that mut_p53 enhances the ability of HGSOC to invade the peritoneum and of basal BC cells to invade extracellular matrix. From NGS data analysis of TP53_silenced cells, we discovered 806 and 1820 lncRNAs differentially expressed in BC and HGSOC cell lines, respectively. Using qRT-PCR, we investigated the 10 gene most differentially expressed both in mut_p53 and wt_p53 cell lines. To sum up, we report a role of mut_p53 both in HGSOC and BC metastatic phenotype, and we identify some lncRNAs (e.g. LINC00704) which could be accountable of this effect. Our future plan is to activate or repress the expression of these candidate genes and evaluate the impact on tumor cell biology

BNC2 is a putative tumor suppressor gene in high-grade serous ovarian carcinoma and impacts cell survival after oxidative stress

Rs3814113 is the single-nucleotide polymorphism (SNP) showing the strongest association with high-grade serous ovarian carcinoma (HGSOC) incidence and is located in an intergenic region about 44\u2009kb downstream of basonuclin 2 (BNC2) gene. Lifetime number of ovulations is associated with increased risk to develop HGSOC, probably because of cell damage of extrauterine M\ufcllerian epithelium by ovulation-induced oxidative stress. However, the impact of low-penetrance HGSOC risk alleles (e.g. rs3814113) on the damage induced by oxidative stress remains unclear. Therefore, the purpose of this study was to investigate whether rs3814113 genetic interval regulates BNC2 expression and whether BNC2 expression levels impact on cell survival after oxidative stress. To do this, we analyzed gene expression levels of BNC2 first in HGSOC data sets and then in an isogenic cell line that we engineered to carry a 5\u2009kb deletion around rs3814113. Finally, we silenced BNC2 and measured surviving cells after hydrogen peroxide (H2O2) treatment to simulate oxidative stress after ovulation. In this paper, we describe that BNC2 expression levels are reduced in HGSOC samples compared with control samples, and that BNC2 expression levels decrease following oxidative stress and ovulation in vitro and in vivo, respectively. Moreover, deletion of 5\u2009kb surrounding rs3814113 decreases BNC2 expression levels in an isogenic cell line, and silencing of BNC2 expression levels increases cell survival after H2O2 treatment. Altogether, our findings suggest that the intergenic region located around rs3814113 regulates BNC2 expression, which in turn affects cell survival after oxidative stress response. Indeed, HGSOC samples present lower BNC2 expression levels that probably, in the initial phases of oncogenic transformation, conferred resistance to oxidative stress and ultimately reduced the clearance of cells with oxidative-induced damages

Exploring the Role of Fallopian Ciliated Cells in the Pathogenesis of High-Grade Serous Ovarian Cancer

High-grade serous epithelial ovarian cancer (HGSOC) is the fifth leading cause of cancer death in women and the first among gynecological malignancies. Despite an initial response to standard chemotherapy, most HGSOC patients relapse. To improve treatment options, we must continue investigating tumor biology. Tumor characteristics (e.g., risk factors and epidemiology) are valuable clues to accomplish this task. The two most frequent risk factors for HGSOC are the lifetime number of ovulations, which is associated with increased oxidative stress in the pelvic area caused by ovulation fluid, and a positive family history due to genetic factors. In the attempt to identify novel genetic factors (i.e., genes) associated with HGSOC, we observed that several genes in linkage with HGSOC are expressed in the ciliated cells of the fallopian tube. This finding made us hypothesize that ciliated cells, despite not being the cell of origin for HGSOC, may take part in HGSOC tumor initiation. Specifically, malfunction of the ciliary beat impairs the laminar fluid flow above the fallopian tube epithelia, thus likely reducing the clearance of oxidative stress caused by follicular fluid. Herein, we review the up-to-date findings dealing with HGSOC predisposition with the hypothesis that fallopian ciliated cells take part in HGSOC onset. Finally, we review the up-to-date literature concerning genes that are located in genomic loci associated with epithelial ovarian cancer (EOC) predisposition that are expressed by the fallopian ciliated cells

Diagnostic and prognostic role of eEF1A in chronic lymphocytic leukaemia

Background. Chronic lymphocytic leukaemia (CLL), the most common form of leukaemia in adults in Western countries, is characterized by the clonal expansion of B cells. Despite major advances in CLL therapy/diagnosis, the medical approach to CLL can be further improved. Here we explore the potential diagnostic/therapeutic role of the elongation factor 1 A (eEF1A) in CLL. Two major isoforms of eEF1A proteins exist: the ubiquitous eEF1A1 and the tissue-specialized eEF1A2. Beside their role in the elongation step of translation, both isoforms are involved in different cellular processes such as cell proliferation and apoptosis. Whereas both eEF1A isoforms play a role in solid and hematologic human tumors, nothing is known in CLL. Methods. eEF1A1/eEF1A2 amounts were quantitated by quantitative real time PCR and western blotting in the lymphocytes of 46 CLL patients vs 26 normal control. eEF1A1 functional role in CLL was investigated in a cellular (MEC-1) and in a subcutaneous xenograft animal model of CLL via its targeting by an aptamer (GT75) or a siRNA (siA1), we previously developed. As control molecules an inactive aptamer (CT75) or siRNA (siGL2) were used. Results. At the mRNA level, eEF1A1 but not eEF1A2 was significantly (p=0,0081) more elevated in CLL lymphocytes compared to control. At the protein level, both eEF1A1 and eEF1A2 were more elevated (p=0,028) in CLL lymphocytes compared to control. Moreover, eEF1A1 but not eEF1A2 protein levels were higher (p=0,0042) in patient which died during the study compared to those surviving. Finally, eEF1A1 targeting by either GT75 or siA1 resulted in MEC-1 viability down regulation (p=0,04) mostly due to autophagy stimulation. In vivo, GT75 or siA1 resulted in tumor growth down-regulation (p=0.014) and extension of animal survival (p=0.014), demonstrating the functional role of eEF1A1 in CLL. Conclusions. The increase of eEF1A1/eEF1A2 protein in lymphocytes of CLL patient cells suggests a role as possible novel CLL markers. The increase of eEF1A1 protein in dead vs surviving patients may confer to eEF1A1 also the role of a novel prognostic marker. This, together with the involvement of eEF1A1 in MEC-1 survival in vitro and in vivo, opens the possibility to consider eEF1A1 also as a novel therapeutic target in CLL

<i>LINC01605</i> Is a Novel Target of Mutant p53 in Breast and Ovarian Cancer Cell Lines

TP53 is the most frequently mutated gene in human cancers. Most TP53 genomic alterations are missense mutations, which cause a loss of its tumour suppressor functions while providing mutant p53 (mut_p53) with oncogenic features (gain-of-function). Loss of p53 tumour suppressor functions alters the transcription of both protein-coding and non-protein-coding genes. Gain-of-function of mut_p53 triggers modification in gene expression as well; however, the impact of mut_p53 on the transcription of the non-protein-coding genes and whether these non-protein-coding genes affect oncogenic properties of cancer cell lines are not fully explored. In this study, we suggested that LINC01605 (also known as lincDUSP) is a long non-coding RNA regulated by mut_p53 and proved that mut_p53 directly regulates LINC01605 by binding to an enhancer region downstream of the LINC01605 locus. We also showed that the loss or downregulation of LINC01605 impairs cell migration in a breast cancer cell line. Eventually, by performing a combined analysis of RNA-seq data generated in mut_TP53-silenced and LINC01605 knockout cells, we showed that LINC01605 and mut_p53 share common gene pathways. Overall, our findings underline the importance of ncRNAs in the mut_p53 network in breast and ovarian cancer cell lines and in particular the importance of LINC01605 in mut_p53 pro-migratory pathways

USP1 links platinum resistance to cancer cell dissemination by regulating Snail stability

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Multiscale pink-beam microCT imaging at the ESRF-ID17 biomedical beamline

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Mutant p53 blocks SESN1/AMPK/PGC-1\u3b1/UCP2 axis increasing mitochondrial O2\u2c9\ub7 production in cancer cells

BACKGROUND: The TP53 tumor suppressor gene is the most frequently altered gene in tumors and mutant p53 gain-of-function isoforms actively promote cancer malignancy. METHODS: A panel of wild-type and mutant p53 cancer cell lines of different tissues, including pancreas, breast, skin, and lung were used, as well as chronic lymphocytic leukemia (CLL) patients with different TP53 gene status. The effects of mutant p53 were evaluated by confocal microscopy, reactive oxygen species production assay, immunoblotting, and quantitative reverse transcription polymerase chain reaction after cellular transfection. RESULTS: We demonstrate that oncogenic mutant p53 isoforms are able to inhibit SESN1 expression and consequently the amount of SESN1/AMPK complex, resulting in the downregulation of the AMPK/PGC-1\u3b1/UCP2 axis and mitochondrial O2-\ub7 production. We also show a correlation between the decrease of reduced thiols with a poorer clinical outcome of CLL patients bearing mutant TP53 gene. The restoration of the mitochondrial uncoupling protein 2 (UCP2) expression, as well as the addition of the radical scavenger N-acetyl-L-cysteine, reversed the oncogenic effects of mutant p53 as cellular hyper-proliferation, antiapoptotic effect, and resistance to drugs. CONCLUSIONS: The inhibition of the SESN1/AMPK/PGC-1\u3b1/UCP2 axis contributes to the pro-oxidant and oncogenic effects of mutant p53, suggesting pro-oxidant drugs as a therapeutic approach for cancer patients bearing mutant TP53 gene

Sleeping beauty genetic screen identifies miR-23b::BTBD7 gene interaction as crucial for colorectal cancer metastasis

Background: Metastatic colorectal cancer (CRC) remains a deadly disease. Identifying locally advanced CRC patients with high risk of developing metastasis and improving outcome of metastatic CRC patients require discovering master regulators of metastasis. In this context, the non-coding part of the human genome is still largely unexplored. Methods: To interrogate the non-coding part of the human genome and disclose regulators of CRC metastasis, we combined a transposon-based forward genetic screen with a novel in vitro assay, which forces cells to grow deprived of cell-substrate and cell-cell contacts (i.e. forced single cell suspension assay - fSCS). Findings: We proved that fSCS selects CRC cells with mesenchymal and pro-metastatic traits. Moreover, we found that the transposon insertions conferred CRC cells resistance to fSCS and thus metastatic advantage. Among the retrieved transposon insertions, we demonstrated that the one located in the 3′UTR of BTBD7 disrupts miR-23b::BTBD7 interaction and contributes to pro-metastatic traits. In addition, miR-23b and BTBD7 correlate with CRC metastasis both in preclinical experiments and in clinical samples. Interpretation: fSCS is a simple and scalable in vitro assay to investigate pro-metastatic traits and transposon-based genetic screens can interrogate the non-coding part of the human genome (e.g. miRNA::target interactions). Finally, both Btbd7 and miR-23b represent promising prognostic biomarkers and therapeutic targets in CRC. Fund: This work was supported by Marie Curie Actions (CIG n. 303877) and Friuli Venezia Giulia region (Grant Agreement n°245574), Italian Association for Cancer Research (AIRC, MFAG n°13589), Italian Ministry of Health (GR-2010-2319387 and PE-2016-02361040) and 5x1000 to CRO Aviano.</p