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Tameni A, Mallia S, Manicardi V, Donati B, Torricelli F, Vitale E, Salviato E, Gambarelli G, Muccioli S, Zanelli M, Ascani S, Martino G, Sanguedolce F, Sauta E, Tamagnini I, Puccio N, Neri A, Ciarrocchi A, Fragliasso V. HELLS regulates transcription in T-cell lymphomas by reducing unscheduled R-loops and by facilitating RNAPII progression. Nucleic Acids Res 2024:gkae239. [PMID: 38597676 DOI: 10.1093/nar/gkae239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 02/26/2024] [Accepted: 04/04/2024] [Indexed: 04/11/2024] Open
Abstract
Chromatin modifiers are emerging as major determinants of many types of cancers, including Anaplastic Large Cell Lymphomas (ALCL), a family of highly heterogeneous T-cell lymphomas for which therapeutic options are still limited. HELLS is a multifunctional chromatin remodeling protein that affects genomic instability by participating in the DNA damage response. Although the transcriptional function of HELLS has been suggested, no clues on how HELLS controls transcription are currently available. In this study, by integrating different multi-omics and functional approaches, we characterized the transcriptional landscape of HELLS in ALCL. We explored the clinical impact of its transcriptional program in a large cohort of 44 patients with ALCL. We demonstrated that HELLS, loaded at the level of intronic regions of target promoters, facilitates RNA Polymerase II (RNAPII) progression along the gene bodies by reducing the persistence of co-transcriptional R-loops and promoting DNA damage resolution. Importantly, selective knockdown of HELLS sensitizes ALCL cells to different chemotherapeutic agents, showing a synergistic effect. Collectively, our work unveils the role of HELLS in acting as a gatekeeper of ALCL genome stability providing a rationale for drug design.
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Affiliation(s)
- Annalisa Tameni
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Selene Mallia
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Veronica Manicardi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Emanuele Vitale
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
- Clinical and Experimental Medicine Ph.D. Program, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Elisa Salviato
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Giulia Gambarelli
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Silvia Muccioli
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Magda Zanelli
- Pathology Unit, Department of Oncology, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - Stefano Ascani
- Pathology Unit, Azienda Ospedaliera Santa Maria di Terni, University of Perugia, 05100 Terni, Italy
| | - Giovanni Martino
- Pathology Unit, Azienda Ospedaliera Santa Maria di Terni, University of Perugia, 05100 Terni, Italy
- Institute of Hematology and CREO, University of Perugia, Perugia 06129, Italy
| | | | - Elisabetta Sauta
- IRCCS Humanitas Clinical and Research Center, via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Ione Tamagnini
- Pathology Unit, Department of Oncology, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - Noemi Puccio
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Antonino Neri
- Scientific Directorate, Azienda USL-IRCCS di Reggio Emilia, Viale Umberto I 50, 42123, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Valentina Fragliasso
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
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2
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Di Chiaro P, Nacci L, Arco F, Brandini S, Polletti S, Palamidessi A, Donati B, Soriani C, Gualdrini F, Frigè G, Mazzarella L, Ciarrocchi A, Zerbi A, Spaggiari P, Scita G, Rodighiero S, Barozzi I, Diaferia GR, Natoli G. Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer. Cancer Cell 2024; 42:662-681.e10. [PMID: 38518775 DOI: 10.1016/j.ccell.2024.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 12/07/2023] [Accepted: 02/27/2024] [Indexed: 03/24/2024]
Abstract
Intratumor morphological heterogeneity of pancreatic ductal adenocarcinoma (PDAC) predicts clinical outcomes but is only partially understood at the molecular level. To elucidate the gene expression programs underpinning intratumor morphological variation in PDAC, we investigated and deconvoluted at single cell level the molecular profiles of histologically distinct clusters of PDAC cells. We identified three major morphological and functional variants that co-exist in varying proportions in all PDACs, display limited genetic diversity, and are associated with a distinct organization of the extracellular matrix: a glandular variant with classical ductal features; a transitional variant displaying abortive ductal structures and mixed endodermal and myofibroblast-like gene expression; and a poorly differentiated variant lacking ductal features and basement membrane, and showing neuronal lineage priming. Ex vivo and in vitro evidence supports the occurrence of dynamic transitions among these variants in part influenced by extracellular matrix composition and stiffness and associated with local, specifically neural, invasion.
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Affiliation(s)
- Pierluigi Di Chiaro
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy.
| | - Lucia Nacci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Fabiana Arco
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Stefania Brandini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Sara Polletti
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Andrea Palamidessi
- IFOM, The FIRC Institute for Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Chiara Soriani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Francesco Gualdrini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Gianmaria Frigè
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Luca Mazzarella
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy; Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, IEO, European Institute of Oncology, IRCCS, Milano, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alessandro Zerbi
- IRCCS Humanitas Research Hospital, Rozzano, Milano, Italy; Humanitas University, Pieve Emanuele - Milano, Italy
| | | | - Giorgio Scita
- IFOM, The FIRC Institute for Molecular Oncology, Via Adamello 16, 20139 Milan, Italy; Department of Oncology and Haemato-Oncology, University of Milan, Milano, Italy
| | - Simona Rodighiero
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Giuseppe R Diaferia
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy.
| | - Gioacchino Natoli
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy.
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3
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Ragazzi M, Besutti G, Mancuso P, Rossi PG, Ciarrocchi A, Donati B, Manzotti G, Giordano D, Frasoldati A, Chiaruccci F, de de Biase D, Coluccelli S, Maloberti T, De Leo A, Piana S, Tallini G. Accuracy of World Health Organisation-grade parameters (necrosis and mitotic activity) and foci of vascular invasion in predicting prognosis of papillary thyroid carcinoma. A case-control validation study. Histopathology 2024. [PMID: 38477417 DOI: 10.1111/his.15173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 01/25/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024]
Abstract
AIMS Tumour necrosis and/or increased mitoses define high-grade papillary thyroid carcinoma (PTC). It is unclear whether angioinvasion is prognostic for PTC. Cut-offs at five or more mitoses/2 mm2 and four or more angioinvasive foci have been empirically defined based upon data from all forms of aggressive non-anaplastic thyroid carcinomas. Performance of tumour necrosis, mitoses and vascular invasion in predicting distant metastases when specifically applied to PTC is undefined. METHODS We analysed 50 consecutive PTC cases with distant metastases (DM-PTC): 16 synchronous and 34 metachronous. A total of 108 non-metastatic PTC (N-DM-PTC, 15.0-year median follow-up) were used as controls. Invasive encapsulated follicular variant PTC was excluded. Necrosis, mitoses and angioinvasion were quantified. Receiver operating characteristics (ROC) and area under the curve (AUC) analyses determined best sensitivity and specificity cut-offs predictive of distant metastases. RESULTS Metastases correlated with necrosis (any extent = 43.8% all DM-PTC, 53.1% metachronous DM-PTC versus 5% N-DM-PTC; P < 0.001), mitoses (P < 0.001) and angioinvasion (P < 0.001). Mitoses at five or more per 2 mm2 was the best cut-off correlating with distant metastases: sensitivity/specificity 42.9%/97.2% all DM-PTC (AUC = 0.78), 18.8%/97.2% synchronous DM-PTC (AUC = 0.63), 54.6%/97.2% metachronous DM-PTC (AUC = 0.85). Angioinvasive foci at five or more was the best cut-off correlating with distant metastases: sensitivity/specificity 36.2%/91.7% all DM-PTC (AUC = 0.75), 25%/91.7% synchronous DM-PTC (AUC = 0.79) and 41.9%/91.7% metachronous DM-PTC (AUC = 0.73). Positive/negative predictive values (PPV/NPV) were: necrosis 22.6%/98.2%; five or more mitoses 32.3%/98.2%; five or more angioinvasive foci 11.8%/97.9%. After multivariable analysis, only necrosis and mitotic activity remained associated with DM-PTC. CONCLUSION Our data strongly support PTC grading, statistically validating World Health Organisation (WHO) criteria to identify poor prognosis PTC. Angioinvasion is not an independent predictor of DM-PTC.
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Affiliation(s)
- Moira Ragazzi
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Giulia Besutti
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
- Radiology Unit, Department of Diagnostic Imaging and Laboratory Medicine, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Pamela Mancuso
- Epidemiology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Paolo Giorgi Rossi
- Epidemiology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Gloria Manzotti
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Davide Giordano
- Otolaryngology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Andrea Frasoldati
- Endocrinology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | | | - Dario de de Biase
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Sara Coluccelli
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Thais Maloberti
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Anatomic Pathology, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Antonio De Leo
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Anatomic Pathology, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Simonetta Piana
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Giovanni Tallini
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Anatomic Pathology, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
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Donati B, Reggiani F, Torricelli F, Santandrea G, Rossi T, Bisagni A, Gasparini E, Neri A, Cortesi L, Ferrari G, Bisagni G, Ragazzi M, Ciarrocchi A. Spatial Distribution of Immune Cells Drives Resistance to Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer. Cancer Immunol Res 2024; 12:120-134. [PMID: 37856875 DOI: 10.1158/2326-6066.cir-23-0076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/22/2023] [Accepted: 10/19/2023] [Indexed: 10/21/2023]
Abstract
Neoadjuvant chemotherapy (NAC) alone or combined with target therapies represents the standard of care for localized triple-negative breast cancer (TNBC). However, only a fraction of patients have a response, necessitating better understanding of the complex elements in the TNBC ecosystem that establish continuous and multidimensional interactions. Resolving such complexity requires new spatially-defined approaches. Here, we used spatial transcriptomics to investigate the multidimensional organization of TNBC at diagnosis and explore the contribution of each cell component to response to NAC. Starting from a consecutive retrospective series of TNBC cases, we designed a case-control study including 24 patients with TNBC of which 12 experienced a pathologic complete response (pCR) and 12 no-response or progression (pNR) after NAC. Over 200 regions of interest (ROI) were profiled. Our computational approaches described a model that recapitulates clinical response to therapy. The data were validated in an independent cohort of patients. Differences in the transcriptional program were detected in the tumor, stroma, and immune infiltrate comparing patients with a pCR with those with pNR. In pCR, spatial contamination between the tumor mass and the infiltrating lymphocytes was observed, sustained by a massive activation of IFN-signaling. Conversely, pNR lesions displayed increased pro-angiogenetic signaling and oxygen-based metabolism. Only modest differences were observed in the stroma, revealing a topology-based functional heterogeneity of the immune infiltrate. Thus, spatial transcriptomics provides fundamental information on the multidimensionality of TNBC and allows an effective prediction of tumor behavior. These results open new perspectives for the improvement and personalization of therapeutic approaches to TNBCs.
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Affiliation(s)
- Benedetta Donati
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Francesca Reggiani
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Giacomo Santandrea
- Pathology Unit, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Teresa Rossi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alessandra Bisagni
- Pathology Unit, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Elisa Gasparini
- Oncology Unit, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Antonino Neri
- Scientific Directorate, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Laura Cortesi
- Department of Oncology and Hematology, Azienda Ospedaliera Policlinico di Modena, Modena, Italy
| | - Guglielmo Ferrari
- Breast Surgery Unit, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Giancarlo Bisagni
- Oncology Unit, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Moira Ragazzi
- Pathology Unit, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
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5
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Mularoni V, Donati B, Tameni A, Manicardi V, Reggiani F, Sauta E, Zanelli M, Tigano M, Vitale E, Torricelli F, Ascani S, Martino G, Inghirami G, Sanguedolce F, Ruffini A, Bavieri A, Luminari S, Pizzi M, Dei Tos AP, Fesce C, Neri A, Ciarrocchi A, Fragliasso V. Long non-coding RNA mitophagy and ALK-negative anaplastic lymphoma-associated transcript: a novel regulator of mitophagy in T-cell lymphoma. Haematologica 2023; 108:3333-3346. [PMID: 37381763 PMCID: PMC10690924 DOI: 10.3324/haematol.2022.282552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/20/2023] [Indexed: 06/30/2023] Open
Abstract
Long non-coding RNA (lncRNA) are emerging as powerful and versatile regulators of transcriptional programs and distinctive biomarkers of progression of T-cell lymphoma. Their role in the aggressive anaplastic lymphoma kinase-negative (ALK-) subtype of anaplastic large cell lymphoma (ALCL) has been elucidated only in part. Starting from our previously identified ALCL-associated lncRNA signature and performing digital gene expression profiling of a retrospective cohort of ALCL, we defined an 11 lncRNA signature able to discriminate among ALCL subtypes. We selected a not previously characterized lncRNA, MTAAT, with preferential expression in ALK- ALCL, for molecular and functional studies. We demonstrated that lncRNA MTAAT contributes to an aberrant mitochondrial turnover restraining mitophagy and promoting cellular proliferation. Functionally, lncRNA MTAAT acts as a repressor of a set of genes related to mitochondrial quality control via chromatin reorganization. Collectively, our work demonstrates the transcriptional role of lncRNA MTAAT in orchestrating a complex transcriptional program sustaining the progression of ALK- ALCL.
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Affiliation(s)
- Valentina Mularoni
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia
| | - Annalisa Tameni
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia
| | - Veronica Manicardi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia
| | - Francesca Reggiani
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia
| | - Elisabetta Sauta
- IRCCS Humanitas Clinical and Research Center, via Manzoni 56, 20089, Rozzano, Milan
| | - Magda Zanelli
- Pathology Unit, Department of Oncology, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, 42123
| | - Marco Tigano
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19144
| | - Emanuele Vitale
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy; Clinical and Experimental Medicine Ph.D. Program, University of Modena and Reggio Emilia, Modena, 41125
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia
| | - Stefano Ascani
- Pathology Unit, Azienda Ospedaliera Santa Maria di Terni, University of Perugia, 05100 Terni
| | - Giovanni Martino
- Pathology Unit, Azienda Ospedaliera Santa Maria di Terni, University of Perugia, 05100 Terni, Italy; Institute of Hematology and CREO, University of Perugia, Perugia 06129
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065
| | | | - Alessia Ruffini
- Hematology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia
| | - Alberto Bavieri
- Hematology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia
| | - Stefano Luminari
- Hematology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia
| | - Marco Pizzi
- Surgical Pathology and Cytopathology Unit, Department of Medicine-DIMED, University of Padova, 35128 Padova
| | - Angelo Paolo Dei Tos
- Surgical Pathology and Cytopathology Unit, Department of Medicine-DIMED, University of Padova, 35128 Padova
| | - Cinzia Fesce
- Hematology Unit, University Hospital, 71122 Foggia
| | - Antonino Neri
- Scientific Directorate, Azienda USL-IRCCS di Reggio Emilia, Viale Umberto I 50, 42123, Reggio Emilia
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia
| | - Valentina Fragliasso
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia.
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Manicardi V, Gugnoni M, Sauta E, Donati B, Vitale E, Torricelli F, Manzotti G, Piana S, Longo C, Ghini F, Ciarrocchi A. Ex vivo mapping of enhancer networks that define the transcriptional program driving melanoma metastasis. Mol Oncol 2023; 17:2728-2742. [PMID: 37408506 DOI: 10.1002/1878-0261.13485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/20/2023] [Accepted: 07/04/2023] [Indexed: 07/07/2023] Open
Abstract
Mortality from vmelanoma is associated with metastatic disease, but the mechanisms leading to spreading of the cancer cells remain obscure. Spatial profiling revealed that melanoma is characterized by a high degree of heterogeneity, which is established by the ability of melanoma cells to switch between different phenotypical stages. This plasticity, likely a heritage from embryonic pathways, accounts for a relevant part of the metastatic potential of these lesions, and requires the rapid and efficient reorganization of the transcriptional landscape of melanoma cells. A large part of the non-coding genome cooperates to control gene expression, specifically through the activity of enhancers (ENHs). In this study, we aimed to identify ex vivo the network of active ENHs and to outline their cooperative interactions in supporting transcriptional adaptation during melanoma metastatic progression. We conducted a genome-wide analysis to map active ENHs distribution in a retrospective cohort of 39 melanoma patients, comparing the profiles obtained in primary (N = 19) and metastatic (N = 20) melanoma lesions. Unsupervised clustering showed that the profile for acetylated histone H3 at lysine 27 (H3K27ac) efficiently segregates lesions into three different clusters corresponding to progressive stages of the disease. We reconstructed the map of super-ENHs (SEs) and cooperative ENHs that associate with metastatic progression in melanoma, which showed that cooperation among regulatory elements is a mandatory requirement for transcriptional plasticity. We also showed that these elements carry out specialized and non-redundant functions, and indicated the existence of a hierarchical organization, with SEs on top as masterminds of the entire transcriptional program and classical ENHs as executors. By providing an innovative vision of how the chromatin landscape of melanoma works during metastatic spreading, our data also point out the need to integrate functional profiling in the analysis of cancer lesions to increase definition and improve interpretation of tumor heterogeneity.
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Affiliation(s)
- Veronica Manicardi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
- Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Italy
| | - Mila Gugnoni
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | | | - Benedetta Donati
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | - Emanuele Vitale
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
- Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | - Gloria Manzotti
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | | | - Caterina Longo
- Skin Cancer Unit, Azienda USL-IRCCS di Reggio Emilia, Italy
| | - Francesco Ghini
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
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Torricelli F, Donati B, Reggiani F, Manicardi V, Piana S, Valli R, Lococo F, Ciarrocchi A. Spatially resolved, high-dimensional transcriptomics sorts out the evolution of biphasic malignant pleural mesothelioma: new paradigms for immunotherapy. Mol Cancer 2023; 22:114. [PMID: 37460925 PMCID: PMC10351128 DOI: 10.1186/s12943-023-01816-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Malignant Pleural Mesothelioma (MPM) is a dreadful disease escaping the classical genetic model of cancer evolution and characterized by wide heterogeneity and transcriptional plasticity. Clinical evolution of MPM is marked by a progressive transdifferentiation that converts well differentiated epithelioid (E) cells into undifferentiated and pleomorphic sarcomatoid (S) phenotypes. Catching the way this transition takes place is necessary to understand how MPM develops and progresses and it is mandatory to improve patients' management and life expectancy. Bulk transcriptomic approaches, while providing a significant overview, failed to resolve the timing of this evolution and to identify the hierarchy of molecular events through which this transition takes place. METHODS We applied a spatially resolved, high-dimensional transcriptomic approach to study MPM morphological evolution. 139 regions across 8 biphasic MPMs (B-MPMs) were profiled using the GeoMx™Digital Spatial Profiler to reconstruct the positional context of transcriptional activities and the spatial topology of MPM cells interactions. Validation was conducted on an independent large cohort of 84 MPMs by targeted digital barcoding analysis. RESULTS Our results demonstrated the existence of a complex circular ecosystem in which, within a strong asbestos-driven inflammatory environment, MPM and immune cells affect each other to support S-transdifferentiation. We also showed that TGFB1 polarized M2-Tumor Associated Macrophages foster immune evasion and that TGFB1 expression correlates with reduced survival probability. CONCLUSIONS Besides providing crucial insights into the multidimensional interactions governing MPM clinical evolution, these results open new perspectives to improve the use of immunotherapy in this disease.
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Affiliation(s)
- F Torricelli
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - B Donati
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - F Reggiani
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - V Manicardi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - S Piana
- Pathology Unit, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - R Valli
- Pathology Unit, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - F Lococo
- Thoracic Surgery Unit, IRCCS-Fondazione Policlinico Gemelli, Roma, Italia
- Catholic University of the Sacred Heart, Roma, Italia
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy.
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8
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Gugnoni M, Lorenzini E, Faria do Valle I, Remondini D, Castellani G, Torricelli F, Sauta E, Donati B, Ragazzi M, Ghini F, Piana S, Ciarrocchi A, Manzotti G. Adding pieces to the puzzle of differentiated-to-anaplastic thyroid cancer evolution: the oncogene E2F7. Cell Death Dis 2023; 14:99. [PMID: 36765037 PMCID: PMC9918458 DOI: 10.1038/s41419-023-05603-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 02/12/2023]
Abstract
Anaplastic Thyroid Cancer (ATC) is the most aggressive and de-differentiated subtype of thyroid cancer. Many studies hypothesized that ATC derives from Differentiated Thyroid Carcinoma (DTC) through a de-differentiation process triggered by specific molecular events still largely unknown. E2F7 is an atypical member of the E2F family. Known as cell cycle inhibitor and keeper of genomic stability, in specific contexts its function is oncogenic, guiding cancer progression. We performed a meta-analysis on 279 gene expression profiles, from 8 Gene Expression Omnibus patient samples datasets, to explore the causal relationship between DTC and ATC. We defined 3 specific gene signatures describing the evolution from normal thyroid tissue to DTC and ATC and validated them in a cohort of human surgically resected ATCs collected in our Institution. We identified E2F7 as a key player in the DTC-ATC transition and showed in vitro that its down-regulation reduced ATC cells' aggressiveness features. RNA-seq and ChIP-seq profiling allowed the identification of the E2F7 specific gene program, which is mainly related to cell cycle progression and DNA repair ability. Overall, this study identified a signature describing DTC de-differentiation toward ATC subtype and unveiled an E2F7-dependent transcriptional program supporting this process.
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Affiliation(s)
- Mila Gugnoni
- Laboratory of Translational Research, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Eugenia Lorenzini
- Laboratory of Translational Research, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | | | - Daniel Remondini
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Gastone Castellani
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Elisabetta Sauta
- Laboratory of Translational Research, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Moira Ragazzi
- Pathology Unit, Department of Oncology and Advanced Technologies, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Francesco Ghini
- Laboratory of Translational Research, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Simonetta Piana
- Pathology Unit, Department of Oncology and Advanced Technologies, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy.
| | - Gloria Manzotti
- Laboratory of Translational Research, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy.
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9
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D’Angelo A, Kilili H, Chapman R, Generali D, Tinhofer I, Luminari S, Donati B, Ciarrocchi A, Giannini R, Moretto R, Cremolini C, Pietrantonio F, Sobhani N, Bonazza D, Prins R, Song SG, Jeon YK, Pisignano G, Cinelli M, Bagby S, Urrutia AO. Immune-related pan-cancer gene expression signatures of patient survival revealed by NanoString-based analyses. PLoS One 2023; 18:e0280364. [PMID: 36649303 PMCID: PMC9844904 DOI: 10.1371/journal.pone.0280364] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
The immune system plays a central role in the onset and progression of cancer. A better understanding of transcriptional changes in immune cell-related genes associated with cancer progression, and their significance in disease prognosis, is therefore needed. NanoString-based targeted gene expression profiling has advantages for deployment in a clinical setting over RNA-seq technologies. We analysed NanoString PanCancer Immune Profiling panel gene expression data encompassing 770 genes, and overall survival data, from multiple previous studies covering 10 different cancer types, including solid and blood malignancies, across 515 patients. This analysis revealed an immune gene signature comprising 39 genes that were upregulated in those patients with shorter overall survival; of these 39 genes, three (MAGEC2, SSX1 and ULBP2) were common to both solid and blood malignancies. Most of the genes identified have previously been reported as relevant in one or more cancer types. Using Cibersort, we investigated immune cell levels within individual cancer types and across groups of cancers, as well as in shorter and longer overall survival groups. Patients with shorter survival had a higher proportion of M2 macrophages and γδ T cells. Patients with longer overall survival had a higher proportion of CD8+ T cells, CD4+ T memory cells, NK cells and, unexpectedly, T regulatory cells. Using a transcriptomics platform with certain advantages for deployment in a clinical setting, our multi-cancer meta-analysis of immune gene expression and overall survival data has identified a specific transcriptional profile associated with poor overall survival.
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Affiliation(s)
- Alberto D’Angelo
- Department of Life Sciences, University of Bath, Bath, United Kingdom
- Oncology Department, Royal United Hospital, Bath, United Kingdom
- * E-mail:
| | - Huseyin Kilili
- Milner Centre, Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Robert Chapman
- Department of Medicine, The Princess Alexandra Hospital, Harlow, United Kingdom
| | - Daniele Generali
- Multidisciplinary Unit of Breast Pathology and Translational Research, Cremona Hospital, Cremona, Italy
| | - Ingeborg Tinhofer
- Department of Radiooncology and Radiotherapy, Charite´ University Hospital, Berlin, Germany
| | - Stefano Luminari
- Hematology Unit, Azienda USL-IRCCS, Reggio Emilia, Italy
- Surgical, Medical and Dental Department of Morphological Sciences Related to Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Benedetta Donati
- Translational Research Laboratory, Azienda USL-IRCCS, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Translational Research Laboratory, Azienda USL-IRCCS, Reggio Emilia, Italy
| | - Riccardo Giannini
- Department of Surgery, Clinical, Molecular and Critical Care Pathology, University of Pisa, Pisa, Italy
| | - Roberto Moretto
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Chiara Cremolini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Navid Sobhani
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Debora Bonazza
- Department of Medical, Surgical and Health Sciences, Cattinara Hospital, University of Trieste, Trieste, Italy
| | - Robert Prins
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Seung Geun Song
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yoon Kyung Jeon
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | | | - Mattia Cinelli
- Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Stefan Bagby
- Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Araxi O. Urrutia
- Milner Centre, Department of Life Sciences, University of Bath, Bath, United Kingdom
- Instituto de Ecologia, UNAM, Ciudad de Mexico, Mexico
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10
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Reggiani F, Donati B, Ragazzi M, Manicardi V, Torricelli F, Sauta E, Gasparini E, Piana S, Sancisi V, Ciarrocchi A. Abstract A22: Deciphering natural killer transcriptional activation in triple-negative breast cancer: A novel opportunity for adoptive cell therapies? Cancer Immunol Res 2022. [DOI: 10.1158/2326-6074.tumimm22-a22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Abstract
Triple-Negative Breast Cancer (TNBC) patients that do not respond to neoadjuvant chemotherapy account for 60-70% of all cases and are orphans of therapeutic alternatives after chemotherapy failure. Despite the great progress that has been made in the application of immune-based strategies, clinical opportunities for TNBC patients are still lacking. We aimed to investigate the molecular mechanisms leading to the activation of the TNBC immunological microenvironment, thus providing novel clues for the design and development of immune-based therapeutic approaches and adoptive immune cell therapies for TNBC patients. We analyzed consecutive TNBC cases treated at AUSL-IRCCS Hospital of Reggio Emilia from 2011 to 2017. 24 Tru-Cut biopsies were selected, comparing 12 patients with pathological complete response (pCR) after neoadjuvant treatment and 12 patients with cancer progression. Then, we performed a morphology-guided transcriptome profiling of the immune infiltrate using our GeoMx-Digital spatial profiler (DSP) to investigate which immune populations were associated with a more favorable outcome. The immune infiltrate of patients showing pCR was significantly enriched for activated Natural Killer (NK) cells, compared to patients with disease progression. Intriguingly, both T-helper CD4- and CD8-T lymphocytes did not reach statistical significance, suggesting a secondary involvement in predicting neoadjuvant efficacy in TNBC patients. We confirmed that NK cells can significantly impair TNBC cell proliferation and viability in vitro and improved the efficacy of chemotherapeutic drugs (paclitaxel, docetaxel). To increase our knowledge of the molecular mechanisms governing NK effector functions toward TNBC, we decided to investigate the specific transcriptional landscape that triggers NK cell activation. We profiled the transcriptome of activated NK cells by RNA-sequencing, identifying several de-regulated pathways involved in NK innate anti-tumor response, including the down-regulation of Immune checkpoint (IC) molecules (CTLA4, CEACAM3, PD1, KIR2DL4, KIR3DX1, KIR3DL3, TIGIT, TIM3, LAG3, etc) and the up-regulation of vesicle-trafficking and autophagy-related proteins (STX5, STX7, BNIP3L, SNAP29, GABARAPL1, RAB4B, etc). To predict upstream transcription regulators, promoters of de-regulated genes were in silico scanned for common binding motifs with the FIMO algorithm, thus identifying a list of candidate Transcription Factors (TFs). Among top-scoring TFs, we identified PAX5 which has been already involved in NK differentiation and cytotoxicity. Other top-scoring TFs are currently under investigation as potential NK Master Regulators of their effector functions, including SMAD3, VEZF1, and MAZ. Overall, our results point out the relevance of NK cells in predicting neoadjuvant treatment response in TNBC patients. Moreover, the modulation of the NK transcriptional program may be a novel tool to potentiate their anti-tumor potential, thus proving novel clues to optimize their application in adoptive cell therapies and in the treatment of TNBC patients.
Citation Format: Francesca Reggiani, Benedetta Donati, Moira Ragazzi, Veronica Manicardi, Federica Torricelli, Elisabetta Sauta, Elisa Gasparini, Simonetta Piana, Valentina Sancisi, Alessia Ciarrocchi. Deciphering natural killer transcriptional activation in triple-negative breast cancer: A novel opportunity for adoptive cell therapies? [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy; 2022 Oct 21-24; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2022;10(12 Suppl):Abstract nr A22.
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Affiliation(s)
- Francesca Reggiani
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Benedetta Donati
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Moira Ragazzi
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Veronica Manicardi
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Federica Torricelli
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Elisabetta Sauta
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Elisa Gasparini
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Simonetta Piana
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Valentina Sancisi
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- 1Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
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11
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Durmo R, Donati B, Rebaud L, Cottereau AS, Ruffini A, Nizzoli ME, Ciavarella S, Vegliante MC, Nioche C, Meignan M, Merli F, Versari A, Ciarrocchi A, Buvat I, Luminari S. Prognostic value of lesion dissemination in doxorubicin, bleomycin, vinblastine, and dacarbazine-treated, interimPET-negative classical Hodgkin Lymphoma patients: A radio-genomic study. Hematol Oncol 2022; 40:645-657. [PMID: 35606338 PMCID: PMC9796042 DOI: 10.1002/hon.3025] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/16/2022] [Indexed: 12/30/2022]
Abstract
We evaluated the prognostic role of the largest distance between two lesions (Dmax), defined by positron emission tomography (PET) in a retrospective cohort of newly diagnosed classical Hodgkin Lymphoma (cHL) patients. We also explored the molecular bases underlying Dmax through a gene expression analysis of diagnostic biopsies. We included patients diagnosed with cHL from 2007 to 2020, initially treated with ABVD, with available baseline PET for review, and with at least two FDG avid lesions. Patients with available RNA from diagnostic biopsy were eligible for gene expression analysis. Dmax was deduced from the three-dimensional coordinates of the baseline metabolic tumor volume (MTV) and its effect on progression free survival (PFS) was evaluated. Gene expression profiles were correlated with Dmax and analyzed using CIBERSORTx algorithm to perform deconvolution. The study was conducted on 155 eligible cHL patients. Using its median value of 20 cm, Dmax was the only variable independently associated with PFS (HR = 2.70, 95% CI 1.1-6.63, pValue = 0.03) in multivariate analysis of PFS for all patients and for those with early complete metabolic response (iPET-). Among patients with iPET-low Dmax was associated with a 4-year PFS of 90% (95% CI 82.0-98.9) significantly better compared to high Dmax (4-year PFS 72.4%, 95% CI 61.9-84.6). From the analysis of gene expression profiles differences in Dmax were mostly associated with variations in the expression of microenvironmental components. In conclusion our results support tumor dissemination measured through Dmax as novel prognostic factor for cHL patients treated with ABVD.
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Affiliation(s)
- Rexhep Durmo
- Nuclear Medicine UnitAzienda USL‐IRCCSReggio EmiliaItaly,PhD Program in Clinical and Experimental Medicine (CEM)University of Modena and Reggio EmiliaModenaItaly
| | - Benedetta Donati
- Translational Research LaboratoryAzienda USL‐IRCCSReggio EmiliaItaly
| | - Louis Rebaud
- Laboratoire d’Imagerie Translationnelle en OncologieInstitut Curie, U1288 Inserm, PSLOrsayFrance,Siemens HealthineersSaint‐DenisFrance
| | | | | | | | - Sabino Ciavarella
- Hematology and Cell Therapy UnitIRCCS‐Istituto Tumori 'Giovanni Paolo II'BariItaly
| | | | - Christophe Nioche
- Laboratoire d’Imagerie Translationnelle en OncologieInstitut Curie, U1288 Inserm, PSLOrsayFrance
| | - Michel Meignan
- Lysa ImagingHenri Mondor University Hospital, AP‐HP, University Paris EastCreteilFrance
| | | | | | | | - Irene Buvat
- Laboratoire d’Imagerie Translationnelle en OncologieInstitut Curie, U1288 Inserm, PSLOrsayFrance
| | - Stefano Luminari
- Hematology UnitAzienda USL‐IRCCSReggio EmiliaItaly,Surgical, Medical and Dental Department of Morphological Sciences Related to Transplant, Oncology and Regenerative MedicineUniversity of Modena and Reggio EmiliaReggio EmiliaItaly
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12
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Lorenzini E, Torricelli F, Zamponi R, Donati B, Manicardi V, Sauta E, Faria do Valle I, Reggiani F, Gugnoni M, Manzotti G, Fragliasso V, Vitale E, Piana S, Sancisi V, Ciarrocchi A. KAP1 is a new non-genetic vulnerability of malignant pleural mesothelioma (MPM). NAR Cancer 2022; 4:zcac024. [PMID: 35910692 PMCID: PMC9336180 DOI: 10.1093/narcan/zcac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/29/2022] [Accepted: 07/16/2022] [Indexed: 11/16/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is a rare and incurable cancer, which incidence is increasing in many countries. MPM escapes the classical genetic model of cancer evolution, lacking a distinctive genetic fingerprint. Omics profiling revealed extensive heterogeneity failing to identify major vulnerabilities and restraining development of MPM-oriented therapies. Here, we performed a multilayered analysis based on a functional genome-wide CRISPR/Cas9 screening integrated with patients molecular and clinical data, to identify new non-genetic vulnerabilities of MPM. We identified a core of 18 functionally-related genes as essential for MPM cells. The chromatin reader KAP1 emerged as a dependency of MPM. We showed that KAP1 supports cell growth by orchestrating the expression of a G2/M-specific program, ensuring mitosis correct execution. Targeting KAP1 transcriptional function, by using CDK9 inhibitors resulted in a dramatic loss of MPM cells viability and shutdown of the KAP1-mediated program. Validation analysis on two independent MPM-patients sets, including a consecutive, retrospective cohort of 97 MPM, confirmed KAP1 as new non-genetic dependency of MPM and proved the association of its dependent gene program with reduced patients’ survival probability. Overall these data: provided new insights into the biology of MPM delineating KAP1 and its target genes as building blocks of its clinical aggressiveness.
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Affiliation(s)
- Eugenia Lorenzini
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
- Cellular and Molecular Biology PhD Program, University of Bologna, 40126 Bologna , Italy
| | - Federica Torricelli
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Raffaella Zamponi
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Benedetta Donati
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Veronica Manicardi
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
- Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia , 41121 Modena , Italy
| | - Elisabetta Sauta
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavi, , 27100 Pavia , Italy
| | - Italo Faria do Valle
- Department of Physics, Center for Complex Network Research, Northeastern University , Boston , MA 02115 , USA
| | - Francesca Reggiani
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Mila Gugnoni
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Gloria Manzotti
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Valentina Fragliasso
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Emanuele Vitale
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
- Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia , 41121 Modena , Italy
| | - Simonetta Piana
- Pathology Unit , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Valentina Sancisi
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
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Donati B, Coudry V, Denoix JM, Ohlerth S, Dittmann M, Richter H, Weishaupt M, Suárez Sánchez-Andrade J. Findings and interobserver agreement in radiography and ultrasonography of the vertebral column of a large population of normally performing horses. PFERDEHEILKUNDE 2022. [DOI: 10.21836/pem20220601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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14
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Pistoni M, Rossi T, Donati B, Torricelli F, Polano M, Ciarrocchi A. Long Noncoding RNA NEAT1 Acts as a Molecular Switch for BRD4 Transcriptional Activity and Mediates Repression of BRD4/WDR5 Target Genes. Mol Cancer Res 2021; 19:799-811. [PMID: 33547232 DOI: 10.1158/1541-7786.mcr-20-0324] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 11/18/2020] [Accepted: 02/03/2021] [Indexed: 11/16/2022]
Abstract
BRD4 is an epigenome reader known to exert key roles at the interface between chromatin remodeling and transcriptional regulation, and is primarily known for its role in promoting gene expression. In selective contexts, however, BRD4 may work as negative regulator of transcription. Here, we reported that BRD4 binds several long noncoding RNAs (lncRNA). Among these, the lncRNA NEAT1 was found to interfere with BRD4 transcriptional activity. Mechanistically, lncNEAT1 forms a complex with BRD4 and WDR5 and maintains them in a low-activity state. Treatment with Bromodomains and Extraterminal (BET) inhibitor caused the lncRNA NEAT1 to dissociate from the BRD4/WDR5 complex, restored the acetyl-transferase capacity of BRD4, and restored the availability of WDR5 to promote histone trimethylation, thereby promoting BRD4/WDR5 transcriptional activity and activation of target gene expression. In addition, the lncRNA NEAT1 then became available to bind and to inhibit EZH2, cooperatively increasing transcriptional activation. IMPLICATIONS: Our results revealed an epigenetic program that involves the interaction between the lncRNA NEAT1 and BRD4, functioning as a molecular switch between BRD4's activator and repressor chromatin complexes.
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Affiliation(s)
- Mariaelena Pistoni
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy.
| | - Teresa Rossi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Maurizio Polano
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, Aviano, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy.
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15
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Ragazzi M, Torricelli F, Donati B, Ciarrocchi A, de Biase D, Tallini G, Zanetti E, Bisagni A, Kuhn E, Giordano D, Frasoldati A, Piana S. Coexisting well-differentiated and anaplastic thyroid carcinoma in the same primary resection specimen: immunophenotypic and genetic comparison of the two components in a consecutive series of 13 cases and a review of the literature. Virchows Arch 2021; 478:265-281. [PMID: 32683537 DOI: 10.1007/s00428-020-02891-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/30/2020] [Accepted: 07/07/2020] [Indexed: 02/08/2023]
Abstract
Anaplastic carcinoma (AC) is a rare but highly aggressive form of thyroid cancer. It mostly arises on a background of pre-existing well-differentiated cancer (WDC); however, whether it evolves directly from a WDC or originates as a second independent neoplasm is still to be defined. To obtain further insights into these mechanisms, we performed morphological, immunohistochemical, and next-generation sequencing analyses to compare AC and its associated WDC in a subset of 13 surgically resected specimens. Histologically, most WDC were of aggressive subtypes. Papillary carcinomas (8 cases; 62%) were tall cell (4/8), columnar (1/8), classic with hobnail features (1/8), classic and follicular variant in the remaining 2 cases; Hürthle cell and follicular carcinomas were present in 5 (38%) and in 1 (8%) patient, respectively. One patient harbored both a PTC, follicular variant, and a Hürthle cell carcinoma. We did not find any correlation between a histotype of WDC and a specific anaplastic growth pattern. Immunohistochemically, ACs retained pankeratin/PAX8 expression but with significantly lower levels than WDCs, and they tended to lose TTF1 expression, as can be expected within a dedifferentiation process. In addition, AC showed a more frequent expression of p63 and/or SMA, a mutated pattern of p53, and an abnormal expression of p16. Genetic analysis showed that the number of mutations was higher in AC than in the associated WDC, confirming a role of the progressive accumulation of genetic damage in this transition. We observed that mutations found in the WDCs were consistently identified in the anaplastic counterparts, further supporting the hypothesis of a developmental link.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/genetics
- Cell Differentiation
- Female
- Genetic Predisposition to Disease
- High-Throughput Nucleotide Sequencing
- Humans
- Immunohistochemistry
- Immunophenotyping
- Male
- Middle Aged
- Molecular Diagnostic Techniques
- Mutation
- Neoplasms, Complex and Mixed/chemistry
- Neoplasms, Complex and Mixed/genetics
- Neoplasms, Complex and Mixed/pathology
- Phenotype
- Predictive Value of Tests
- Thyroid Carcinoma, Anaplastic/chemistry
- Thyroid Carcinoma, Anaplastic/genetics
- Thyroid Carcinoma, Anaplastic/pathology
- Thyroid Carcinoma, Anaplastic/surgery
- Thyroid Neoplasms/chemistry
- Thyroid Neoplasms/genetics
- Thyroid Neoplasms/pathology
- Thyroid Neoplasms/surgery
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Affiliation(s)
- Moira Ragazzi
- Pathology Unit, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Dario de Biase
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Molecular Diagnostic Unit, Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Azienda USL di Bologna, University of Bologna, Bologna, Italy
| | - Eleonora Zanetti
- Pathology Unit, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Alessandra Bisagni
- Pathology Unit, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Elisabetta Kuhn
- Division of Pathology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Department of Biomedical, Surgical, and Dental Sciences, University of Milan, Milan, Italy
| | - Davide Giordano
- Otolaryngology Unit, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Andrea Frasoldati
- Endocrinology Unit, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Simonetta Piana
- Pathology Unit, Arcispedale Santa Maria Nuova, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy.
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16
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Donati B, Ferrari A, Ruffini A, Manzotti G, Fragliasso V, Merli F, Zanelli M, Valli R, Luminari S, Ciarrocchi A. Gene expression profile unveils diverse biological effect of serum vitamin D in Hodgkin's and diffuse large B-cell lymphoma. Hematol Oncol 2020; 39:205-214. [PMID: 33215701 DOI: 10.1002/hon.2827] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/05/2020] [Accepted: 11/14/2020] [Indexed: 12/21/2022]
Abstract
The primary function of 25(OH)Vitamin D (VitD) is to control calcium; however, recent evidence associated serum VitD deficiency to high aggressiveness and worse outcome in different type of malignancies including lymphomas, and the reasons of such effect are to be defined. In this study, we investigated the association of VitD blood levels with gene expression in a retrospective cohort of 181 lymphomas (104 diffuse large B-cell lymphomas [DLBCLs] and 77 classical Hodgkin's lymphomas [cHLs]) of whom 116 with available gene expression profiles (52 DLBCLs and 64 cHLs, respectively). In DLBCL, VitD deficiency did not cause significant alteration in gene expression suggesting different mechanisms of action including a possible systemic effect or an effect on pharmacokinetics. By contrast, in cHLs, VitD deficiency induced profound changes in the transcriptional program leading to the NF-κB-mediated activation of stress-protective and pro-survival pathways. Coherently, VitD signaling defined by vitamin D Receptor (VDR) expression analysis, resulted highly activated in cHLs but not in DLBCLs. Even if preliminary, these data represent the first evidence of a direct role of VitD in the biology of cHL and suggest a multimodality and disease-specific activity of this vitamin in lymphomas.
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Affiliation(s)
- Benedetta Donati
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Angela Ferrari
- Hematology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alessia Ruffini
- Gruppo Amici Dell'Ematologia Foundation_GrADE, Reggio Emilia, Italy
| | - Gloria Manzotti
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Valentina Fragliasso
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Francesco Merli
- Hematology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Magda Zanelli
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Riccardo Valli
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Stefano Luminari
- Hematology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
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Gobbi G, Donati B, Valle IFD, Reggiani F, Torricelli F, Remondini D, Castellani G, Ambrosetti DC, Ciarrocchi A, Sancisi V. Abstract B33: Genome-scale CRISPR/Cas9 screening identifies Hippo pathway as key determinant for susceptibility to BET inhibitors in lung cancer. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.hippo19-b33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Lung cancer is the main cause of cancer-related mortality worldwide. Despite the availability of different therapeutic options, including chemotherapy, target therapy, and immunotherapy, prognosis for lung cancer patients remains poor. Among innovative therapeutic approaches, inhibitors of the bromodomain and extraterminal domain containing proteins (BETi) have proven efficacy in preclinical settings and are currently in clinical trials for hematologic and solid tumors, including lung cancer. BETi downregulate key oncogenes to which cancer cells are addicted, causing a decrease in proliferation and an increase in apoptosis and differentiation. However, biomarkers that can help to select patients for this treatment are still lacking. To discover the mechanisms responsible of susceptibility and/or resistance to BETi, we performed a genome-scale knockout screening using the CRISPR/Cas9 technology in lung cancer cells. Through this approach, we identified three genes belonging to Hippo pathway, LATS2, TAOK1, and NF2, as mediators of susceptibility to BETi. Hippo pathway is an oncosuppressor pathway that converges on the phosphorylation of YAP1 and TAZ. YAP1 and TAZ are two transcriptional coactivators that interact with TEAD family proteins in nucleus for the activation of pro-oncogenic transcriptional programs. Phosphorylated YAP1 and TAZ are excluded from nucleus, degraded, and unable to enhance the expression of their target genes. We showed that LATS2, TAOK1, and NF2 support susceptibility to BETi, restraining TAZ nuclear localization and activity. We observed that TAZ knockout increases sensitivity whereas TAZ overexpression supports resistance to BETi. Furthermore, we showed that TAZ, YAP1, and TEAD are direct targets of BRD4 and their expression is downregulated by BETi treatment in a large panel of cancer cell lines. Noticeably, molecular alterations in YAP1, TAZ or in the Hippo genes LATS2, TAOK1, and NF2 are present in 19% of all non-small cell lung cancer patients, and overexpression or amplification of TAZ correlates with a worse outcome in lung adenocarcinoma patients. Our data demonstrate that Hippo pathway genes are required for susceptibility to BETi by restraining TAZ activity as transcriptional coactivator, and suggest that this mechanism can be exploited to detect and overcome drug resistance in lung cancer. BETi-mediated downregulation of the YAP1/TAZ/TEAD transcriptional activity provides a rationale for using these drugs to counteract the activity of these pro-oncogenic transcription factors.
Citation Format: Giulia Gobbi, Benedetta Donati, Italo Faria Do Valle, Francesca Reggiani, Federica Torricelli, Daniel Remondini, Gastone Castellani, Davide Carlo Ambrosetti, Alessia Ciarrocchi, Valentina Sancisi. Genome-scale CRISPR/Cas9 screening identifies Hippo pathway as key determinant for susceptibility to BET inhibitors in lung cancer [abstract]. In: Proceedings of the AACR Special Conference on the Hippo Pathway: Signaling, Cancer, and Beyond; 2019 May 8-11; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(8_Suppl):Abstract nr B33.
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18
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Luminari S, Donati B, Casali M, Valli R, Santi R, Puccini B, Kovalchuk S, Ruffini A, Fama A, Berti V, Fragliasso V, Zanelli M, Vergoni F, Versari A, Rigacci L, Merli F, Ciarrocchi A. A Gene Expression-based Model to Predict Metabolic Response After Two Courses of ABVD in Hodgkin Lymphoma Patients. Clin Cancer Res 2019; 26:373-383. [PMID: 31645353 DOI: 10.1158/1078-0432.ccr-19-2356] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 09/12/2019] [Accepted: 10/15/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Early response to ABVD, assessed with interim FDG-PET (iPET), is prognostic for classical Hodgkin lymphoma (cHL) and supports the use of response adapted therapy. The aim of this study was to identify a gene-expression profile on diagnostic biopsy to predict iPET positivity (iPET+). EXPERIMENTAL DESIGN Consecutive untreated patients with stage I-IV cHL who underwent iPET after two cycles of ABVD were identified. Expression of 770 immune-related genes was analyzed by digital expression profiling (NanoString Technology). iPET was centrally reviewed according to the five-point Deauville scale (DS 1-5). An iPET+ predictive model was derived by multivariate regression analysis and assessed in a validation set identified using the same inclusion criteria. RESULTS A training set of 121 and a validation set of 117 patients were identified, with 23 iPET+ cases in each group. Sixty-three (52.1%), 19 (15.7%), and 39 (32.2%) patients had stage I-II, III, and IV, respectively. Diagnostic biopsy of iPET+ cHLs showed transcriptional profile distinct from iPET-. Thirteen genes were stringently associated with iPET+. This signature comprises two functionally stromal-related nodes. Lymphocytes/monocytes ratio (LMR) was also associated to iPET+. In the training cohort a 5-gene/LMR integrated score predicted iPET+ [AUC, 0.88; 95% confidence interval (CI), 0.80-0.96]. The score achieved a 100% sensitivity to identify DS5 cases. Model performance was confirmed in the validation set (AUC, 0.68; 95% CI, 0.52-0.84). Finally, iPET score was higher in patients with event versus those without. CONCLUSIONS In cHL, iPET is associated with a genetic signature and can be predicted by applying an integrated gene-based model on the diagnostic biopsy.
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Affiliation(s)
- Stefano Luminari
- Hematology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy.
- Surgical, Medical and Dental Department of Morphological Sciences related to Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | | | - Riccardo Valli
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | | | | | | | - Alessia Ruffini
- Hematology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
- Gruppo Amici Dell'Ematologia Foundation_GrADE, Reggio Emilia, Italy
| | - Angelo Fama
- Hematology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | | | - Valentina Fragliasso
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Magda Zanelli
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | | | - Annibale Versari
- Nuclear Medicine, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Luigi Rigacci
- Hematology and Stem Cell Transplant AO San Camillo Forlanini, Roma, Italy
| | - Francesco Merli
- Hematology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy.
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Rossi T, Pistoni M, Sancisi V, Gobbi G, Torricelli F, Donati B, Ribisi S, Gugnoni M, Ciarrocchi A. RAIN Is a Novel Enhancer-Associated lncRNA That Controls RUNX2 Expression and Promotes Breast and Thyroid Cancer. Mol Cancer Res 2019; 18:140-152. [PMID: 31624086 DOI: 10.1158/1541-7786.mcr-19-0564] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/04/2019] [Accepted: 10/14/2019] [Indexed: 11/16/2022]
Abstract
Enhancer (ENH)-associated long noncoding RNAs (lncRNA) are a peculiar class of RNAs produced by transcriptionally active ENHs, owning potential gene-regulatory function. Here, we characterized RAIN, a novel ENH-associated lncRNA. Analysis of RAIN expression in a retrospective cohort of human thyroid cancers showed that the expression of this lncRNA is restricted to cancer cells and strongly correlates with the expression of the cancer-promoting transcription factor RUNX2. We showed that RAIN, serving as a cis-regulatory element, promotes RUNX2 expression by two mechanisms. Binding WDR5 and facilitating its localization on the RUNX2 promoter, RAIN modifies the transcriptional status of the RUNX2 locus facilitating transcription initiation. In parallel, RAIN acts as decoy for negative elongation factor complex, restraining its inhibitory function on transcription elongation. In both thyroid and breast cancer cells, RAIN promotes oncogenic features. Using RNA-sequencing profiling, we showed that RAIN orchestrates the expression of a network of cancer-promoting transcription regulators, suggesting that RAIN affects cancer cell phenotype by coordinating the expression of a complex transcriptional network. IMPLICATIONS: Our data contribute to understand lncRNA function in gene regulation and to consolidate their role in cancer.
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Affiliation(s)
- Teresa Rossi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale (AUSL)-IRCCS, Reggio Emilia, Italy
| | - Mariaelena Pistoni
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale (AUSL)-IRCCS, Reggio Emilia, Italy
| | - Valentina Sancisi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale (AUSL)-IRCCS, Reggio Emilia, Italy
| | - Giulia Gobbi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale (AUSL)-IRCCS, Reggio Emilia, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale (AUSL)-IRCCS, Reggio Emilia, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale (AUSL)-IRCCS, Reggio Emilia, Italy
| | - Salvatore Ribisi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale (AUSL)-IRCCS, Reggio Emilia, Italy
| | - Mila Gugnoni
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale (AUSL)-IRCCS, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale (AUSL)-IRCCS, Reggio Emilia, Italy.
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Gobbi G, Donati B, Do Valle IF, Reggiani F, Torricelli F, Remondini D, Castellani G, Ambrosetti DC, Ciarrocchi A, Sancisi V. The Hippo pathway modulates resistance to BET proteins inhibitors in lung cancer cells. Oncogene 2019; 38:6801-6817. [PMID: 31406246 DOI: 10.1038/s41388-019-0924-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/19/2019] [Accepted: 05/13/2019] [Indexed: 11/09/2022]
Abstract
Inhibitors of BET proteins (BETi) are anti-cancer drugs that have shown efficacy in pre-clinical settings and are currently in clinical trials for different types of cancer, including non-small cell lung cancer (NSCLC). Currently, no predictive biomarker is available to identify patients that may benefit from this treatment. To uncover the mechanisms of resistance to BETi, we performed a genome-scale CRISPR/Cas9 screening in lung cancer cells. We identified three Hippo pathway genes, LATS2, TAOK1, and NF2, as key determinants for sensitivity to BETi. The knockout of these genes induces resistance to BETi, by promoting TAZ nuclear localization and transcriptional activity. Conversely, TAZ expression promotes resistance to these drugs. We also showed that TAZ, YAP, and their partner TEAD are direct targets of BRD4 and that treatment with BETi downregulates their expression. Noticeably, molecular alterations in one or more of these genes are present in a large fraction of NSCLC patients and TAZ amplification or overexpression correlates with a worse outcome in lung adenocarcinoma. Our data define the central role of Hippo pathway in mediating resistance to BETi and provide a rationale for using BETi to counter-act YAP/TAZ-mediated pro-oncogenic activity.
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Affiliation(s)
- Giulia Gobbi
- Laboratory of Translational Research, Azienda USL di Reggio Emilia - IRCCS, Reggio Emilia, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda USL di Reggio Emilia - IRCCS, Reggio Emilia, Italy
| | - Italo Faria Do Valle
- Department of Physics, Center for Complex Network Research, Northeastern University, Boston, MA, USA
| | - Francesca Reggiani
- Laboratory of Translational Research, Azienda USL di Reggio Emilia - IRCCS, Reggio Emilia, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda USL di Reggio Emilia - IRCCS, Reggio Emilia, Italy
| | - Daniel Remondini
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Gastone Castellani
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | | | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL di Reggio Emilia - IRCCS, Reggio Emilia, Italy
| | - Valentina Sancisi
- Laboratory of Translational Research, Azienda USL di Reggio Emilia - IRCCS, Reggio Emilia, Italy.
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Manzotti G, Torricelli F, Donati B, Sancisi V, Gugnoni M, Ciarrocchi A. HDACs control RUNX2 expression in cancer cells through redundant and cell context-dependent mechanisms. J Exp Clin Cancer Res 2019; 38:346. [PMID: 31395086 PMCID: PMC6686443 DOI: 10.1186/s13046-019-1350-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 07/29/2019] [Indexed: 12/15/2022]
Abstract
Background RUNX2 is a Runt-related transcription factor required during embryogenesis for skeletal development and morphogenesis of other organs including thyroid and breast gland. Consistent evidence indicates that RUNX2 expression is aberrantly reactivated in cancer and supports tumor progression. The mechanisms leading to RUNX2 expression in cancer has only recently began to emerge. Previously, we showed that suppressing the activity of the epigenetic regulators HDACs significantly represses RUNX2 expression highlighting a role for these enzymes in RUNX2 reactivation in cancer. However, the molecular mechanisms by which HDACs control RUNX2 are still largely unexplored. Here, to fill this gap, we investigated the role of different HDACs in RUNX2 expression regulation in breast and thyroid cancer, tumors that majorly rely on RUNX2 for their development and progression. Methods Proliferation assays and evaluation of RUNX2 mRNA levels by qRT-PCR were used to evaluate the effect of several HDACi and specific siRNAs on a panel of cancer cell lines. Moreover, ChIP and co-IP assays were performed to elucidate the molecular mechanism underneath the RUNX2 transcriptional regulation. Finally, RNA-sequencing unveiled a new subset of genes whose transcription is regulated by the complex RUNX2-HDAC6. Results In this study, we showed that Class I HDACs and in particular HDAC1 are required for RUNX2 efficient transcription in cancer. Furthermore, we found an additional and cell-specific function of HDAC6 in driving RUNX2 expression in thyroid cancer cells. In this model, HDAC6 likely stabilizes the assembly of the transcriptional complex, which includes HDAC1, on the RUNX2 P2 promoter potentiating its transcription. Since a functional interplay between RUNX2 and HDAC6 has been suggested, we used RNA-Seq profiling to consolidate this evidence in thyroid cancer and to extend the knowledge on this cooperation in a setting in which HDAC6 also controls RUNX2 expression. Conclusions Overall, our data provide new insights into the molecular mechanisms controlling RUNX2 in cancer and consolidate the rationale for the use of HDACi as potential pharmacological strategy to counteract the pro-oncogenic program controlled by RUNX2 in cancer cells. Electronic supplementary material The online version of this article (10.1186/s13046-019-1350-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gloria Manzotti
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Valentina Sancisi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Mila Gugnoni
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy.
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22
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Donati B, Casali M, Fama A, Puccini B, Zanelli M, Valli R, Santi R, Vergoni F, Ruffini A, Berti V, Rigacci L, Merli F, Ciarrocchi A, Luminari S. A GENE EXPRESSION-BASED SCORE TO PREDICT INTERIM PET POSITIVITY IN HODGKIN LYMPHOMA PATIENTS TREATED WITH ABVD. Hematol Oncol 2019. [DOI: 10.1002/hon.17_2629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- B. Donati
- Laboratory of Translational Research; AUSL IRCCS; Reggio Emilia Italy
| | - M. Casali
- Nuclear Medicine; AUSL IRCCS; Reggio Emilia Italy
| | - A. Fama
- Hematology; AUSL IRCCS; Reggio Emilia Italy
| | - B. Puccini
- Hematology; Azienda Ospedaliero Universitaria Careggi; Firenze Italy
| | - M. Zanelli
- Pathology; AUSL IRCCS; Reggio Emilia Italy
| | - R. Valli
- Pathology; AUSL IRCCS; Reggio Emilia Italy
| | - R. Santi
- Pathological Histology and Molecular Diagnostics; Azienda Ospedaliero Universitaria Careggi; Firenze Italy
| | - F. Vergoni
- Pathological Histology and Molecular Diagnostics; Azienda Ospedaliero Universitaria Careggi; Firenze Italy
| | - A. Ruffini
- Hematology; GRuppo Amici dell'Ematologia Foundation_GrADE; Reggio Emilia Italy
| | - V. Berti
- Nuclear Medicine; University of Firenze; Firenze Italy
| | - L. Rigacci
- Hematology and Stem Cell Transplant; AO San Camillo Forlanini, Roma and Hematology of Azienda Ospedaliero Universitaria Careggi; Firenze Italy
| | - F. Merli
- Hematology; AUSL IRCCS; Reggio Emilia Italy
| | - A. Ciarrocchi
- Laboratory of Translational Research; AUSL IRCCS; Reggio Emilia Italy
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Pelusi S, Baselli G, Pietrelli A, Dongiovanni P, Donati B, McCain MV, Meroni M, Fracanzani AL, Romagnoli R, Petta S, Grieco A, Miele L, Soardo G, Bugianesi E, Fargion S, Aghemo A, D'Ambrosio R, Xing C, Romeo S, De Francesco R, Reeves HL, Valenti LVC. Rare Pathogenic Variants Predispose to Hepatocellular Carcinoma in Nonalcoholic Fatty Liver Disease. Sci Rep 2019; 9:3682. [PMID: 30842500 PMCID: PMC6403344 DOI: 10.1038/s41598-019-39998-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/23/2019] [Indexed: 12/12/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a rising cause of hepatocellular carcinoma (HCC). We examined whether inherited pathogenic variants in candidate genes (n = 181) were enriched in patients with NAFLD-HCC. To this end, we resequenced peripheral blood DNA of 142 NAFLD-HCC, 59 NAFLD with advanced fibrosis, and 50 controls, and considered 404 healthy individuals from 1000 G. Pathogenic variants were defined according to ClinVar, likely pathogenic as rare variants predicted to alter protein activity. In NAFLD-HCC patients, we detected an enrichment in pathogenic (p = 0.024), and likely pathogenic variants (p = 1.9*10-6), particularly in APOB (p = 0.047). APOB variants were associated with lower circulating triglycerides and higher HDL cholesterol (p < 0.01). A genetic risk score predicted NAFLD-HCC (OR 4.96, 3.29-7.55; p = 5.1*10-16), outperforming the diagnostic accuracy of common genetic risk variants, and of clinical risk factors (p < 0.05). In conclusion, rare pathogenic variants in genes involved in liver disease and cancer predisposition are associated with NAFLD-HCC development.
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Affiliation(s)
- Serena Pelusi
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Internal Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Translational Medicine, Department of Transfusion Medicine and Hepatology, Milan, Italy
| | - Guido Baselli
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessandro Pietrelli
- Internal Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Paola Dongiovanni
- Internal Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Benedetta Donati
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Misti Vanette McCain
- Northern Institute for Cancer Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Marica Meroni
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Anna Ludovica Fracanzani
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Internal Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Renato Romagnoli
- Department of Surgical Sciences, Liver Transplantation Center, University of Turin, Turin, Italy
| | - Salvatore Petta
- Section of Gastroenterology, DIBIMIS, University of Palermo, 90127, Palermo, Italy
| | - Antonio Grieco
- Internal Medicine and Gastroenterology Area, Fondazione Policlinico Universitario A. Gemelli, Catholic University of Rome, 00168, Rome, Italy
| | - Luca Miele
- Internal Medicine and Gastroenterology Area, Fondazione Policlinico Universitario A. Gemelli, Catholic University of Rome, 00168, Rome, Italy
| | - Giorgio Soardo
- Clinic of Internal Medicine-Liver Unit, Department of Experimental and Clinical Medical Sciences, University of Udine, Udine, Italy
| | - Elisabetta Bugianesi
- Division of Gastroenterology, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Silvia Fargion
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Internal Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessio Aghemo
- Division of Gastroenterology and Hepatology Unit, Humanitas Research Hospital and Humanitas University, Rozzano (MI), Italy
| | - Roberta D'Ambrosio
- "A.M. e A. Migliavacca" Center for the Study of Liver Disease, Division of Gastroenterology and Hepatology, Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milano, Italy
| | - Chao Xing
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Stefano Romeo
- Sahlgrenska Center for Cardiovascular and Metabolic Research, Wallenberg Laboratory, Cardiology Department, University of Gothenburg, Gothenburg, Sweden
- Clinical Nutrition Unit, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Raffaele De Francesco
- Istituto Nazionale di Genetica Molecolare (INGM), Romeo ed Enrica Invernizzi, Bioinformatic group, Milan, Italy
| | - Helen Louise Reeves
- Northern Institute for Cancer Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK
- Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Luca Vittorio Carlo Valenti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
- Internal Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
- Translational Medicine, Department of Transfusion Medicine and Hepatology, Milan, Italy.
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de Biase D, Torricelli F, Ragazzi M, Donati B, Kuhn E, Visani M, Acquaviva G, Pession A, Tallini G, Piana S, Ciarrocchi A. Not the same thing: metastatic PTCs have a different background than ATCs. Endocr Connect 2018; 7:1370-1379. [PMID: 30400028 PMCID: PMC6280609 DOI: 10.1530/ec-18-0386] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 10/30/2018] [Indexed: 02/05/2023]
Abstract
Anaplastic thyroid cancer (ATC) is a rare but highly aggressive form of thyroid cancer. By contrast, differentiated papillary thyroid cancer (PTC) only rarely behave aggressively and develop distant metastasis. Whether distantly metastatic PTC (DM-PTC) and ATC share a common genetic background is still to be defined. We used next-generation sequencing (NGS) to explore the genetic background of a cohort of ATC and DM-PTC and a group of well-differentiated PTCs that did not developed distant metastasis as control (ctrl-PTC). A panel of 128 amplicons within 21 thyroid cancer-related genes was analyzed in a set of 151 thyroid cancer samples including 66 ATCs and DM-PTCs. We showed that the ATC/DM-PTC group had an overall mutational load higher than ctrl-PTCs and that ATCs and DM-PTCs are characterized by a different genetic background, with the exception of mutations in the TERT promoter that were overrepresented in both ATCs (61.1%) and DM-PTCs (48.2%) vs non-aggressive ctrl-PTCs (7.6%). In ATCs, TERT promoter mutations were frequently associated with TP53 mutations, while in the DM-PTCs no significant co-occurrence was observed. No significant association of MED12 mutations with aggressiveness of thyroid cancer was observed in our analysis. Finally, correlation analysis showed that increasing number of mutations negatively impact on patient overall survival also within the ATC and DM-PTC group. In conclusions, overall our analysis further highlights the relevance of TERT promoter mutations in driving aggressiveness and provides new pieces of information in the definition of aggressiveness evolution of thyroid cancer lesions.
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Affiliation(s)
- Dario de Biase
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) – Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
- Correspondence should be addressed to A Ciarrocchi or D de Biase: or
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale AUSL-IRCCS, Reggio Emilia, Italy
| | - Moira Ragazzi
- Pathology Unit, Azienda Unità Sanitaria Locale AUSL-IRCCS, Reggio Emilia, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale AUSL-IRCCS, Reggio Emilia, Italy
| | - Elisabetta Kuhn
- Pathology Unit, Azienda Unità Sanitaria Locale AUSL-IRCCS, Reggio Emilia, Italy
| | - Michela Visani
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) – Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Giorgia Acquaviva
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) – Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) – Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) – Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Simonetta Piana
- Pathology Unit, Azienda Unità Sanitaria Locale AUSL-IRCCS, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale AUSL-IRCCS, Reggio Emilia, Italy
- Correspondence should be addressed to A Ciarrocchi or D de Biase: or
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Abstract
BRD4, member of the Bromodomain and Extraterminal (BET) protein family, is largely acknowledged in cancer for its role in super-enhancers (SEs) organization and oncogenes expression regulation. Inhibition of BRD4 shortcuts the communication between SEs and target promoters with a subsequent cell-specific repression of oncogenes to which cancer cells are addicted and cell death. To date, this is the most credited mechanism of action of BET inhibitors, a class of small molecules targeting BET proteins which are currently in clinical trials in several cancer settings. However, recent evidence indicates that BRD4 relevance in cancer goes beyond its role in transcription regulation and identifies this protein as a keeper of genome stability. Indeed, a non-transcriptional role of BRD4 in controlling DNA damage checkpoint activation and repair as well as telomere maintenance has been proposed, throwing new lights into the multiple functions of this protein and opening new perspectives on the use of BETi in cancer. Here we discuss the current available information on non-canonical, non-transcriptional functions of BRD4 and on their implications in cancer biology. Integrating this information with the already known BRD4 role in gene expression regulation, we propose a “common” model to explain BRD4 genomic function. Furthermore, in light of the transversal function of BRD4, we provide new interpretation for the cytotoxic activity of BETi and we discuss new possibilities for a wide and focused employment of these drugs in clinical settings.
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Affiliation(s)
- Benedetta Donati
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Eugenia Lorenzini
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emilia, Italy.
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26
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Gallo C, Fragliasso V, Donati B, Torricelli F, Tameni A, Piana S, Ciarrocchi A. The bHLH transcription factor DEC1 promotes thyroid cancer aggressiveness by the interplay with NOTCH1. Cell Death Dis 2018; 9:871. [PMID: 30158530 PMCID: PMC6115386 DOI: 10.1038/s41419-018-0933-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/30/2018] [Accepted: 08/01/2018] [Indexed: 02/06/2023]
Abstract
Aberrant re-activation of transcription factors occurs frequently in cancer. Recently, we found the basic helix-loop-helix transcription factors DEC1 and DEC2 significantly up-regulated in a model of highly aggressive thyroid cancer, raising the hypothesis that these factors might be part of the program driving progression of these tumors. Here, we investigated for the first time the function of DEC1 and DEC2 in thyroid cancer. Using both gain- and loss-of-function approaches, we showed that DEC1 more than DEC2 sustains progression of thyroid cancer by promoting cell growth and invasiveness. We demonstrated that DEC1 controls NOTCH1 expression and that the interplay with the NOTCH pathway is relevant for DEC1 function in thyroid cancer. We confirmed this observation in vivo showing that DEC1 expression is a specific feature of tumor cells, that this transcription factor is significantly over-expressed in all major thyroid cancer histotypes and that its expression correlated with NOTCH1 in these tumors. Finally, we performed RNA-sequencing to define the DEC1-associated gene expression profile in thyroid cancer cells and we discovered that DEC1 drives the expression of many cell cycle-related genes, uncovering a potential new function for this transcription factor in cancer.
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Affiliation(s)
- Cristina Gallo
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - Valentina Fragliasso
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - Annalisa Tameni
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - Simonetta Piana
- Pathology Unit, Department of Oncology, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy.
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27
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Donati B, Fürst AE, Hässig M, Jackson MA. Epidemiology of fractures: The role of kick injuries in equine fractures. Equine Vet J 2018; 50:580-586. [PMID: 29441693 DOI: 10.1111/evj.12819] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 12/23/2017] [Accepted: 01/26/2018] [Indexed: 11/29/2022]
Abstract
BACKGROUND Fractures occur commonly in equids and often are associated with complications and a poor outcome. There are no reports on the epidemiology of fractures in a heterogeneous equine population. OBJECTIVES To study the epidemiology of fractures in a heterogeneous equine population, focusing on differences between fractures resulting from a kick and fractures, resulting from other causes and investigating predictors for recovery. STUDY DESIGN Retrospective case series. METHODS Data of all equids presented to the Equine Department, Vetsuisse Faculty, University of Zurich between 1990 and 2014 and diagnosed with a fracture were reviewed and those with a known cause were included in this study. Mann-Whitney and chi-squared tests were used to compare recovery rates of fractures resulting from a kick and fractures resulting from other causes, and a logistic regression was carried out for multivariate analysis of the most important factors affecting recovery. RESULTS Here, 1144 cases fulfilled the inclusion criteria. Of all fractures (with a known cause), 43.6% were the result of a kick from another equid. Kicks often produced open fractures (44.7%) that involved bones of the limbs (85.6%). Overall recovery was 70.1%. Logistic regression showed that high-grade lameness accompanying the fracture and severe comminution negatively affected recovery. MAIN LIMITATIONS The equids in this study were drawn from a referred population, which likely precluded the inclusion of both minor fractures and catastrophic fractures that necessitated immediate euthanasia. Moreover, many cases were excluded because the cause of the fracture could not be determined from the patient record. CONCLUSIONS Kicks are the most common cause of fractures in a heterogeneous equine population and measures to reduce the incidence of kicks are necessary in group-housing systems.
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Affiliation(s)
- B Donati
- Equine Department, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - A E Fürst
- Equine Department, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - M Hässig
- Section of Herd Health, Department of Farm Animals, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - M A Jackson
- Equine Department, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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28
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Affiliation(s)
- Benedetta Donati
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRRCS, Reggio Emilia, Italy
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, Internal Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Policlinico Hospital, Università degli Studi di Milano, Milano, Italy
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Magnussen C, Niiranen T, Ojeda F, Costanzo S, Blankenberg S, Donati B, Jousilahti P, Linneberg A, Jorgensen T, Soederberg S, Kuulasmaa K, Zeller T, Iacoviello L, Salomaa V, Schnabel R. P4617Gender differences and similarities in atrial fibrillation epidemiology, risk factors and mortality in community cohorts. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx504.p4617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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30
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Donati B, Pietrelli A, Pingitore P, Dongiovanni P, Caddeo A, Walker L, Baselli G, Pelusi S, Rosso C, Vanni E, Daly A, Mancina RM, Grieco A, Miele L, Grimaudo S, Craxi A, Petta S, De Luca L, Maier S, Soardo G, Bugianesi E, Colli F, Romagnoli R, Anstee QM, Reeves HL, Fracanzani AL, Fargion S, Romeo S, Valenti L. Telomerase reverse transcriptase germline mutations and hepatocellular carcinoma in patients with nonalcoholic fatty liver disease. Cancer Med 2017; 6:1930-1940. [PMID: 28677271 PMCID: PMC5548883 DOI: 10.1002/cam4.1078] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 03/25/2017] [Accepted: 03/27/2017] [Indexed: 12/18/2022] Open
Abstract
In an increasing proportion of cases, hepatocellular carcinoma (HCC) develops in patients with nonalcoholic fatty liver disease (NAFLD). Mutations in telomerase reverse transcriptase (hTERT) are associated with familial liver diseases. The aim of this study was to examine telomere length and germline hTERT mutations as associated with NAFLD‐HCC. In 40 patients with NAFLD‐HCC, 45 with NAFLD‐cirrhosis and 64 healthy controls, peripheral blood telomere length was evaluated by qRT‐PCR and hTERT coding regions and intron–exon boundaries sequenced. We further analyzed 78 patients affected by primary liver cancer (NAFLD‐PLC, 76 with HCC). Enrichment of rare coding mutations (allelic frequency <0.001) was evaluated by Burden test. Functional consequences were estimated in silico and by over‐expressing protein variants in HEK‐293 cells. We found that telomere length was reduced in individuals with NAFLD‐HCC versus those with cirrhosis (P = 0.048) and healthy controls (P = 0.0006), independently of age and sex. We detected an enrichment of hTERT mutations in NAFLD‐HCC, that was confirmed when we further considered a larger cohort of NAFLD‐PLC, and was more marked in female patients (P = 0.03). No mutations were found in cirrhosis and local controls, and only one in 503 healthy Europeans from the 1000 Genomes Project (allelic frequency = 0.025 vs. <0.001; P = 0.0005). Mutations with predicted functional impact, including the frameshift Glu113Argfs*79 and missense Glu668Asp, cosegregated with liver disease in two families. Three patients carried missense mutations (Ala67Val in homozygosity, Pro193Leu and His296Pro in heterozygosity) in the N‐terminal template‐binding domain (P = 0.037 for specific enrichment). Besides Glu668Asp, the Ala67Val variant resulted in reduced intracellular protein levels. In conclusion, we detected an association between shorter telomeres in peripheral blood and rare germline hTERT mutations and NAFLD‐HCC.
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Affiliation(s)
- Benedetta Donati
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, 20122, Italy
| | - Alessandro Pietrelli
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, 20122, Italy.,Istituto Nazionale di Genetica Molecolare (INGM), Romeo ed Enrica Invernizzi, Bioinformatics Group, Milan, 20122, Italy
| | - Piero Pingitore
- Sahlgrenska Center for Cardiovascular and Metabolic Research, Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Paola Dongiovanni
- Internal Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, 20122, Italy
| | - Andrea Caddeo
- Sahlgrenska Center for Cardiovascular and Metabolic Research, Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Lucy Walker
- The Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, United Kingdom
| | - Guido Baselli
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, 20122, Italy
| | - Serena Pelusi
- Internal Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, 20122, Italy
| | - Chiara Rosso
- Division of Gastroenterology, Department of Medical Sciences, University of Torino, Torino, 10126, Italy
| | - Ester Vanni
- Division of Gastroenterology, Department of Medical Sciences, University of Torino, Torino, 10126, Italy
| | - Ann Daly
- The Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, United Kingdom
| | - Rosellina Margherita Mancina
- Sahlgrenska Center for Cardiovascular and Metabolic Research, Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Antonio Grieco
- Internal Medicine and Gastroenterology Area, Fondazione Policlinico Universitario A. Gemelli, Catholic University of Rome, Rome, 00168, Italy
| | - Luca Miele
- Internal Medicine and Gastroenterology Area, Fondazione Policlinico Universitario A. Gemelli, Catholic University of Rome, Rome, 00168, Italy
| | - Stefania Grimaudo
- Section of Gastroenterology, DIBIMIS, University of Palermo, Palermo, 90127, Italy
| | - Antonio Craxi
- Section of Gastroenterology, DIBIMIS, University of Palermo, Palermo, 90127, Italy
| | - Salvatore Petta
- Section of Gastroenterology, DIBIMIS, University of Palermo, Palermo, 90127, Italy
| | - Laura De Luca
- Clinic of Internal Medicine-Liver Unit, Department of Experimental and Clinical Medical Sciences, University of Udine, Udine, 33100, Italy
| | - Silvia Maier
- Clinic of Internal Medicine-Liver Unit, Department of Experimental and Clinical Medical Sciences, University of Udine, Udine, 33100, Italy
| | - Giorgio Soardo
- Clinic of Internal Medicine-Liver Unit, Department of Experimental and Clinical Medical Sciences, University of Udine, Udine, 33100, Italy
| | - Elisabetta Bugianesi
- Division of Gastroenterology, Department of Medical Sciences, University of Torino, Torino, 10126, Italy
| | - Fabio Colli
- Department of Surgical Sciences, Liver Transplantation Center, University of Torino, Torino, 10126, Italy
| | - Renato Romagnoli
- Department of Surgical Sciences, Liver Transplantation Center, University of Torino, Torino, 10126, Italy
| | - Quentin M Anstee
- The Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, United Kingdom.,Liver Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Helen L Reeves
- The Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, United Kingdom.,Northern Institute for Cancer Research, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Anna Ludovica Fracanzani
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, 20122, Italy.,Internal Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, 20122, Italy
| | - Silvia Fargion
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, 20122, Italy.,Internal Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, 20122, Italy
| | - Stefano Romeo
- Sahlgrenska Center for Cardiovascular and Metabolic Research, Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden.,Clinical Nutrition Unit, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, 88100, Italy
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, 20122, Italy.,Internal Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, 20122, Italy
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31
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Abstract
Telomeres consist of repeat DNA sequences located at the terminal portion of chromosomes that shorten during mitosis, protecting the tips of chromosomes. During chronic degenerative conditions associated with high cell replication rate, progressive telomere attrition is accentuated, favoring senescence and genomic instability. Several lines of evidence suggest that this process is involved in liver disease progression: (a) telomere shortening and alterations in the expression of proteins protecting the telomere are associated with cirrhosis and hepatocellular carcinoma; (b) advanced liver damage is a feature of a spectrum of genetic diseases impairing telomere function, and inactivating germline mutations in the telomerase complex (including human Telomerase Reverse Transcriptase (hTERT) and human Telomerase RNA Component (hTERC)) are enriched in cirrhotic patients independently of the etiology; and (c) experimental models suggest that telomerase protects from liver fibrosis progression. Conversely, reactivation of telomerase occurs during hepatocarcinogenesis, allowing the immortalization of the neoplastic clone. The role of telomere attrition may be particularly relevant in the progression of nonalcoholic fatty liver, an emerging cause of advanced liver disease. Modulation of telomerase or shelterins may be exploited to prevent liver disease progression, and to define specific treatments for different stages of liver disease.
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Affiliation(s)
- Benedetta Donati
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Policlinico Milano, 20122 Milano, Italy.
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Policlinico Milano, 20122 Milano, Italy.
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Donati B, Motta BM, Pingitore P, Meroni M, Pietrelli A, Alisi A, Petta S, Xing C, Dongiovanni P, del Menico B, Rametta R, Mancina RM, Badiali S, Fracanzani AL, Craxì A, Fargion S, Nobili V, Romeo S, Valenti L. The rs2294918 E434K variant modulates patatin-like phospholipase domain-containing 3 expression and liver damage. Hepatology 2016; 63:787-98. [PMID: 26605757 DOI: 10.1002/hep.28370] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 11/23/2015] [Indexed: 12/23/2022]
Abstract
UNLABELLED The patatin-like phosholipase domain-containing 3 (PNPLA3) rs738409 polymorphism (I148M) is a major determinant of hepatic fat and predisposes to the full spectrum of liver damage in nonalcoholic fatty liver disease (NAFLD). The aim of this study was to evaluate whether additional PNPLA3 coding variants contribute to NAFLD susceptibility, first in individuals with contrasting phenotypes (with early-onset NAFLD vs. very low aminotransferases) and then in a large validation cohort. Rare PNPLA3 variants were not detected by sequencing coding regions and intron-exon boundaries either in 142 patients with early-onset NAFLD nor in 100 healthy individuals with alanine aminotransferase <22/20 IU/mL. Besides rs738409 I148M, the rs2294918 G>A polymorphism (E434K sequence variant) was over-represented in NAFLD (adjusted P = 0.01). In 1,447 subjects with and without NAFLD, the 148M-434E (P < 0.0001), but not the 148M-434K, haplotype (P > 0.9), was associated with histological NAFLD and steatohepatitis. Both the I148M (P = 0.0002) and E434K variants (P = 0.044) were associated with serum ALT levels, by interacting with each other, in that the 434K hampered the association with liver damage of the 148M allele (P = 0.006). The E434K variant did not affect PNPLA3 enzymatic activity, but carriers of the rs2294918 A allele (434K) displayed lower hepatic PNPLA3 messenger RNA and protein levels (P < 0.05). CONCLUSIONS Rare loss-of-function PNPLA3 variants were not detected in early-onset NAFLD. However, PNPLA3 rs2294918 E434K decreased PNPLA3 expression, lessening the effect of the I148M variant on the predisposition to steatosis and liver damage. This suggests that the PNPLA3 I148M variant has a codominant negative effect on triglycerides mobilization from lipid droplets, mediated by inhibition of other lipases.
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Affiliation(s)
- Benedetta Donati
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Policlinico, Milano, Italy
| | - Benedetta Maria Motta
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Policlinico, Milano, Italy.,Sahlgrenska Center for Cardiovascular and Metabolic Research, Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Piero Pingitore
- Sahlgrenska Center for Cardiovascular and Metabolic Research, Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Marica Meroni
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Policlinico, Milano, Italy
| | - Alessandro Pietrelli
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Policlinico, Milano, Italy.,Istituto Nazionale Genetica Molecolare (INGM), "Romeo ed Enrica Invernizzi", Bioinformatic Group, Milano, Italy
| | - Anna Alisi
- Hepato-Metabolic Unit, Ospedale Bambin Gesù, Roma, Italy
| | - Salvatore Petta
- Department of Gastroenterology, Università di Palermo, Palermo, Italy
| | - Chao Xing
- UT Southwestern Medical Center, Dallas, TX
| | - Paola Dongiovanni
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Policlinico, Milano, Italy
| | - Benedetta del Menico
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Policlinico, Milano, Italy
| | - Raffaela Rametta
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Policlinico, Milano, Italy
| | - Rosellina Margherita Mancina
- Sahlgrenska Center for Cardiovascular and Metabolic Research, Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Sara Badiali
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Policlinico, Milano, Italy
| | - Anna Ludovica Fracanzani
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Policlinico, Milano, Italy
| | - Antonio Craxì
- Department of Gastroenterology, Università di Palermo, Palermo, Italy
| | - Silvia Fargion
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Policlinico, Milano, Italy
| | - Valerio Nobili
- Hepato-Metabolic Unit, Ospedale Bambin Gesù, Roma, Italy
| | - Stefano Romeo
- Sahlgrenska Center for Cardiovascular and Metabolic Research, Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden.,Clinical Nutrition Unit, Department of Medical and Surgical Sciences, University Magna Graecia, Catanzaro, Italy.,Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Policlinico, Milano, Italy
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Baudet C, Donati B, Sinaimeri B, Crescenzi P, Gautier C, Matias C, Sagot MF. Cophylogeny reconstruction via an approximate Bayesian computation. Syst Biol 2014; 64:416-31. [PMID: 25540454 PMCID: PMC4395844 DOI: 10.1093/sysbio/syu129] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/18/2014] [Indexed: 12/27/2022] Open
Abstract
Despite an increasingly vast literature on cophylogenetic reconstructions for studying host–parasite associations, understanding the common evolutionary history of such systems remains a problem that is far from being solved. Most algorithms for host–parasite reconciliation use an event-based model, where the events include in general (a subset of) cospeciation, duplication, loss, and host switch. All known parsimonious event-based methods then assign a cost to each type of event in order to find a reconstruction of minimum cost. The main problem with this approach is that the cost of the events strongly influences the reconciliation obtained. Some earlier approaches attempt to avoid this problem by finding a Pareto set of solutions and hence by considering event costs under some minimization constraints. To deal with this problem, we developed an algorithm, called Coala, for estimating the frequency of the events based on an approximate Bayesian computation approach. The benefits of this method are 2-fold: (i) it provides more confidence in the set of costs to be used in a reconciliation, and (ii) it allows estimation of the frequency of the events in cases where the data set consists of trees with a large number of taxa. We evaluate our method on simulated and on biological data sets. We show that in both cases, for the same pair of host and parasite trees, different sets of frequencies for the events lead to equally probable solutions. Moreover, often these solutions differ greatly in terms of the number of inferred events. It appears crucial to take this into account before attempting any further biological interpretation of such reconciliations. More generally, we also show that the set of frequencies can vary widely depending on the input host and parasite trees. Indiscriminately applying a standard vector of costs may thus not be a good strategy.
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Affiliation(s)
- C Baudet
- INRIA Grenoble Rhône-Alpes, 38330 Montbonnot Saint-Martin, France; Université de Lyon, F-69000 Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622 Villeurbanne, France; Università di Firenze, Dipartimento di Sistemi e Informatica, I-50134 Firenze, Italy; and Laboratoire Statistique et Génome, UMR CNRS 8071 & USC INRA, Université d'Évry INRIA Grenoble Rhône-Alpes, 38330 Montbonnot Saint-Martin, France; Université de Lyon, F-69000 Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622 Villeurbanne, France; Università di Firenze, Dipartimento di Sistemi e Informatica, I-50134 Firenze, Italy; and Laboratoire Statistique et Génome, UMR CNRS 8071 & USC INRA, Université d'Évry
| | - B Donati
- INRIA Grenoble Rhône-Alpes, 38330 Montbonnot Saint-Martin, France; Université de Lyon, F-69000 Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622 Villeurbanne, France; Università di Firenze, Dipartimento di Sistemi e Informatica, I-50134 Firenze, Italy; and Laboratoire Statistique et Génome, UMR CNRS 8071 & USC INRA, Université d'Évry INRIA Grenoble Rhône-Alpes, 38330 Montbonnot Saint-Martin, France; Université de Lyon, F-69000 Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622 Villeurbanne, France; Università di Firenze, Dipartimento di Sistemi e Informatica, I-50134 Firenze, Italy; and Laboratoire Statistique et Génome, UMR CNRS 8071 & USC INRA, Université d'Évry INRIA Grenoble Rhône-Alpes, 38330 Montbonnot Saint-Martin, France; Université de Lyon, F-69000 Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622 Villeurbanne, France; Università di Firenze, Dipartimento di Sistemi e Informatica, I-50134 Firenze, Italy; and Laboratoire Statistique et Génome, UMR CNRS 8071 & USC INRA, Université d'Évry
| | - B Sinaimeri
- INRIA Grenoble Rhône-Alpes, 38330 Montbonnot Saint-Martin, France; Université de Lyon, F-69000 Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622 Villeurbanne, France; Università di Firenze, Dipartimento di Sistemi e Informatica, I-50134 Firenze, Italy; and Laboratoire Statistique et Génome, UMR CNRS 8071 & USC INRA, Université d'Évry INRIA Grenoble Rhône-Alpes, 38330 Montbonnot Saint-Martin, France; Université de Lyon, F-69000 Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622 Villeurbanne, France; Università di Firenze, Dipartimento di Sistemi e Informatica, I-50134 Firenze, Italy; and Laboratoire Statistique et Génome, UMR CNRS 8071 & USC INRA, Université d'Évry
| | - P Crescenzi
- INRIA Grenoble Rhône-Alpes, 38330 Montbonnot Saint-Martin, France; Université de Lyon, F-69000 Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622 Villeurbanne, France; Università di Firenze, Dipartimento di Sistemi e Informatica, I-50134 Firenze, Italy; and Laboratoire Statistique et Génome, UMR CNRS 8071 & USC INRA, Université d'Évry
| | - C Gautier
- INRIA Grenoble Rhône-Alpes, 38330 Montbonnot Saint-Martin, France; Université de Lyon, F-69000 Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622 Villeurbanne, France; Università di Firenze, Dipartimento di Sistemi e Informatica, I-50134 Firenze, Italy; and Laboratoire Statistique et Génome, UMR CNRS 8071 & USC INRA, Université d'Évry INRIA Grenoble Rhône-Alpes, 38330 Montbonnot Saint-Martin, France; Université de Lyon, F-69000 Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622 Villeurbanne, France; Università di Firenze, Dipartimento di Sistemi e Informatica, I-50134 Firenze, Italy; and Laboratoire Statistique et Génome, UMR CNRS 8071 & USC INRA, Université d'Évry
| | - C Matias
- INRIA Grenoble Rhône-Alpes, 38330 Montbonnot Saint-Martin, France; Université de Lyon, F-69000 Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622 Villeurbanne, France; Università di Firenze, Dipartimento di Sistemi e Informatica, I-50134 Firenze, Italy; and Laboratoire Statistique et Génome, UMR CNRS 8071 & USC INRA, Université d'Évry
| | - M-F Sagot
- INRIA Grenoble Rhône-Alpes, 38330 Montbonnot Saint-Martin, France; Université de Lyon, F-69000 Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622 Villeurbanne, France; Università di Firenze, Dipartimento di Sistemi e Informatica, I-50134 Firenze, Italy; and Laboratoire Statistique et Génome, UMR CNRS 8071 & USC INRA, Université d'Évry INRIA Grenoble Rhône-Alpes, 38330 Montbonnot Saint-Martin, France; Université de Lyon, F-69000 Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622 Villeurbanne, France; Università di Firenze, Dipartimento di Sistemi e Informatica, I-50134 Firenze, Italy; and Laboratoire Statistique et Génome, UMR CNRS 8071 & USC INRA, Université d'Évry
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Trépo E, Nahon P, Bontempi G, Valenti L, Falleti E, Nischalke HD, Hamza S, Corradini SG, Burza MA, Guyot E, Donati B, Spengler U, Hillon P, Toniutto P, Henrion J, Franchimont D, Devière J, Mathurin P, Moreno C, Romeo S, Deltenre P. Association between the PNPLA3 (rs738409 C>G) variant and hepatocellular carcinoma: Evidence from a meta-analysis of individual participant data. Hepatology 2014; 59:2170-7. [PMID: 24114809 DOI: 10.1002/hep.26767] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 09/19/2013] [Indexed: 12/12/2022]
Abstract
UNLABELLED The incidence of hepatocellular carcinoma (HCC) is increasing in Western countries. Although several clinical factors have been identified, many individuals never develop HCC, suggesting a genetic susceptibility. However, to date, only a few single-nucleotide polymorphisms have been reproducibly shown to be linked to HCC onset. A variant (rs738409 C>G, encoding for p.I148M) in the PNPLA3 gene is associated with liver damage in chronic liver diseases. Interestingly, several studies have reported that the minor rs738409[G] allele is more represented in HCC cases in chronic hepatitis C (CHC) and alcoholic liver disease (ALD). However, a significant association with HCC related to CHC has not been consistently observed, and the strength of the association between rs738409 and HCC remains unclear. We performed a meta-analysis of individual participant data including 2,503 European patients with cirrhosis to assess the association between rs738409 and HCC, particularly in ALD and CHC. We found that rs738409 was strongly associated with overall HCC (odds ratio [OR] per G allele, additive model=1.77; 95% confidence interval [CI]: 1.42-2.19; P=2.78 × 10(-7) ). This association was more pronounced in ALD (OR=2.20; 95% CI: 1.80-2.67; P=4.71 × 10(-15) ) than in CHC patients (OR=1.55; 95% CI: 1.03-2.34; P=3.52 × 10(-2) ). After adjustment for age, sex, and body mass index, the variant remained strongly associated with HCC. CONCLUSION Overall, these results suggest that rs738409 exerts a marked influence on hepatocarcinogenesis in patients with cirrhosis of European descent and provide a strong argument for performing further mechanistic studies to better understand the role of PNPLA3 in HCC development.
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Affiliation(s)
- Eric Trépo
- Department of Gastroenterology, Hepatopancreatology and Digestive Oncology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium; Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium
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35
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Nobili V, Donati B, Panera N, Vongsakulyanon A, Alisi A, Dallapiccola B, Valenti L. A 4-polymorphism risk score predicts steatohepatitis in children with nonalcoholic fatty liver disease. J Pediatr Gastroenterol Nutr 2014. [PMID: 24345846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
OBJECTIVE Nonalcoholic fatty liver disease (NAFLD) has become the most common cause of chronic liver disease in industrialized countries in adults and children, following the trail of the epidemic diffusion of obesity. Nonalcoholic steatohepatitis (NASH) is a potentially serious form of NAFLD linked with a significant increase in overall and liver-related morbidity and mortality. Because diagnosis still requires liver biopsy, there is urgent need of developing noninvasive early markers. The aim of the present study was to assess whether the simultaneous detection of genetic risk factors could predict NASH. METHOD We enrolled 152 untreated, consecutive obese children and adolescents with biopsy-proven NAFLD and increased liver enzymes. The PNPLA3 rs738409 C>G (I148 M), SOD2 rs4880 C>T, KLF6 rs3750861 G>A, and LPIN1 rs13412852 C>T polymorphisms were detected by Taqman assays. RESULTS A multivariate logistic model based on the genetic risk factors significantly predicted NASH (area under the receiver-operating characteristic curve [AUC] 0.75, 95% confidence interval [CI] 0.67-0.82, P < 0.0001), performing better than a clinical risk score identified at stepwise regression based on age, aspartate aminotransferase levels, and diastolic blood pressure (AUC 0.66, 95% CI 0.57-0.75). A single cutoff value of the genetic risk score had 90% sensitivity and 36% specificity for NASH. A risk score combining the clinical and genetic risk factors resulted in an AUC of 0.80 (95% CI 0.73-0.87). CONCLUSIONS A score based on genetic risk factors significantly predicts NASH in obese children with increased liver enzymes, representing a proof-of-principle that genetic scores may be useful to predict long-term outcomes of the disease and guide clinical management.
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Affiliation(s)
- Valerio Nobili
- *Liver Research Unit, Bambino Gesù Children's Hospital and Research Institute, Roma †Department of Pathophysiology and Transplantation, section Internal Medicine, Universita' degli Studi di Milano, Fondazione Ca' Granda IRCCS Ospedale Maggiore Policlinico, Milan ‡Scientific direction, Bambino Gesù Children's Hospital and Research Institute, Roma, Italy
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Dongiovanni P, Donati B, Fares R, Lombardi R, Mancina RM, Romeo S, Valenti L. PNPLA3 I148M polymorphism and progressive liver disease. World J Gastroenterol 2013; 19:6969-6978. [PMID: 24222941 PMCID: PMC3819533 DOI: 10.3748/wjg.v19.i41.6969] [Citation(s) in RCA: 176] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/06/2013] [Accepted: 09/17/2013] [Indexed: 02/06/2023] Open
Abstract
The 148 Isoleucine to Methionine protein variant (I148M) of patatin-like phospholipase domain-containing 3 (PNPLA3), a protein is expressed in the liver and is involved in lipid metabolism, has recently been identified as a major determinant of liver fat content. Several studies confirmed that the I148M variant predisposes towards the full spectrum of liver damage associated with fatty liver: from simple steatosis to steatohepatitis and progressive fibrosis. Furthermore, the I148M variant represents a major determinant of progression of alcohol related steatohepatitis to cirrhosis, and to influence fibrogenesis and related clinical outcomes in chronic hepatitis C virus hepatitis, and possibly chronic hepatitis B virus hepatitis, hereditary hemochromatosis and primary sclerosing cholangitis. All in all, studies suggest that the I148M polymorphism may represent a general modifier of fibrogenesis in liver diseases. Remarkably, the effect of the I148M variant on fibrosis was independent of that on hepatic steatosis and inflammation, suggesting that it may affect both the quantity and quality of hepatic lipids and the biology of non-parenchymal liver cells besides hepatocytes, directly promoting fibrogenesis. Therefore, PNPLA3 is a key player in liver disease progression. Assessment of the I148M polymorphism will possibly inform clinical practice in the future, whereas the determination of the effect of the 148M variant will reveal mechanisms involved in hepatic fibrogenesis.
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MESH Headings
- Carcinoma, Hepatocellular
- Cholangitis, Sclerosing/enzymology
- Cholangitis, Sclerosing/genetics
- Cholangitis, Sclerosing/pathology
- Disease Progression
- Fatty Liver/complications
- Fatty Liver/enzymology
- Fatty Liver/genetics
- Fatty Liver/pathology
- Fatty Liver, Alcoholic/complications
- Fatty Liver, Alcoholic/enzymology
- Fatty Liver, Alcoholic/genetics
- Fatty Liver, Alcoholic/pathology
- Genetic Predisposition to Disease
- Hemochromatosis/enzymology
- Hemochromatosis/genetics
- Hemochromatosis/pathology
- Hepatitis B, Chronic/enzymology
- Hepatitis B, Chronic/genetics
- Hepatitis B, Chronic/pathology
- Hepatitis C, Chronic/complications
- Hepatitis C, Chronic/enzymology
- Hepatitis C, Chronic/genetics
- Hepatitis C, Chronic/pathology
- Humans
- Lipase/genetics
- Liver Cirrhosis/enzymology
- Liver Cirrhosis/genetics
- Liver Cirrhosis/pathology
- Liver Cirrhosis, Alcoholic/enzymology
- Liver Cirrhosis, Alcoholic/genetics
- Liver Cirrhosis, Alcoholic/pathology
- Liver Neoplasms/enzymology
- Liver Neoplasms/genetics
- Liver Neoplasms/pathology
- Membrane Proteins/genetics
- Non-alcoholic Fatty Liver Disease
- Phenotype
- Polymorphism, Genetic
- Risk Factors
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Valenti L, Motta BM, Soardo G, Iavarone M, Donati B, Sangiovanni A, Carnelutti A, Dongiovanni P, Rametta R, Bertelli C, Facchetti F, Colombo M, Fargion S, Fracanzani AL. PNPLA3 I148M polymorphism, clinical presentation, and survival in patients with hepatocellular carcinoma. PLoS One 2013; 8:e75982. [PMID: 24155878 PMCID: PMC3796509 DOI: 10.1371/journal.pone.0075982] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/19/2013] [Indexed: 12/16/2022] Open
Abstract
Background & Aims Aim of this study was to evaluate whether the PNPLA3 I148M polymorphism, previously associated with hepatocellular carcinoma (HCC) risk, influences the clinical presentation of HCC and survival. Methods we considered 460 consecutive HCC patients referred to tertiary care centers in Northern Italy, 353 with follow-up data. Results Homozygosity for PNPLA3 148M at risk allele was enriched in HCC patients with alcoholic liver disease or nonalcoholic fatty liver disease (ALD&NAFLD: relative risk 5.9, 95% c.i. 3.5–9.9; other liver diseases: relative risk 1.9, 95% c.i. 1.1–3.4). In ALD&NAFLD patients, the PNPLA3 148M allele was associated with younger age, shorter history of cirrhosis, less advanced (Child A) cirrhosis at HCC diagnosis, and lower HCC differentiation grade (p<0.05). Homozygosity for PNPLA3 148M was associated with reduced survival in the overall series (p = 0.009), and with a higher number of HCC lesions at presentation (p = 0.007) and reduced survival in ALD&NAFLD patients (p = 0.003; median survival 30, 95% c.i. 20–39 vs. 45, 95% c.i. 38–52 months), but not in those with HCC related to other etiologies (p = 0.86; 48, 95% c.i. 32–64 vs. 55, 95% c.i. 43–67 months). At multivariate Cox regression analysis, homozygosity for PNPLA3 148M was the only negative predictor of survival in ALD&NAFLD patients (HR of death 1.57, 95% c.i. 1.12–2.78). Conclusions PNPLA3 148M is over-represented in ALD&NAFLD HCC patients, and is associated with occurrence at a less advanced stage of liver disease in ALD&NAFLD. In ALD&NAFLD, PNPLA3 148M is associated with more diffuse HCC at presentation, and with reduced survival.
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Affiliation(s)
- Luca Valenti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milano, Italy
- Internal Medicine, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca' Granda - Ospedale Maggiore Policlinico Milano, Milano, Italy
- * E-mail:
| | - Benedetta Maria Motta
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milano, Italy
| | | | - Massimo Iavarone
- First Diviosion of Gastroenterology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca' Granda - Ospedale Maggiore Policlinico Milano, Milano, Italy
| | - Benedetta Donati
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milano, Italy
| | - Angelo Sangiovanni
- First Diviosion of Gastroenterology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca' Granda - Ospedale Maggiore Policlinico Milano, Milano, Italy
| | | | - Paola Dongiovanni
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milano, Italy
| | - Raffaela Rametta
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milano, Italy
| | - Cristina Bertelli
- Internal Medicine, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca' Granda - Ospedale Maggiore Policlinico Milano, Milano, Italy
| | - Floriana Facchetti
- First Diviosion of Gastroenterology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca' Granda - Ospedale Maggiore Policlinico Milano, Milano, Italy
| | - Massimo Colombo
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milano, Italy
- First Diviosion of Gastroenterology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca' Granda - Ospedale Maggiore Policlinico Milano, Milano, Italy
| | - Silvia Fargion
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milano, Italy
- Internal Medicine, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca' Granda - Ospedale Maggiore Policlinico Milano, Milano, Italy
| | - Anna Ludovica Fracanzani
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milano, Italy
- Internal Medicine, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca' Granda - Ospedale Maggiore Policlinico Milano, Milano, Italy
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Viganò M, Valenti L, Lampertico P, Facchetti F, Motta BM, D'Ambrosio R, Romagnoli S, Dongiovanni P, Donati B, Fargion S, Colombo M. Patatin-like phospholipase domain-containing 3 I148M affects liver steatosis in patients with chronic hepatitis B. Hepatology 2013; 58:1245-52. [PMID: 23564580 DOI: 10.1002/hep.26445] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 04/03/2013] [Indexed: 12/14/2022]
Abstract
UNLABELLED Steatosis is a common histopathological feature of chronic hepatitis B (CHB) and has been associated with severity of liver disease. Recently, the rs738409 I148M patatin-like phospholipase domain-containing 3 (PNPLA3) polymorphism has been demonstrated to influence steatosis susceptibility and fibrosis progression in patients with different liver diseases, but no data are yet available for CHB. The aim of this study was to evaluate whether PNPLA3 I148M influences steatosis susceptibility in a large series of patients with CHB. We enrolled 235 treatment-naïve CHB patients consecutively examined by percutaneous liver biopsy. In ≥2-cm-long liver tissue cores, steatosis and fibrosis were staged by Kleiner and METAVIR scores, respectively. The I148M polymorphism was determined by Taqman assays. Steatosis was present in 146 (62%) patients, of whom 24 (10%) had severe (>33% of hepatocytes) steatosis. Steatosis was independently associated with age (odds ratio [OR]: 2.67; confidence interval [CI]: 1.50-4.92; for age ≥50 years), body mass index (BMI; OR, 2.84; CI, 1.30-6.76; for BMI ≥27.5 kg/m(2) ), diabetes or impaired fasting glucose (OR, 4.45; CI, 1.10-30.0), and PNPLA3 148M allele (OR, 1.62; CI, 1.00-7.00; for each 148M allele). Independent predictors of severe steatosis were BMI (OR, 3.60; CI, 1.39-9.22; for BMI ≥27.5 kg/m(2) ) and PNPLA3 148M allele (OR, 6.03; CI, 1.23-5.0; for each 148M allele). PNPLA3 148M alleles were associated with a progressive increase in severe steatosis in patients with acquired cofactors, such severe overweight and a history of alcohol intake (P = 0.005). CONCLUSION In CHB patients, the PNPLA3 I148M polymorphism influences susceptibility to steatosis and, in particular, when associated with severe overweight and alcohol intake, severe steatosis.
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Affiliation(s)
- Mauro Viganò
- Hepatology Unit, Ospedale San Giuseppe, Università degli Studi di Milano, Milano, Italy
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Nobili V, Bedogni G, Donati B, Alisi A, Valenti L. The I148M variant of PNPLA3 reduces the response to docosahexaenoic acid in children with non-alcoholic fatty liver disease. J Med Food 2013; 16:957-60. [PMID: 24074360 DOI: 10.1089/jmf.2013.0043] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The aim of this secondary analysis of a randomized controlled trial was to test whether the I148M variant of Patatin-like phospholipase domain-containing protein-3 (PNPLA3) is associated with the response to docosahexaenoic acid (DHA) in children with non-alcoholic fatty liver disease (NAFLD). Sixty children with NAFLD were randomized in equal numbers to DHA 250 mg/day, DHA 500 mg/day or placebo. Coherently with the primary analysis, the probability of more severe steatosis after 24 months of DHA supplementation was 50% lower [95% confidence interval (CI) -59% to -42%)] in the combined DHA 250 and 500 mg/day groups versus placebo. The present secondary analysis revealed an independent effect of PNPLA3 status on the response to DHA. In fact, the probability of more severe steatosis was higher (37%, 95% CI 26-48%) for the PNPLA3 M/M versus I/M genotype and lower (-12%, 95% CI -21% to -3%) for the I/I versus I/M genotype (Somers' D for repeated measures). We conclude that the 148M allele of PNPLA3 is associated with lower response, and the 148I allele with greater response, to DHA supplementation in children with NAFLD.
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Affiliation(s)
- Valerio Nobili
- 1 Hepatometabolic Unit, Bambino Gesù Children's Hospital , Roma, Italy
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Petta S, Valenti L, Marchesini G, Di Marco V, Licata A, Cammà C, Barcellona MR, Cabibi D, Donati B, Fracanzani A, Grimaudo S, Parrinello G, Pipitone RM, Torres D, Fargion S, Licata G, Craxì A. PNPLA3 GG genotype and carotid atherosclerosis in patients with non-alcoholic fatty liver disease. PLoS One 2013; 8:e74089. [PMID: 24069270 PMCID: PMC3775795 DOI: 10.1371/journal.pone.0074089] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 07/26/2013] [Indexed: 12/15/2022] Open
Abstract
Background and Aim To evaluate if the presence of carotid atherosclerosis in patients with NAFLD, could be related to gene variants influencing hepatic fat accumulation and the severity of liver damage. Methods We recorded anthropometric, metabolic and histological data(Kleiner score) of 162 consecutive, biopsy-proven Sicilian NAFLD patients. Intima-media thickness(IMT), IMT thickening(IMT≥1 mm) and carotid plaques(focal thickening of >1.3 mm at the level of common carotid artery) were evaluated using ultrasonography. IL28B rs12979860 C>T, PNPLA3 rs738409 C>G, GCKR rs780094 C>T, LYPLAL1 rs12137855 C>T, and NCAN rs2228603 C>T single nucleotide polymorphisms were also assessed. The results were validated in a cohort of 267 subjects with clinical or histological diagnosis of NAFLD from Northern Italy, 63 of whom had follow-up examinations. Results Carotid plaques, IMT thickening and mean maximum IMT were similar in the two cohorts, whereas the prevalence of diabetes, obesity, NASH, and PNPLA3 GG polymorphism(21%vs.13%, p = 0.02) were significantly higher in the Sicilian cohort. In this cohort, the prevalence of carotid plaques and IMT thickening was higher in PNPLA3 GG compared to CC/CG genotype(53%vs.32%, p = 0.02; 62%vs.28%, p<0.001, respectively). These associations were confirmed at multivariate analyses (OR2.94;95%C.I. 1.12–7.71, p = 0.02, and OR4.11;95%C.I. 1.69–9.96, p = 0.002, respectively), although have been observed only in patients <50years. Also in the validation cohort, PNPLA3 GG genotype was independently associated with IMT thickening in younger patients only (OR: 6.00,95%C.I. 1.36–29, p = 0.01), and to IMT progression (p = 0.05) in patients with follow-up examinations. Conclusion PNPLA3 GG genotype is associated with higher severity of carotid atherosclerosis in younger patients with NAFLD. Mechanisms underlying this association, and its clinical relevance need further investigations.
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Affiliation(s)
- Salvatore Petta
- Di.Bi.M.I.S, Sezione di Gastroenterologia, Università di Palermo, Palermo, Italia
- * E-mail:
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, Section Internal Medicine, Università degli Studi, Fondazione Ca’ Granda IRCCS Ospedale Maggiore Policlinico, Milano, Italy
| | - Giulio Marchesini
- Dipartimento di Medicina e Gastroenterologia, “Alma Mater Studiorum,” Università di Bologna, Bologna, Italy
| | - Vito Di Marco
- Di.Bi.M.I.S, Sezione di Gastroenterologia, Università di Palermo, Palermo, Italia
| | - Anna Licata
- Di.Bi.M.I.S, Sezione di Gastroenterologia, Università di Palermo, Palermo, Italia
| | - Calogero Cammà
- Di.Bi.M.I.S, Sezione di Gastroenterologia, Università di Palermo, Palermo, Italia
| | | | - Daniela Cabibi
- Dipartimento di Patologia umana, Università di Palermo, Palermo, Italia
| | - Benedetta Donati
- Department of Pathophysiology and Transplantation, Section Internal Medicine, Università degli Studi, Fondazione Ca’ Granda IRCCS Ospedale Maggiore Policlinico, Milano, Italy
| | - Anna Fracanzani
- Department of Pathophysiology and Transplantation, Section Internal Medicine, Università degli Studi, Fondazione Ca’ Granda IRCCS Ospedale Maggiore Policlinico, Milano, Italy
| | - Stefania Grimaudo
- Di.Bi.M.I.S, Sezione di Gastroenterologia, Università di Palermo, Palermo, Italia
| | - Gaspare Parrinello
- Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S), Università di Palermo, Palermo, Italia
| | | | - Daniele Torres
- Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S), Università di Palermo, Palermo, Italia
| | - Silvia Fargion
- Department of Pathophysiology and Transplantation, Section Internal Medicine, Università degli Studi, Fondazione Ca’ Granda IRCCS Ospedale Maggiore Policlinico, Milano, Italy
| | - Giuseppe Licata
- Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S), Università di Palermo, Palermo, Italia
| | - Antonio Craxì
- Di.Bi.M.I.S, Sezione di Gastroenterologia, Università di Palermo, Palermo, Italia
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Abstract
Despite the involvement of genetic alterations in neoplastic cell transformation, it is increasingly evident that abnormal epigenetic patterns, such as those affecting DNA methylation and histone posttranslational modifications (PTMs), play an essential role in the early stages of tumor development. This finding, together with the evidence that epigenetic changes are reversible, enabled the development of new antineoplastic therapeutic approaches known as epigenetic therapies. Epigenetic modifications are involved in the control of gene expression, and their aberrant distribution is thought to participate in neoplastic transformation by causing the deregulation of crucial cellular pathways. Epigenetic drugs are able to revert the defective gene expression profile of cancer cells and, consequently, reestablish normal molecular pathways. Considering the emerging interest in epigenetic therapeutics, this review focuses on the approaches affecting DNA methylation, evaluates novel strategies and those already approved for clinical use, and compares their therapeutic potential.
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Affiliation(s)
- Stefano Amatori
- Molecular Pathology and Oncology Lab. "PaoLa," Department of Biomolecular Sciences, University of Urbino "Carlo Bo," Fano, Italy
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Amatori S, Papalini F, Lazzarini R, Donati B, Bagaloni I, Rippo MR, Procopio A, Pelicci PG, Catalano A, Fanelli M. Decitabine, differently from DNMT1 silencing, exerts its antiproliferative activity through p21 upregulation in malignant pleural mesothelioma (MPM) cells. Lung Cancer 2009; 66:184-90. [PMID: 19233506 DOI: 10.1016/j.lungcan.2009.01.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Revised: 10/21/2008] [Accepted: 01/19/2009] [Indexed: 01/12/2023]
Abstract
Malignant pleural mesothelioma (MPM) is a locally aggressive neoplasm, principally linked to asbestos fibres exposure. Strong evidences associate this pollutant with induction of DNA breaks, aberrant chromosomes segregation and important chromosomal rearrangements, considered crucial events in malignant transformation. A considerable contribution to cellular transformation in MPM is also given by the presence of high genomic instability, as well as by the increased DNA methylation, and consequent decreased expression, of tumor-suppressor genes. In this study we first demonstrated that MPM cells are characterized by a decreased methylation level of pericentromeric DNA sequences which can justify, at least in part, the genomic instability observed in this neoplasia. Concomitantly, we found a paradoxical increased expression of DNMT1, the most expressed DNA methyltransferases in MPM cells, DNMT3a and all five isoforms of DNMT3b. Thus, we compared two experimental strategies, DNMT1 silencing and usage of a demethylating agent (5-aza-2'-deoxycytidine or Decitabine), both theoretically able to revert the locally hypermethylated phenotype and considered potential future therapeutic approaches for MPM. Interestingly, both strategies substantially decrease cell survival of MPM cells but the antitumor activity of Decitabine, differently from DNMT1 silencing, is mediated, at least in part, by a p53-independent p21 upregulation, and is characterized by the arrest of MPM cells at the G2/M phase of the cell cycle. These results indicate that the two approaches act probably through different mechanisms and, thus, that DNMT1 silencing can be considered an effective alternative to Decitabine for cancer treatment.
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Affiliation(s)
- S Amatori
- Molecular Pathology and Oncology Lab. M.Paola, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61032 Fano, PU, Italy
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Iacoviello L, Di Castelnuovo A, D'Orazio A, Donati B. Cigarette smoking doubles the risk of myocardial infarction in carriers of a protective polymorphism in the blood coagulation factor VII gene. Thromb Haemost 1999; 81:658. [PMID: 10235457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Remuzzi G, Benigni A, Dodesini P, Schieppati A, Gotti E, Livio M, Mecca G, Donati B, de Gaetano G. Platelet function in patients on maintenance hemodialysis: depressed or enhanced? Clin Nephrol 1982; 17:60-3. [PMID: 7067167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Uremic patients on long-term hemodialysis show a paradoxical association of hemorrhages on the one hand and thrombotic complications or atherosclerosis on the other. Platelet function has been found to be depressed in some cases but enhanced in others. In 19 patients, both platelet aggregation and prostaglandin formation appeared to be significantly enhanced in response to low concentrations of arachidonic acid but significantly reduced with high concentrations. It is suggested that this double functional abnormality of uremic platelets may contribute to the complex vascular disturbances of hemodialyzed patients.
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