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Giansanti V, Giannese F, Botrugno OA, Gandolfi G, Balestrieri C, Antoniotti M, Tonon G, Cittaro D. Scalable Integration of Multiomic Single Cell Data Using Generative Adversarial Networks. Bioinformatics 2024:btae300. [PMID: 38696763 DOI: 10.1093/bioinformatics/btae300] [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] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/22/2024] [Accepted: 04/30/2024] [Indexed: 05/04/2024]
Abstract
MOTIVATION Single cell profiling has become a common practice to investigate the complexity of tissues, organs and organisms. Recent technological advances are expanding our capabilities to profile various molecular layers beyond the transcriptome such as, but not limited to, the genome, the epigenome and the proteome. Depending on the experimental procedure, these data can be obtained from separate assays or from the very same cells. Despite development of computational methods for data integration is an active research field, most of the available strategies have been devised for the joint analysis of two modalities and cannot accommodate a high number of them. RESULTS We here propose a multiomic data integration framework based on Wasserstein Generative Adversarial Networks (MOWGAN) suitable for the analysis of paired or unpaired data with high number of modalities (>2). At the core of our strategy is a single network trained on all modalities together, limiting the computational burden when many molecular layers are evaluated. AVAILABILITY Source code of our framework is available at https://github.com/vgiansanti/MOWGAN. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Valentina Giansanti
- Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Milan, Italy
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milan, Italy
| | | | - Oronza A Botrugno
- Functional Genomics of Cancer Unit, IRCCS San Raffaele Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Giorgia Gandolfi
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milan, Italy
| | - Chiara Balestrieri
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milan, Italy
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marco Antoniotti
- Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Milan, Italy
- Bicocca Bioinformatics Biostatistics and Bioimaging Centre-B4, Università degli Studi di Milano-Bicocca, Milan, Italy
- Istituto di Bioimmagini e Fisiologia Molecolare, Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Giovanni Tonon
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milan, Italy
- Functional Genomics of Cancer Unit, IRCCS San Raffaele Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Davide Cittaro
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milan, Italy
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2
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Potenza A, Balestrieri C, Spiga M, Albarello L, Pedica F, Manfredi F, Cianciotti BC, De Lalla C, Botrugno OA, Faccani C, Stasi L, Tassi E, Bonfiglio S, Scotti GM, Redegalli M, Biancolini D, Camisa B, Tiziano E, Sirini C, Casucci M, Iozzi C, Abbati D, Simeoni F, Lazarevic D, Elmore U, Fiorentini G, Di Lullo G, Casorati G, Doglioni C, Tonon G, Dellabona P, Rosati R, Aldrighetti L, Ruggiero E, Bonini C. Revealing and harnessing CD39 for the treatment of colorectal cancer and liver metastases by engineered T cells. Gut 2023; 72:1887-1903. [PMID: 37399271 DOI: 10.1136/gutjnl-2022-328042] [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: 06/14/2022] [Accepted: 06/02/2023] [Indexed: 07/05/2023]
Abstract
OBJECTIVE Colorectal tumours are often densely infiltrated by immune cells that have a role in surveillance and modulation of tumour progression but are burdened by immunosuppressive signals, which might vary from primary to metastatic stages. Here, we deployed a multidimensional approach to unravel the T-cell functional landscape in primary colorectal cancers (CRC) and liver metastases, and genome editing tools to develop CRC-specific engineered T cells. DESIGN We paired high-dimensional flow cytometry, RNA sequencing and immunohistochemistry to describe the functional phenotype of T cells from healthy and neoplastic tissue of patients with primary and metastatic CRC and we applied lentiviral vectors (LV) and CRISPR/Cas9 genome editing technologies to develop CRC-specific cellular products. RESULTS We found that T cells are mainly localised at the front edge and that tumor-infiltrating T cells co-express multiple inhibitory receptors, which largely differ from primary to metastatic sites. Our data highlighted CD39 as the major driver of exhaustion in both primary and metastatic colorectal tumours. We thus simultaneously redirected T-cell specificity employing a novel T-cell receptor targeting HER-2 and disrupted the endogenous TCR genes (TCR editing (TCRED)) and the CD39 encoding gene (ENTPD1), thus generating TCREDENTPD1KOHER-2-redirected lymphocytes. We showed that the absence of CD39 confers to HER-2-specific T cells a functional advantage in eliminating HER-2+ patient-derived organoids in vitro and in vivo. CONCLUSION HER-2-specific CD39 disrupted engineered T cells are promising advanced medicinal products for primary and metastatic CRC.
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Affiliation(s)
- Alessia Potenza
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Balestrieri
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Martina Spiga
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luca Albarello
- Pathology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federica Pedica
- Pathology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Manfredi
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Claudia De Lalla
- Experimental Immunology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Oronza A Botrugno
- Functional Genomics of Cancer Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Cristina Faccani
- Experimental Immunology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Lorena Stasi
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elena Tassi
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Bonfiglio
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Maria Scotti
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Miriam Redegalli
- Pathology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Donatella Biancolini
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Barbara Camisa
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Innovative Immunotherapies Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elena Tiziano
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Innovative Immunotherapies Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Camilla Sirini
- Innovative Immunotherapies Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Monica Casucci
- Innovative Immunotherapies Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Iozzi
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Danilo Abbati
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabio Simeoni
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Dejan Lazarevic
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ugo Elmore
- Gastrointestinal Surgery Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Guido Fiorentini
- Gastrointestinal Surgery Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Di Lullo
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Casorati
- Experimental Immunology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Claudio Doglioni
- Pathology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Giovanni Tonon
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Functional Genomics of Cancer Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Paolo Dellabona
- Experimental Immunology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Riccardo Rosati
- Vita-Salute San Raffaele University, Milan, Italy
- Gastrointestinal Surgery Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luca Aldrighetti
- Vita-Salute San Raffaele University, Milan, Italy
- Hepatobiliary Surgery Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eliana Ruggiero
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Bonini
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
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Berardi A, Botrugno OA, Quilici G, Manteiga JMG, Bachi A, Tonon G, Musco G. Nizp1 is a specific
NUP98
‐
NSD1
functional interactor that regulates
NUP98
‐
NSD1
‐dependent oncogenic programs. FEBS J 2022; 290:1782-1797. [PMID: 36271682 DOI: 10.1111/febs.16664] [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] [Received: 08/05/2022] [Revised: 09/27/2022] [Accepted: 10/21/2022] [Indexed: 11/05/2022]
Abstract
NSD1, NSD2 and NSD3 proteins constitute a family of histone 3 lysine 36 (H3K36) methyltransferases with similar domain architecture, but diversified activities, in part, dependent on their non-enzymatic domains. These domains, despite their high sequence identity, recruit the hosting proteins to different chromatin regions through the recognition of diverse epigenetic marks and/or associations to distinct interactors. In this sense, the PHDvC5HCH finger tandem domain represents a paradigmatic example of functional divergence within the NSD family. In this work, we prove and give a structural rationale for the uniqueness of the PHDvC5HCH domain of NSD1 in recognizing the C2HR Zinc finger domain of Nizp1 (NSD1 interacting Zn finger protein). Importantly, we show that, in a leukaemogenic context, Nizp1 is pivotal in driving the unscheduled expression of HoxA genes and of genes involved in the type I IFN pathway, triggered by the expression of the fusion protein NUP98-NSD1. These data provide the first insight into the pathophysiological relevance of the Nizp1-NSD1 functional association. Targeting of this interaction might open new therapeutic windows to inhibit the NUP98-NSD1 oncogenic properties.
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Affiliation(s)
- Andrea Berardi
- Biomolecular NMR, Division of Genetics and Cell Biology IRCCS Ospedale San Raffaele Milan Italy
| | - Oronza A. Botrugno
- Functional Genomics of Cancer, Division of Experimental Oncology IRCCS Ospedale San Raffaele Milan Italy
| | - Giacomo Quilici
- Biomolecular NMR, Division of Genetics and Cell Biology IRCCS Ospedale San Raffaele Milan Italy
| | | | - Angela Bachi
- Functional Proteomics Group IFOM‐FIRC Institute of Molecular Oncology Milan Italy
| | - Giovanni Tonon
- Functional Genomics of Cancer, Division of Experimental Oncology IRCCS Ospedale San Raffaele Milan Italy
| | - Giovanna Musco
- Biomolecular NMR, Division of Genetics and Cell Biology IRCCS Ospedale San Raffaele Milan Italy
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Zuppone S, Assalini C, Minici C, Botrugno OA, Curnis F, Degano M, Corti A, Montorsi F, Salonia A, Vago R. A Novel RGD-4C-Saporin Conjugate Inhibits Tumor Growth in Mouse Models of Bladder Cancer. Front Oncol 2022; 12:846958. [PMID: 35480108 PMCID: PMC9035931 DOI: 10.3389/fonc.2022.846958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Although toxin may have some advantages compared to chemotherapeutic drugs in cancer therapy, e.g. a potent cytotoxic activity and a reduced risk of resistance, their successful application in the treatments to solid tumors still remains to be fully demonstrated. In this study, we genetically modified the structure of the plant-derived single-chain ribosome inactivating protein saporin (SAP) by fusing its N-terminus to the ACDCRGDCFCG peptide (RGD-4C), an αv-integrin ligand, and explored the anti-tumor activity of the resulting protein (called RGD-SAP) in vitro and in vivo, using a model of muscle invasive bladder cancer. We found that the RGD-4C targeting domain enhances the cytotoxic activity of SAP against various tumor cell lines, in a manner dependent on αv-integrin expression levels. In a subcutaneous syngeneic model of bladder cancer, RGD-SAP significantly reduced tumor growth in a dose-dependent manner. Furthermore, systemic administration of RGD-SAP in combination with mitomycin C, a chemotherapeutic drug currently used to treat patients with bladder cancer, increased the survival of mice bearing orthotopic bladder cancer with no evidence of systemic toxicity. Overall, the results suggest that RGD-SAP represents an efficient drug that could be exploited, either alone or in combination with the state-of-the-art therapies, for the treatment of bladder cancer and, potentially, of other solid tumors.
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Affiliation(s)
- Stefania Zuppone
- Urological Research Institute, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Chiara Assalini
- Urological Research Institute, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Claudia Minici
- Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Oronza A. Botrugno
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Flavio Curnis
- Tumor Biology and Vascular Targeting Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Massimo Degano
- Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Angelo Corti
- Tumor Biology and Vascular Targeting Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milano, Italy
| | - Francesco Montorsi
- Urological Research Institute, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milano, Italy
| | - Andrea Salonia
- Urological Research Institute, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milano, Italy
| | - Riccardo Vago
- Urological Research Institute, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milano, Italy
- *Correspondence: Riccardo Vago,
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5
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Tedesco M, Giannese F, Lazarević D, Giansanti V, Rosano D, Monzani S, Catalano I, Grassi E, Zanella ER, Botrugno OA, Morelli L, Panina Bordignon P, Caravagna G, Bertotti A, Martino G, Aldrighetti L, Pasqualato S, Trusolino L, Cittaro D, Tonon G. Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin. Nat Biotechnol 2022; 40:235-244. [PMID: 34635836 DOI: 10.1038/s41587-021-01031-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [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: 10/05/2020] [Accepted: 07/22/2021] [Indexed: 02/08/2023]
Abstract
Recent efforts have succeeded in surveying open chromatin at the single-cell level, but high-throughput, single-cell assessment of heterochromatin and its underlying genomic determinants remains challenging. We engineered a hybrid transposase including the chromodomain (CD) of the heterochromatin protein-1α (HP-1α), which is involved in heterochromatin assembly and maintenance through its binding to trimethylation of the lysine 9 on histone 3 (H3K9me3), and developed a single-cell method, single-cell genome and epigenome by transposases sequencing (scGET-seq), that, unlike single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq), comprehensively probes both open and closed chromatin and concomitantly records the underlying genomic sequences. We tested scGET-seq in cancer-derived organoids and human-derived xenograft (PDX) models and identified genetic events and plasticity-driven mechanisms contributing to cancer drug resistance. Next, building upon the differential enrichment of closed and open chromatin, we devised a method, Chromatin Velocity, that identifies the trajectories of epigenetic modifications at the single-cell level. Chromatin Velocity uncovered paths of epigenetic reorganization during stem cell reprogramming and identified key transcription factors driving these developmental processes. scGET-seq reveals the dynamics of genomic and epigenetic landscapes underlying any cellular processes.
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Affiliation(s)
- Martina Tedesco
- Università Vita-Salute San Raffaele, Milano, Italy
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | | | - Dejan Lazarević
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
| | - Valentina Giansanti
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano, Italy
| | - Dalia Rosano
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Silvia Monzani
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IEO, IRCCS European Institute of Oncology, Milano, Italy
| | - Irene Catalano
- Department of Oncology, University of Torino School of Medicine, Candiolo, Torino, Italy
- Candiolo Cancer Institute FPO- IRCCS, Candiolo, Torino, Italy
| | - Elena Grassi
- Department of Oncology, University of Torino School of Medicine, Candiolo, Torino, Italy
- Candiolo Cancer Institute FPO- IRCCS, Candiolo, Torino, Italy
| | | | - Oronza A Botrugno
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Leonardo Morelli
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
| | - Paola Panina Bordignon
- Università Vita-Salute San Raffaele, Milano, Italy
- Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy
| | - Giulio Caravagna
- Department of Mathematics and Geosciences, University of Trieste, Trieste, Italy
| | - Andrea Bertotti
- Department of Oncology, University of Torino School of Medicine, Candiolo, Torino, Italy
- Candiolo Cancer Institute FPO- IRCCS, Candiolo, Torino, Italy
| | - Gianvito Martino
- Università Vita-Salute San Raffaele, Milano, Italy
- Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy
| | - Luca Aldrighetti
- Hepatobiliary Surgery Division, IRCCS San Raffaele Hospital, Milano, Italy
| | - Sebastiano Pasqualato
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IEO, IRCCS European Institute of Oncology, Milano, Italy
| | - Livio Trusolino
- Department of Oncology, University of Torino School of Medicine, Candiolo, Torino, Italy
- Candiolo Cancer Institute FPO- IRCCS, Candiolo, Torino, Italy
| | - Davide Cittaro
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy.
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy.
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy.
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Botrugno OA, Tonon G. Genomic Instability and Replicative Stress in Multiple Myeloma: The Final Curtain? Cancers (Basel) 2021; 14:cancers14010025. [PMID: 35008191 PMCID: PMC8750813 DOI: 10.3390/cancers14010025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 11/12/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 12/02/2022] Open
Abstract
Simple Summary Genomic instability is recognized as a driving force in most cancers as well as in the haematological cancer multiple myeloma and remains among the leading cause of drug resistance. Several evidences suggest that replicative stress exerts a fundamental role in fuelling genomic instability. Notably, cancer cells rely on a single protein, ATR, to cope with the ensuing DNA damage. In this perspective, we provide an overview depicting how replicative stress represents an Achilles heel for multiple myeloma, which could be therapeutically exploited either alone or in combinatorial regimens to preferentially ablate tumor cells. Abstract Multiple Myeloma (MM) is a genetically complex and heterogeneous hematological cancer that remains incurable despite the introduction of novel therapies in the clinic. Sadly, despite efforts spanning several decades, genomic analysis has failed to identify shared genetic aberrations that could be targeted in this disease. Seeking alternative strategies, various efforts have attempted to target and exploit non-oncogene addictions of MM cells, including, for example, proteasome inhibitors. The surprising finding that MM cells present rampant genomic instability has ignited concerted efforts to understand its origin and exploit it for therapeutic purposes. A credible hypothesis, supported by several lines of evidence, suggests that at the root of this phenotype there is intense replicative stress. Here, we review the current understanding of the role of replicative stress in eliciting genomic instability in MM and how MM cells rely on a single protein, Ataxia Telangiectasia-mutated and Rad3-related protein, ATR, to control and survive the ensuing, potentially fatal DNA damage. From this perspective, replicative stress per se represents not only an opportunity for MM cells to increase their evolutionary pool by increasing their genomic heterogeneity, but also a vulnerability that could be leveraged for therapeutic purposes to selectively target MM tumor cells.
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Affiliation(s)
- Oronza A. Botrugno
- Functional Genomics of Cancer Unit, Experimental Oncology Division, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Correspondence: (O.A.B.); (G.T.); Tel.: +39-02-2643-6661 (O.A.B.); +39-02-2643-5624 (G.T.); Fax: +39-02-2643-6352 (O.A.B. & G.T.)
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Experimental Oncology Division, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Correspondence: (O.A.B.); (G.T.); Tel.: +39-02-2643-6661 (O.A.B.); +39-02-2643-5624 (G.T.); Fax: +39-02-2643-6352 (O.A.B. & G.T.)
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7
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Botrugno OA, Bianchessi S, Zambroni D, Frenquelli M, Belloni D, Bongiovanni L, Girlanda S, Di Terlizzi S, Ferrarini M, Ferrero E, Ponzoni M, Marcatti M, Tonon G. ATR addiction in multiple myeloma: synthetic lethal approaches exploiting established therapies. Haematologica 2020; 105:2440-2447. [PMID: 33054085 PMCID: PMC7556682 DOI: 10.3324/haematol.2018.215210] [Citation(s) in RCA: 8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 11/13/2019] [Indexed: 11/09/2022] Open
Abstract
Therapeutic strategies designed to tinker with cancer cell DNA damage response have led to the widespread use of PARP inhibitors for BRCA1/2-mutated cancers. In the haematological cancer multiple myeloma, we sought to identify analogous synthetic lethality mechanisms that could be leveraged upon established cancer treatments. The combination of ATR inhibition using the compound VX-970 with a drug eliciting interstrand cross-links, melphalan, was tested in in vitro, ex vivo, and most notably in vivo models. Cell proliferation, induction of apoptosis, tumor growth and animal survival were assessed. The combination of ATM inhibition with a drug triggering double strand breaks, doxorucibin, was also probed. We found that ATR inhibition is strongly synergistic with melphalan, even in resistant cells. The combination was dramatically effective in targeting myeloma primary patient cells and cell lines reducing cell proliferation and inducing apoptosis. The combination therapy significantly reduced tumor burden and prolonged survival in animal models. Conversely, ATM inhibition only marginally impacted on myeloma cell survival, even in combination with doxorucibin at high doses. These results indicate that myeloma cells extensively rely on ATR, but not on ATM, for DNA repair. Our findings posit that adding an ATR inhibitor such as VX-970 to established therapeutic regimens may provide a remarkably broad benefit to myeloma patients.
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Affiliation(s)
- Oronza A. Botrugno
- Functional Genomics of Cancer Unit, Experimental Oncology Division, IRCCS San Raffaele Scientific Institute
| | - Silvia Bianchessi
- Laboratory of Lymphoid Organ Development, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute
| | - Desirée Zambroni
- ALEMBIC, Advanced Light and Electron Microscopy Bio-Imaging Center, IRCCS San Raffaele Scientific Institute
| | - Michela Frenquelli
- Functional Genomics of Cancer Unit, Experimental Oncology Division, IRCCS San Raffaele Scientific Institute
| | - Daniela Belloni
- B-Cell Neoplasia Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute
| | | | - Stefania Girlanda
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Hospital
| | - Simona Di Terlizzi
- FRACTAL, Flow Cytometry Resource Advanced Cytometry Technical Applications Laboratory, IRCCS San Raffaele Scientific Institute
| | - Marina Ferrarini
- B-Cell Neoplasia Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute
| | - Elisabetta Ferrero
- B-Cell Neoplasia Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute
| | | | - Magda Marcatti
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Hospital
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Experimental Oncology Division, IRCCS San Raffaele Scientific Institute
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
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8
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Fioravanti R, Romanelli A, Mautone N, Di Bello E, Rovere A, Corinti D, Zwergel C, Valente S, Rotili D, Botrugno OA, Dessanti P, Vultaggio S, Vianello P, Cappa A, Binda C, Mattevi A, Minucci S, Mercurio C, Varasi M, Mai A. Tranylcypromine-Based LSD1 Inhibitors: Structure-Activity Relationships, Antiproliferative Effects in Leukemia, and Gene Target Modulation. ChemMedChem 2020; 15:643-658. [PMID: 32003940 DOI: 10.1002/cmdc.201900730] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 12/25/2019] [Indexed: 01/07/2023]
Abstract
LSD1 is a lysine demethylase highly involved in initiation and development of cancer. To design highly effective covalent inhibitors, a strategy is to fill its large catalytic cleft by designing tranylcypromine (TCP) analogs decorated with long, hindered substituents. We prepared three series of TCP analogs, carrying aroyl- and arylacetylamino (1 a-h), Z-amino acylamino (2 a-o), or double-substituted benzamide (3 a-n) residues at the C4 or C3 position of the phenyl ring. Further fragments obtained by chemical manipulation applied on the TCP scaffold (compounds 4 a-i) were also prepared. When tested against LSD1, most of 1 and 3 exhibited IC50 values in the low nanomolar range, with 1 e and 3 a,d,f,g being also the most selective respect to monoamine oxidases. In MV4-11 AML and NB4 APL cells compounds 3 were the most potent, displaying up to sub-micromolar cell growth inhibition against both cell lines (3 a) or against NB4 cells (3 c). The most potent compounds in cellular assays were also able to induce the expression of LSD1 target genes, such as GFI-1b, ITGAM, and KCTD12, as functional read-out for LSD1 inhibition. Mouse and human intrinsic clearance data highlighted the high metabolic stability of compounds 3 a, 3 d and 3 g. Further studies will be performed on the new compounds 3 a and 3 c to assess their anticancer potential in different cancer contexts.
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Affiliation(s)
- Rossella Fioravanti
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy
| | - Annalisa Romanelli
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy
| | - Nicola Mautone
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy
| | - Elisabetta Di Bello
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy
| | - Annarita Rovere
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy
| | - Davide Corinti
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy
| | - Clemens Zwergel
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy.,Department of Medicine of Precision, University of Studi della Campania Luigi Vanvitelli, Vico L. De Crecchio 7, 80138, Naples, Italy
| | - Sergio Valente
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy
| | - Oronza A Botrugno
- Department of Experimental Oncology, IEO - European Institute of Oncology IRCCS, via Adamello 16, 20139, Milan, Italy.,IRCCS San Raffaele Scientific Institute, Via Olgettina Milano, 58, 20132, Milan, Italy
| | - Paola Dessanti
- Department of Experimental Oncology, IEO - European Institute of Oncology IRCCS, via Adamello 16, 20139, Milan, Italy.,Oryzon Genomics S.A., Sant Ferran, 08940 Cornellà de Llobregat, Barcelona, Spain
| | - Stefania Vultaggio
- Department of Experimental Oncology, IEO - European Institute of Oncology IRCCS, via Adamello 16, 20139, Milan, Italy
| | - Paola Vianello
- Department of Experimental Oncology, IEO - European Institute of Oncology IRCCS, via Adamello 16, 20139, Milan, Italy
| | - Anna Cappa
- Department of Experimental Oncology, IEO - European Institute of Oncology IRCCS, via Adamello 16, 20139, Milan, Italy.,Experimental Therapeutics Program, IFOM-FIRC Institute of Molecular Oncology Foundation, via Adamello 16, 20139, Milan, Italy
| | - Claudia Binda
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Saverio Minucci
- Department of Experimental Oncology, IEO - European Institute of Oncology IRCCS, via Adamello 16, 20139, Milan, Italy.,Department of Biosciences, University of Milan, Via Festa del Perdono 7, 20122, Milano, Italy
| | - Ciro Mercurio
- Department of Experimental Oncology, IEO - European Institute of Oncology IRCCS, via Adamello 16, 20139, Milan, Italy.,Experimental Therapeutics Program, IFOM-FIRC Institute of Molecular Oncology Foundation, via Adamello 16, 20139, Milan, Italy
| | - Mario Varasi
- Department of Experimental Oncology, IEO - European Institute of Oncology IRCCS, via Adamello 16, 20139, Milan, Italy.,Experimental Therapeutics Program, IFOM-FIRC Institute of Molecular Oncology Foundation, via Adamello 16, 20139, Milan, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy
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9
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Vianello P, Sartori L, Amigoni F, Cappa A, Fagá G, Fattori R, Legnaghi E, Ciossani G, Mattevi A, Meroni G, Moretti L, Cecatiello V, Pasqualato S, Romussi A, Thaler F, Trifiró P, Villa M, Botrugno OA, Dessanti P, Minucci S, Vultaggio S, Zagarrí E, Varasi M, Mercurio C. Thieno[3,2-b]pyrrole-5-carboxamides as New Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1. Part 2: Structure-Based Drug Design and Structure–Activity Relationship. J Med Chem 2017; 60:1693-1715. [DOI: 10.1021/acs.jmedchem.6b01019] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Paola Vianello
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Luca Sartori
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Federica Amigoni
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Anna Cappa
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Giovanni Fagá
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Raimondo Fattori
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Elena Legnaghi
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Giuseppe Ciossani
- Department
of Biology and Biotechnology, University of Pavia, Via Ferrata
1, 27100 Pavia, Italy
| | - Andrea Mattevi
- Department
of Biology and Biotechnology, University of Pavia, Via Ferrata
1, 27100 Pavia, Italy
| | - Giuseppe Meroni
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Loris Moretti
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Valentina Cecatiello
- Crystallography
Unit, Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
- IFOM- The FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139 Milano, Italy
| | - Sebastiano Pasqualato
- Crystallography
Unit, Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Alessia Romussi
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Florian Thaler
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Paolo Trifiró
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Manuela Villa
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Oronza A. Botrugno
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Paola Dessanti
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Saverio Minucci
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
- Department
of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy
| | - Stefania Vultaggio
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Elisa Zagarrí
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Mario Varasi
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Ciro Mercurio
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
- Genextra Group, DAC s.r.l., Via
Adamello 16, 20139 Milano, Italy
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10
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Sartori L, Mercurio C, Amigoni F, Cappa A, Fagá G, Fattori R, Legnaghi E, Ciossani G, Mattevi A, Meroni G, Moretti L, Cecatiello V, Pasqualato S, Romussi A, Thaler F, Trifiró P, Villa M, Vultaggio S, Botrugno OA, Dessanti P, Minucci S, Zagarrí E, Carettoni D, Iuzzolino L, Varasi M, Vianello P. Thieno[3,2-b]pyrrole-5-carboxamides as New Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1. Part 1: High-Throughput Screening and Preliminary Exploration. J Med Chem 2017; 60:1673-1692. [DOI: 10.1021/acs.jmedchem.6b01018] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Luca Sartori
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Ciro Mercurio
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
- Genextra
Group, DAC s.r.l., Via Adamello 16, 20139 Milano, Italy
| | - Federica Amigoni
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Anna Cappa
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Giovanni Fagá
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Raimondo Fattori
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Elena Legnaghi
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Giuseppe Ciossani
- Department
of Biology and Biotechnology, University of Pavia, Via Ferrata
1, 27100 Pavia, Italy
| | - Andrea Mattevi
- Department
of Biology and Biotechnology, University of Pavia, Via Ferrata
1, 27100 Pavia, Italy
| | - Giuseppe Meroni
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Loris Moretti
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Valentina Cecatiello
- Crystallography
Unit, Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
- IFOM- The FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139 Milano, Italy
| | - Sebastiano Pasqualato
- Crystallography
Unit, Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Alessia Romussi
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Florian Thaler
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Paolo Trifiró
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Manuela Villa
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Stefania Vultaggio
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Oronza A. Botrugno
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Paola Dessanti
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Saverio Minucci
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
- Department
of Biosciences, University of Milan, Via Celoria, 26, 20133 Milano, Italy
| | - Elisa Zagarrí
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | | | | | - Mario Varasi
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Paola Vianello
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
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11
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Mehdipour P, Santoro F, Botrugno OA, Romanenghi M, Pagliuca C, Matthews GM, Johnstone RW, Minucci S. HDAC3 activity is required for initiation of leukemogenesis in acute promyelocytic leukemia. Leukemia 2017; 31:995-997. [DOI: 10.1038/leu.2017.3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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12
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Vianello P, Botrugno OA, Cappa A, Dal Zuffo R, Dessanti P, Mai A, Marrocco B, Mattevi A, Meroni G, Minucci S, Stazi G, Thaler F, Trifiró P, Valente S, Villa M, Varasi M, Mercurio C. Discovery of a Novel Inhibitor of Histone Lysine-Specific Demethylase 1A (KDM1A/LSD1) as Orally Active Antitumor Agent. J Med Chem 2016; 59:1501-17. [DOI: 10.1021/acs.jmedchem.5b01209] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Paola Vianello
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Oronza A. Botrugno
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Anna Cappa
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Roberto Dal Zuffo
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Paola Dessanti
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Antonello Mai
- Department
of Drug Chemistry and Technologies, Sapienza University of Rome, P.le
A. Moro 5, 00185 Rome, Italy
- Pasteur Institute-Cenci Bolognetti Foundation, Sapienza
University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Biagina Marrocco
- Department
of Drug Chemistry and Technologies, Sapienza University of Rome, P.le
A. Moro 5, 00185 Rome, Italy
| | - Andrea Mattevi
- Department
of Biology and Biotechnology, University of Pavia, Via Ferrata
1, 27100 Pavia, Italy
| | - Giuseppe Meroni
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Saverio Minucci
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
- Department
of Biosciences, University of Milan, Via Celoria, 26, 20133 Milan, Italy
| | - Giulia Stazi
- Department
of Drug Chemistry and Technologies, Sapienza University of Rome, P.le
A. Moro 5, 00185 Rome, Italy
| | - Florian Thaler
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Paolo Trifiró
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Sergio Valente
- Department
of Drug Chemistry and Technologies, Sapienza University of Rome, P.le
A. Moro 5, 00185 Rome, Italy
| | - Manuela Villa
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Mario Varasi
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Ciro Mercurio
- Department
of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
- Genextra Group, DAC s.r.l., Via
Adamello 16, 20139 Milan, Italy
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13
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Chiaradonna F, Barozzi I, Miccolo C, Bucci G, Palorini R, Fornasari L, Botrugno OA, Pruneri G, Masullo M, Passafaro A, Galimberti VE, Fantin VR, Richon VM, Pece S, Viale G, Di Fiore PP, Draetta G, Pelicci PG, Minucci S, Chiocca S. Redox-Mediated Suberoylanilide Hydroxamic Acid Sensitivity in Breast Cancer. Antioxid Redox Signal 2015; 23:15-29. [PMID: 25897982 PMCID: PMC4492673 DOI: 10.1089/ars.2014.6189] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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] [Indexed: 12/23/2022]
Abstract
AIMS Vorinostat (suberoylanilide hydroxamic acid; SAHA) is a histone deacetylase inhibitor (HDACi) approved in the clinics for the treatment of T-cell lymphoma and with the potential to be effective also in breast cancer. We investigated the responsiveness to SAHA in human breast primary tumors and cancer cell lines. RESULTS We observed a differential response to drug treatment in both human breast primary tumors and cancer cell lines. Gene expression analysis of the breast cancer cell lines revealed that genes involved in cell adhesion and redox pathways, especially glutathione metabolism, were differentially expressed in the cell lines resistant to SAHA compared with the sensitive ones, indicating their possible association with drug resistance mechanisms. Notably, such an association was also observed in breast primary tumors. Indeed, addition of buthionine sulfoximine (BSO), a compound capable of depleting cellular glutathione, significantly enhanced the cytotoxicity of SAHA in both breast cancer cell lines and primary breast tumors. INNOVATION We identify and validate transcriptional differences in genes involved in redox pathways, which include potential predictive markers of sensitivity to SAHA. CONCLUSION In breast cancer, it could be relevant to evaluate the expression of antioxidant genes that may favor tumor resistance as a factor to consider for potential clinical application and treatment with epigenetic drugs (HDACis).
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Affiliation(s)
- Ferdinando Chiaradonna
- 1 Department of Biotechnology and Biosciences, University of Milano-Bicocca , Milan, Italy .,2 SYSBIO Centre of Systems Biology , Milan, Italy
| | - Iros Barozzi
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
| | - Claudia Miccolo
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
| | - Gabriele Bucci
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
| | - Roberta Palorini
- 1 Department of Biotechnology and Biosciences, University of Milano-Bicocca , Milan, Italy .,2 SYSBIO Centre of Systems Biology , Milan, Italy
| | - Lorenzo Fornasari
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
| | - Oronza A Botrugno
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
| | - Giancarlo Pruneri
- 4 Department of Pathology, European Institute of Oncology , Milan, Italy
| | - Michele Masullo
- 4 Department of Pathology, European Institute of Oncology , Milan, Italy
| | - Alfonso Passafaro
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
| | | | - Valeria R Fantin
- 6 Oncology Research Unit, Pfizer Global Research and Development , La Jolla, California
| | | | - Salvatore Pece
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
| | - Giuseppe Viale
- 4 Department of Pathology, European Institute of Oncology , Milan, Italy
| | - Pier Paolo Di Fiore
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
| | - Giulio Draetta
- 8 Institute for Applied Cancer, The University of Texas MD Anderson Cancer Center Science , Houston, Texas
| | - Pier Giuseppe Pelicci
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
| | - Saverio Minucci
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy .,9 Department of Biosciences, University of Milan , Milan, Italy
| | - Susanna Chiocca
- 3 Department of Experimental Oncology, European Institute of Oncology , Milan, Italy
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14
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Valente S, Rodriguez V, Mercurio C, Vianello P, Saponara B, Cirilli R, Ciossani G, Labella D, Marrocco B, Monaldi D, Ruoppolo G, Tilset M, Botrugno OA, Dessanti P, Minucci S, Mattevi A, Varasi M, Mai A. Pure enantiomers of benzoylamino-tranylcypromine: LSD1 inhibition, gene modulation in human leukemia cells and effects on clonogenic potential of murine promyelocytic blasts. Eur J Med Chem 2015; 94:163-74. [DOI: 10.1016/j.ejmech.2015.02.060] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 02/27/2015] [Accepted: 02/28/2015] [Indexed: 12/12/2022]
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15
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Valente S, Rodriguez V, Mercurio C, Vianello P, Saponara B, Cirilli R, Ciossani G, Labella D, Marrocco B, Ruoppolo G, Botrugno OA, Dessanti P, Minucci S, Mattevi A, Varasi M, Mai A. Pure Diastereomers of a Tranylcypromine-Based LSD1 Inhibitor: Enzyme Selectivity and In-Cell Studies. ACS Med Chem Lett 2015; 6:173-7. [PMID: 25699146 DOI: 10.1021/ml500424z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 10/18/2014] [Accepted: 12/08/2014] [Indexed: 12/13/2022] Open
Abstract
The pure four diastereomers (11a-d) of trans-benzyl (1-((4-(2-aminocyclopropyl)phenyl)amino)-1-oxo-3-phenylpropan-2-yl)carbamate hydrochloride 11, previously described by us as LSD1 inhibitor, were obtained by enantiospecific synthesis/chiral HPLC separation method. Tested in LSD1 and MAO assays, 11b (S,1S,2R) and 11d (R,1S,2R) were the most potent isomers against LSD1 and were less active against MAO-A and practically inactive against MAO-B. In cells, all the four diastereomers induced Gfi-1b and ITGAM gene expression in NB4 cells, accordingly with their LSD1 inhibition, and 11b and 11d inhibited the colony forming potential in murine promyelocytic blasts.
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Affiliation(s)
- Sergio Valente
- Department
of Drug Chemistry and Technologies, Sapienza University of Roma, P.le
A. Moro 5, 00185 Roma, Italy
| | - Veronica Rodriguez
- Department
of Drug Chemistry and Technologies, Sapienza University of Roma, P.le
A. Moro 5, 00185 Roma, Italy
| | - Ciro Mercurio
- Genextra
Group, DAC s.r.l., Via Adamello 16, 20139 Milano, Italy
| | - Paola Vianello
- Dipartimento
di Oncologia Sperimentale, IEO−European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Bruna Saponara
- Department
of Therapeutic Research and Medicines Evaluation, Italian National Institute of Health, Via Regina Elena 299, 00161 Roma, Italy
| | - Roberto Cirilli
- Department
of Therapeutic Research and Medicines Evaluation, Italian National Institute of Health, Via Regina Elena 299, 00161 Roma, Italy
| | - Giuseppe Ciossani
- Department
of Biology and Biotechnology, University of Pavia, Via Ferrata
1, 27100 Pavia, Italy
| | - Donatella Labella
- Department
of Drug Chemistry and Technologies, Sapienza University of Roma, P.le
A. Moro 5, 00185 Roma, Italy
| | - Biagina Marrocco
- Department
of Drug Chemistry and Technologies, Sapienza University of Roma, P.le
A. Moro 5, 00185 Roma, Italy
| | - Giovanni Ruoppolo
- Department
of Sense Organs, Sapienza University of Roma, P.le A. Moro 5, 00185 Roma, Italy
| | - Oronza A. Botrugno
- Dipartimento
di Oncologia Sperimentale, IEO−European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Paola Dessanti
- Dipartimento
di Oncologia Sperimentale, IEO−European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Saverio Minucci
- Dipartimento
di Oncologia Sperimentale, IEO−European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
- Department
of Biosciences, University of Milan, 20100 Milan, Italy
| | - Andrea Mattevi
- Department
of Biology and Biotechnology, University of Pavia, Via Ferrata
1, 27100 Pavia, Italy
| | - Mario Varasi
- Dipartimento
di Oncologia Sperimentale, IEO−European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Antonello Mai
- Department
of Drug Chemistry and Technologies, Sapienza University of Roma, P.le
A. Moro 5, 00185 Roma, Italy
- Pasteur
Institute−Cenci Bolognetti Foundation, Sapienza University of Roma, P.le A. Moro 5, 00185 Roma, Italy
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16
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Rodriguez V, Valente S, Rovida S, Rotili D, Stazi G, Lucidi A, Ciossani G, Mattevi A, Botrugno OA, Dessanti P, Mercurio C, Vianello P, Minucci S, Varasi M, Mai A. Pyrrole- and indole-containing tranylcypromine derivatives as novel lysine-specific demethylase 1 inhibitors active on cancer cells. Med Chem Commun 2015. [DOI: 10.1039/c4md00507d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new series of pyrrole/indole-containing tranylcypromine analogues is reported as potent and selective LSD1 inhibitors active in leukemia.
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17
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Vianello P, Botrugno OA, Cappa A, Ciossani G, Dessanti P, Mai A, Mattevi A, Meroni G, Minucci S, Thaler F, Tortorici M, Trifiró P, Valente S, Villa M, Varasi M, Mercurio C. Synthesis, biological activity and mechanistic insights of 1-substituted cyclopropylamine derivatives: a novel class of irreversible inhibitors of histone demethylase KDM1A. Eur J Med Chem 2014; 86:352-63. [PMID: 25173853 DOI: 10.1016/j.ejmech.2014.08.068] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [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: 06/12/2014] [Revised: 08/25/2014] [Accepted: 08/26/2014] [Indexed: 11/25/2022]
Abstract
Histone demethylase KDM1A (also known as LSD1) has become an attractive therapeutic target for the treatment of cancer as well as other disorders such as viral infections. We report on the synthesis of compounds derived from the expansion of tranylcypromine as a chemical scaffold for the design of novel demethylase inhibitors. These compounds, which are substituted on the cyclopropyl core moiety, were evaluated for their ability to inhibit KDM1A in vitro as well as to function in cells by modulating the expression of Gfi-1b, a well recognized KDM1A target gene. The molecules were all found to covalently inhibit KDM1A and to become increasingly selective against human monoamine oxidases MAO A and MAO B through the introduction of bulkier substituents on the cyclopropylamine ring. Structural and biochemical analysis of selected trans isomers showed that the two stereoisomers are endowed with similar inhibitory activities against KDM1A, but form different covalent adducts with the FAD co-enzyme.
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Affiliation(s)
- Paola Vianello
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.
| | - Oronza A Botrugno
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Anna Cappa
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Giuseppe Ciossani
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy
| | - Paola Dessanti
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Antonello Mai
- Pasteur Institute - Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, University "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy.
| | - Giuseppe Meroni
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Saverio Minucci
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy; Department of Biosciences, University of Milan, Via Celoria, 26, 20133 Milan, Italy
| | - Florian Thaler
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.
| | - Marcello Tortorici
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy
| | - Paolo Trifiró
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Sergio Valente
- Pasteur Institute - Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, University "La Sapienza", P.le A. Moro 5, 00185 Roma, Italy
| | - Manuela Villa
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Mario Varasi
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Ciro Mercurio
- Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
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18
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Robert T, Vanoli F, Chiolo I, Shubassi G, Bernstein KA, Rothstein R, Botrugno OA, Parazzoli D, Oldani A, Minucci S, Foiani M. HDACs link the DNA damage response, processing of double-strand breaks and autophagy. Nature 2011; 471:74-79. [PMID: 21368826 DOI: 10.1038/nature09803] [Citation(s) in RCA: 309] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 01/11/2011] [Indexed: 11/09/2022]
Abstract
Protein acetylation is mediated by histone acetyltransferases (HATs) and deacetylases (HDACs), which influence chromatin dynamics, protein turnover and the DNA damage response. ATM and ATR mediate DNA damage checkpoints by sensing double-strand breaks and single-strand-DNA-RFA nucleofilaments, respectively. However, it is unclear how acetylation modulates the DNA damage response. Here we show that HDAC inhibition/ablation specifically counteracts yeast Mec1 (orthologue of human ATR) activation, double-strand-break processing and single-strand-DNA-RFA nucleofilament formation. Moreover, the recombination protein Sae2 (human CtIP) is acetylated and degraded after HDAC inhibition. Two HDACs, Hda1 and Rpd3, and one HAT, Gcn5, have key roles in these processes. We also find that HDAC inhibition triggers Sae2 degradation by promoting autophagy that affects the DNA damage sensitivity of hda1 and rpd3 mutants. Rapamycin, which stimulates autophagy by inhibiting Tor, also causes Sae2 degradation. We propose that Rpd3, Hda1 and Gcn5 control chromosome stability by coordinating the ATR checkpoint and double-strand-break processing with autophagy.
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Affiliation(s)
- Thomas Robert
- Fondazione IFOM (Istituto FIRC di Oncologia Molecolare), IFOM-IEO Campus, via Adamello 16, Milan 20139, Italy
| | - Fabio Vanoli
- Fondazione IFOM (Istituto FIRC di Oncologia Molecolare), IFOM-IEO Campus, via Adamello 16, Milan 20139, Italy
| | - Irene Chiolo
- Fondazione IFOM (Istituto FIRC di Oncologia Molecolare), IFOM-IEO Campus, via Adamello 16, Milan 20139, Italy.,LBNL, Department of Genome Biology, Berkeley, California 94710-2722, USA
| | - Ghadeer Shubassi
- Fondazione IFOM (Istituto FIRC di Oncologia Molecolare), IFOM-IEO Campus, via Adamello 16, Milan 20139, Italy
| | - Kara A Bernstein
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032-2704, USA
| | - Rodney Rothstein
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032-2704, USA
| | | | | | | | - Saverio Minucci
- European Institute of Oncology, IFOM-IEO campus, Milan 20139, Italy.,DSBB-Università degli Studi di Milano, Milan 20139, Italy
| | - Marco Foiani
- Fondazione IFOM (Istituto FIRC di Oncologia Molecolare), IFOM-IEO Campus, via Adamello 16, Milan 20139, Italy.,DSBB-Università degli Studi di Milano, Milan 20139, Italy
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19
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Di Micco R, Sulli G, Dobreva M, Liontos M, Botrugno OA, Gargiulo G, dal Zuffo R, Matti V, d'Ario G, Montani E, Mercurio C, Hahn WC, Gorgoulis V, Minucci S, d'Adda di Fagagna F. Interplay between oncogene-induced DNA damage response and heterochromatin in senescence and cancer. Nat Cell Biol 2011. [PMID: 21336312 DOI: 10.1038/ncb2170.interplay] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Two major mechanisms have been causally implicated in the establishment of cellular senescence: the activation of the DNA damage response (DDR) pathway and the formation of senescence-associated heterochromatic foci (SAHF). Here we show that in human fibroblasts resistant to premature p16(INK4a) induction, SAHF are preferentially formed following oncogene activation but are not detected during replicative cellular senescence or on exposure to a variety of senescence-inducing stimuli. Oncogene-induced SAHF formation depends on DNA replication and ATR (ataxia telangiectasia and Rad3-related). Inactivation of ATM (ataxia telangiectasia mutated) or p53 allows the proliferation of oncogene-expressing cells that retain increased heterochromatin induction. In human cancers, levels of heterochromatin markers are higher than in normal tissues, and are independent of the proliferative index or stage of the tumours. Pharmacological and genetic perturbation of heterochromatin in oncogene-expressing cells increase DDR signalling and lead to apoptosis. In vivo, a histone deacetylase inhibitor (HDACi) causes heterochromatin relaxation, increased DDR, apoptosis and tumour regression. These results indicate that heterochromatin induced by oncogenic stress restrains DDR and suggest that the use of chromatin-modifying drugs in cancer therapies may benefit from the study of chromatin and DDR status of tumours.
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Affiliation(s)
- Raffaella Di Micco
- IFOM Foundation - FIRC Institute of Molecular Oncology Foundation, Milan, Italy
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20
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Binda C, Valente S, Romanenghi M, Pilotto S, Cirilli R, Karytinos A, Ciossani G, Botrugno OA, Forneris F, Tardugno M, Edmondson DE, Minucci S, Mattevi A, Mai A. Biochemical, structural, and biological evaluation of tranylcypromine derivatives as inhibitors of histone demethylases LSD1 and LSD2. J Am Chem Soc 2010; 132:6827-33. [PMID: 20415477 DOI: 10.1021/ja101557k] [Citation(s) in RCA: 221] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
LSD1 and LSD2 histone demethylases are implicated in a number of physiological and pathological processes, ranging from tumorigenesis to herpes virus infection. A comprehensive structural, biochemical, and cellular study is presented here to probe the potential of these enzymes for epigenetic therapies. This approach employs tranylcypromine as a chemical scaffold for the design of novel demethylase inhibitors. This drug is a clinically validated antidepressant known to target monoamine oxidases A and B. These two flavoenzymes are structurally related to LSD1 and LSD2. Mechanistic and crystallographic studies of tranylcypromine inhibition reveal a lack of selectivity and differing covalent modifications of the FAD cofactor depending on the enantiomeric form. These findings are pharmacologically relevant, since tranylcypromine is currently administered as a racemic mixture. A large set of tranylcypromine analogues were synthesized and screened for inhibitory activities. We found that the common evolutionary origin of LSD and MAO enzymes, despite their unrelated functions and substrate specificities, is reflected in related ligand-binding properties. A few compounds with partial enzyme selectivity were identified. The biological activity of one of these new inhibitors was evaluated with a cellular model of acute promyelocytic leukemia chosen since its pathogenesis includes aberrant activities of several chromatin modifiers. Marked effects on cell differentiation and an unprecedented synergistic activity with antileukemia drugs were observed. These data demonstrate that these LSD1/2 inhibitors are of potential relevance for the treatment of promyelocytic leukemia and, more generally, as tools to alter chromatin state with promise of a block of tumor progression.
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Affiliation(s)
- Claudia Binda
- Department of Genetics and Microbiology, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy
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21
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Zanardi A, Giorgetti L, Botrugno OA, Minucci S, Milani P, Pelicci PG, Carbone R. Immunocell-array for molecular dissection of multiple signaling pathways in mammalian cells. Mol Cell Proteomics 2007; 6:939-47. [PMID: 17293591 DOI: 10.1074/mcp.t600051-mcp200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The knowledge of signaling pathways that are triggered by physiological and pathological conditions or drug treatment is essential for the comprehension of the biological events that regulate cellular responses. Recently novel platforms based on "reverse-phase protein arrays" have proven to be useful in the study of different pathways, but they still lack the possibility to detect events in the complexity of a cellular context. We developed an "immunocell-array" of cells on chip where, upon cell plating, growing, drug treatment, and fixation, by spotting specific antibodies we can detect the localization and state of hundreds of proteins involved in specific signaling pathways. By applying this technology to mammalian cells we analyzed signaling proteins involved in the response to DNA damage and identified a chromatin remodeling pathway following bleomycin treatment. We propose our technology as a new tool for the array-based multiplexed analysis of signaling pathways in drug response screening, for the proteomics of profiling patient cells, and ultimately for the high throughput screening of antibodies for immunofluorescence applications.
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22
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Carbone R, Botrugno OA, Ronzoni S, Insinga A, Di Croce L, Pelicci PG, Minucci S. Recruitment of the histone methyltransferase SUV39H1 and its role in the oncogenic properties of the leukemia-associated PML-retinoic acid receptor fusion protein. Mol Cell Biol 2006; 26:1288-96. [PMID: 16449642 PMCID: PMC1367206 DOI: 10.1128/mcb.26.4.1288-1296.2006] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Leukemia-associated fusion proteins establish aberrant transcriptional programs, which result in the block of hematopoietic differentiation, a prominent feature of the leukemic phenotype. The dissection of the mechanisms of deregulated transcription by leukemia fusion proteins is therefore critical for the design of tailored antileukemic strategies, aimed at reestablishing the differentiation program of leukemic cells. The acute promyelocytic leukemia (APL)-associated fusion protein PML-retinoic acid receptor (RAR) behaves as an aberrant transcriptional repressor, due to its ability to induce chromatin modifications (histone deacetylation and DNA methylation) and silencing of PML-RAR target genes. Here, we indicate that the ultimate result of PML-RAR action is to impose a heterochromatin-like structure on its target genes, thereby establishing a permanent transcriptional silencing. This effect is mediated by the previously described association of PML-RAR with chromatin-modifying enzymes (histone deacetylases and DNA methyltransferases) and by recruitment of the histone methyltransferase SUV39H1, responsible for trimethylation of lysine 9 of histone H3.
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MESH Headings
- Cell Differentiation
- DNA Methylation
- Gene Silencing
- Histone Methyltransferases
- Histone-Lysine N-Methyltransferase/genetics
- Histone-Lysine N-Methyltransferase/metabolism
- Histones/chemistry
- Histones/metabolism
- Humans
- Leukemia, Promyelocytic, Acute/genetics
- Leukemia, Promyelocytic, Acute/metabolism
- Leukemia, Promyelocytic, Acute/pathology
- Methylation
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Models, Biological
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Promyelocytic Leukemia Protein
- Protein Methyltransferases
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
- Transfection
- Tumor Suppressor Proteins/genetics
- Tumor Suppressor Proteins/metabolism
- U937 Cells
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Affiliation(s)
- Roberta Carbone
- Department of Experimental Oncology, European Institute of Oncology, and Department of Biomolecular Sciences and Biotechnologies, University of Milan, Italy
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23
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Botrugno OA, Paris S, Za L, Gualdoni S, Cattaneo A, Bachi A, de Curtis I. Characterization of the endogenous GIT1-betaPIX complex, and identification of its association to membranes. Eur J Cell Biol 2005; 85:35-46. [PMID: 16373173 DOI: 10.1016/j.ejcb.2005.09.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [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: 07/01/2005] [Revised: 09/21/2005] [Accepted: 09/22/2005] [Indexed: 12/25/2022] Open
Abstract
G protein-coupled receptor kinase interactors (GITs) are adaptor proteins with ADP-ribosylating factor--GTPase-activating protein (ARF-GAP) activity that form complexes with the p21-activated kinase-interacting exchange factor (PIX) guanine nucleotide exchanging factors for Rac and Cdc42. In this study we have characterized the endogenous GIT1/p95-APP1/Cat1 (GIT1)- PIX complexes in neuronal and non-neuronal cells. In COS7 cells, immunocytochemical analysis shows the localization of endogenous GIT1 in the perinuclear region of the cell, as well as at the cell periphery, where GIT1 co-localizes with filamentous actin. The perinuclear localization of endogenous GIT1 was confirmed in avian fibroblasts. In COS7 cells, immunoprecipitation and microsequencing experiments with either anti-GIT1 or anti-betaPIX antibodies unequivocally show that betaPIX is uniquely associated with GIT1 in lysates from these cells, while GIT2/PKL/p95-APP2/Cat2 (GIT2) is undetectable in the endogenous complexes. Moreover, this analysis demonstrates that betaPIX is the limiting factor for the formation of the endogenous complexes, since a small fraction of GIT1 can be co-immunoprecipitated with most betaPIX from these cells. Saponin treatment of unfixed cells indicates that betaPIX-bound GIT1 is preferentially retained in the saponin-resistant fraction when compared to betaPIX-free GIT1. Moreover, analysis by tissue fractionation shows that a significant fraction of the endogenous GIT1-betaPIX complex is firmly associated to membranes from brain homogenates. Our findings show the specific localization of the complex at intracellular membranes, and indicate a correlation between the association of GIT1 to betaPIX, and the localization of the endogenous complex at membranes.
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Affiliation(s)
- Oronza A Botrugno
- Cell Adhesion Unit, Department of Molecular Biology and Functional Genomics, San Raffaele Scientific Institute, Via Olgettina 58, I-20132 Milano, Italy
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24
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Botrugno OA, Fayard E, Annicotte JS, Haby C, Brennan T, Wendling O, Tanaka T, Kodama T, Thomas W, Auwerx J, Schoonjans K. Synergy between LRH-1 and beta-catenin induces G1 cyclin-mediated cell proliferation. Mol Cell 2004; 15:499-509. [PMID: 15327767 DOI: 10.1016/j.molcel.2004.07.009] [Citation(s) in RCA: 233] [Impact Index Per Article: 11.7] [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: 01/26/2004] [Revised: 05/27/2004] [Accepted: 06/09/2004] [Indexed: 12/29/2022]
Abstract
LRH-1 is an orphan nuclear receptor predominantly expressed in tissues of endodermal origin, where it controls development and cholesterol homeostasis. We show here that LRH-1 induces cell proliferation through the concomitant induction of cyclin D1 and E1, an effect that is potentiated by its interaction with beta-catenin. Whereas beta-catenin coactivates LRH-1 on the cyclin E1 promoter, LRH-1 acts as a potent tissue-restricted coactivator of beta-catenin on the cyclin D1 promoter. The implication of LRH-1 in cell proliferation highlights an unanticipated crosstalk between LRH-1 and the beta-catenin/Tcf4 signaling pathway, which is relevant for the renewal of intestinal crypt cells.
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Affiliation(s)
- Oronza A Botrugno
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université Louis Pasteur, 67404 Illkirch, France
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25
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Schoonjans K, Annicotte JS, Huby T, Botrugno OA, Fayard E, Ueda Y, Chapman J, Auwerx J. Liver receptor homolog 1 controls the expression of the scavenger receptor class B type I. EMBO Rep 2002; 3:1181-7. [PMID: 12446566 PMCID: PMC1308324 DOI: 10.1093/embo-reports/kvf238] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.2] [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] [Indexed: 12/11/2022] Open
Abstract
The scavenger receptor class B type I (SR-BI), which mediates selective cellular cholesterol uptake from high-density lipoproteins (HDLs), plays a key role in reverse cholesterol transport. The orphan nuclear receptor liver receptor homolog 1 (LRH-1) and SR-BI are co-expressed in liver and ovary, suggesting that LRH-1 might control the expression of SR-BI in these tissues. LRH-1 induces human and mouse SR-BI promoter activity by binding to an LRH-1 response element in the promoter. Retroviral expression of LRH-1 robustly induces SR-BI, an effect associated with histone H3 acetylation on the SR-BI promoter. The decrease in SR-BI mRNA levels in livers of LRH-1(+/-) animals provides in vivo evidence that LRH-1 regulates SR-BI expression. Our data demonstrate that SR-BI is an LRH-1 target gene and underscore the pivotal role of LRH-1 in reverse cholesterol transport.
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Affiliation(s)
- Kristina Schoonjans
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS/INSERM/Université Louis Pasteur, 67404 Illkirch, France
- Tel: +33 3 8865 3419/3425; Fax: +33 3 8865 3201; or
| | - Jean-Sebastien Annicotte
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS/INSERM/Université Louis Pasteur, 67404 Illkirch, France
- J.s. Annicotte and T. Huby contributed equally to this work
| | - Thierry Huby
- Unité 551 INSERM, Hôpital de la Pitié, 75651 Paris, France
- J.s. Annicotte and T. Huby contributed equally to this work
| | - Oronza A. Botrugno
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS/INSERM/Université Louis Pasteur, 67404 Illkirch, France
| | - Elisabeth Fayard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS/INSERM/Université Louis Pasteur, 67404 Illkirch, France
| | - Yukihiko Ueda
- Shiga Medical Center Research Institute, 5-4-30 Moriyama, Shiga 524-8524, Japan
| | - John Chapman
- Unité 551 INSERM, Hôpital de la Pitié, 75651 Paris, France
| | - Johan Auwerx
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS/INSERM/Université Louis Pasteur, 67404 Illkirch, France
- Institut Clinique de la Souris (ICS), BP 10142, 67404 Illkirch, France
- Tel: +33 3 8865 3419/3425; Fax: +33 3 8865 3201; or
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26
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Potenza MA, Botrugno OA, De Salvia MA, Lerro G, Nacci C, Marasciulo FL, Andriantsitohaina R, Mitolo-Chieppa D. Endothelial COX-1 and -2 differentially affect reactivity of MVB in portal hypertensive rats. Am J Physiol Gastrointest Liver Physiol 2002; 283:G587-94. [PMID: 12181171 DOI: 10.1152/ajpgi.00391.2001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Expression of constitutive and inducible cyclooxygenase (COX-1 and COX-2, respectively) and the role of prostanoids were investigated in the aorta and mesenteric vascular bed (MVB) from the portal vein-ligated rat (PVL) as a model of portal hypertension. Functional experiments were carried out in MVB from PVL and sham-operated rats in the absence or presence of the nonselective COX inhibitor indomethacin or the selective inhibitors of COX-1 (SC-560) or COX-2 (NS-398). Western blots of COX-1 and COX-2 proteins were evaluated in aorta and MVB, and PGI(2) production by enzyme immunoassay of 6-keto-PGF(1alpha) was evaluated in the aorta. In the presence of functional endothelium, decreased contraction to norepinephrine (NE) and increased vasodilatation to ACh were observed in MVB from PVL. Exposure of MVB to indomethacin, SC-560, or NS-398 reversed the hyporeactivity to NE and the increased endothelial vasodilatation to ACh in PVL, with NS-398 being more potent than the other two inhibitors. Upregulation of COX-1 and COX-2 expressions was detected in aorta and MVB from PVL portal hypertensive rats, and increased production of 6-keto-PGF(1alpha) was observed in aorta from portal hypertensive rats. These results suggest that generation of endothelial vasodilator prostanoids, from COX-1 and COX-2 isoforms, accounts for the increased mesenteric blood flow in portal hypertension.
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Affiliation(s)
- M A Potenza
- Section of Pharmacology, Department of Pharmacology and Human Physiology, Medical School, University of Bari, 70124 Bari, Italy
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27
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Brendel C, Schoonjans K, Botrugno OA, Treuter E, Auwerx J. The small heterodimer partner interacts with the liver X receptor alpha and represses its transcriptional activity. Mol Endocrinol 2002; 16:2065-76. [PMID: 12198243 DOI: 10.1210/me.2001-0194] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The small heterodimer partner SHP (NR0B2) is an unusual nuclear receptor that lacks the typical DNA binding domain common to most nuclear receptors. SHP has been reported to act as a corepressor for several nuclear receptors, but its exact mechanism of action is still elusive. Here we show that SHP can interact with the liver X receptors LXRalpha (NR1H3) and LXRbeta (NR1H2), as demonstrated by glutathione-S-transferase pull-down assays, mammalian two-hybrid, and coimmunoprecipitation experiments. In transfection assays, SHP inhibits the expression of an artificial reporter driven by an LXR-response element and represses the transcriptional activation by LXR of the human ATP-binding cassette transporter 1 (ABCA1) promoter. Treatment of Caco-2 cells with bile acids, which activate farnesoid X receptor and subsequently induce SHP, leads to the repression of the human ABCG1 gene, an established LXR target gene. These results demonstrate that SHP is able to interact with LXR and to modulate its transcriptional activity.
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Affiliation(s)
- Carole Brendel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale/Université Louis Pasteur, BP 1042, 67404 Illkirch, France
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